Re: [ccp4bb] poly-dN model
Hi Reza, If you are looking for a molecular replacement model, we typically use single-stranded or double-stranded poly-uridine, which you can generate with Coot. Best, -Jinwei - Jinwei Zhang Laboratory of Molecular Biology NIDDK, NIH 50 South Drive, Room 4503 Bethesda, MD 20892 Tel: 301-402-4703 https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral Position at NIH — Structures, Interactions and Mechanisms of Noncoding RNAs and RNPs.
Dear Colleagues, We are looking for a new member to join our group at the Laboratory of Molecular Biology at NIDDK, in NIH’s main campus in Bethesda, MD, USA. Set in an exciting and burgeoning field, the lab explores novel structures, mechanisms and interactions of large noncoding RNAs in bacterial, viral and eukaryotic gene regulation, stress response and antiviral immunity. We employ multidisciplinary tools such as RNA crystallography, single-particle Cryo-EM, small-angle X-ray scattering, fluorescence spectroscopy, chemical biology, and many other biochemical and biophysical tools. If you are interested or know of a suitable candidate, please contact me at jinwei.zh...@nih.gov. Detailed ad is below Thank you, -Jinwei Position Description: A fully funded postdoctoral position (up to 5 years) is available in the Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab addresses a widening gap between the accelerated discovery and functional description of the noncoding transcriptome, and the lack of structural and mechanistic understanding of complex noncoding RNAs and RNPs. We seek a new member to join our diverse group to study gene-regulatory riboswitches, highly structured viral RNAs, long noncoding and circular RNAs and their complexes with other RNAs and immune proteins, etc. We develop and apply innovative technologies such as rational RNA design and engineering, RNA crystallography, RNA cryo-EM, XFEL, ultrafast SAXS/WAXS, single-molecule fluorescence, fluorescence lifetime, crosslinking-mass spec., etc. See https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html and recent publications below for details: Bou-Nader C. et al., & Zhang, J. (2021) Structural basis for host tRNA control of HIV-1 Gag localization., under review. Suddala K.C & Zhang, J. (2019) High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove, Nat. Struct. & Mol. Biol., 26, 1114–1122. Li S. et al., & Zhang, J. (2019) Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions, Nat. Struct. & Mol. Biol., 26, 1094–1105. Hood, I.V. et al., & Zhang, J. (2019). Crystal structure of an Adenovirus Virus-Associated RNA, Nat. Commun. 10:2871 The well-supported lab has dedicated access to state-of-the-art equipment in structural biology (Mosquito, Dragonfly, Rock Imager, Akta Pures, FSEC, etc.; regular synchrotron access for X-ray crystallography; Titan Krios and Glacios for single-particle Cryo-EM; SAXS, AFM, NMR, etc), biochemistry, biophysics (ITC, DSC, SPR, BLI, AUC, DLS, SEC-MALS, CD, fluorescence, thermophoresis, iSCAMS, etc), fermentation, advanced mass spec, genomics and sequencing, and proteomics core facilities with hands-on training or service by dedicated PhD-level staff scientists. Incoming fellows are also encouraged to bring your own ideas that you could develop into research programs that you can then take to your independent PI positions. The NIH, NIDDK, and LMB are committed to the continued education and career development of trainees through numerous courses and workshops offered by OITE, FAES, and NIDDK. Requirements: Interested candidates must have received (or be expecting) a Ph.D. or M.D. within the past five years in molecular biology, structural biology, biochemistry, RNA biology, or a related discipline, have excellent oral and written communication skills, and be strongly self-motivated to design and participate in innovative and rigorous research projects. Prior experiences in structural biology are not required, as training will be provided. To apply: Please email a cover letter indicating preferred start date, CV, a brief summary of research interests, accomplishments, and career goals, and names and contact information for at least three references to: Dr. Jinwei Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse community in its training and employment programs. DHHS/NIH is an Equal Opportunity Employer. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral Position at the NIH on Structural Biology of Noncoding RNAs and RNPs
Dear Colleagues, I am looking for a new member to join our group at the Laboratory of Molecular Biology at NIDDK, in NIH’s main campus in Bethesda, MD, USA. Set in an exciting and burgeoning field, the lab explores novel structures, mechanisms and interactions of large noncoding RNAs in bacterial, viral and eukaryotic gene regulation, stress response and antiviral immunity. We employ multidisciplinary tools such as X-ray crystallography, single-particle Cryo-EM, small-angle X-ray scattering, fluorescence spectroscopy, chemical biology, and many other biochemical and biophysical tools. If you are interested or know of a suitable candidate, please contact me at jinwei.zh...@nih.gov. Detailed ad is below. Thank you, -Jinwei Position Description: A postdoctoral position is available in the Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab addresses a widening gap between the accelerated discovery and functional description of the noncoding transcriptome, and the lack of structural and mechanistic understanding of complex noncoding RNAs and RNPs. We seek a new member to join our diverse group to study gene-regulatory riboswitches, highly structured viral RNAs, long noncoding and circular RNAs and their RNP complexes. See https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html for details. The lab is part of the Earl Stadtman Investigator program for high-risk, high-impact research at the NIH intramural program consisting of 1100 labs. The lab has dedicated access to complete suites of state-of-the-art equipment in structural biology (Mosquito, Dragonfly, Rock Imager, Akta Pures, FSEC, etc., and regular synchrotron access for X-ray crystallography; Titan Krios and Glacios for single-particle Cryo-EM; SAXS, AFM, NMR, etc), cutting-edge biochemistry, biophysics (ITC, DSC, SPR, BLI, AUC, DLS, SEC-MALS, CD, fluorescence, thermophoresis, iSCAMS, etc), fermentation, advanced mass spec, genomics and sequencing, and proteomics core facilities with hands-on training or service by PhD-level staff scientists. We apply innovative technologies to study RNA and RNP structure, dynamics, and interactions, such as rational RNA design and engineering, RNA cryo-EM, XFEL, ultrafast SAXS/WAXS, single-molecule fluorescence, crosslinking-mass spec., etc. Ongoing projects include structural and mechanistic elucidations of the T-box riboswitches in bacteria and Gcn2 kinase in eukaryotes in cellular stress responses. A second area addresses how numerous viral and host structured noncoding RNAs differentially manipulate immune protein activities such as PKR. For details refer to recent publications: Suddala K.C & Zhang, J. (2019) High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove, Nat. Struct. & Mol. Biol., 26, 1114–1122. Li S. et al., & Zhang, J. (2019) Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions, Nat. Struct. & Mol. Biol., 26, 1094–1105. Hood, I.V. et al., & Zhang, J. (2019). Crystal structure of an Adenovirus Virus-Associated RNA, Nat. Commun. 10:2871 Incoming fellows are also encouraged to bring your own ideas that you could develop into research programs that you can then take to your independent PI positions. The NIH, NIDDK, and LMB are committed to the continued education and career development of trainees through numerous courses and workshops offered by OITE, FAES, and NIDDK. Requirements: Interested candidates must have received (or be expecting) a Ph.D. or M.D. within the past five years in molecular biology, structural biology, biochemistry, cell biology, or a related discipline, have excellent oral and written communication skills, and be strongly self-motivated to participate in and design innovative and rigorous research projects. Prior experiences in structural biology are not required. To apply: Please email a cover letter indicating preferred start date, CV, a brief summary of research interests, accomplishments, and career goals, and names and contact information for at least three references to: Dr. Jinwei Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse community in its training and employment programs. DHHS/NIH is an Equal Opportunity Employer. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Noncoding RNA Structural Biology trainee position at NIH
A postdoctoral or technician position is immediately available in the Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab addresses a widening gap between the accelerated discovery and functional description of the noncoding transcriptome, and a paucity of 3D structures and mechanistic understanding of complex noncoding RNAs. We seek a new member to join our diverse group to study gene-regulatory riboswitches, highly structured viral RNAs, circular and other structured long noncoding RNAs, and their protein complexes. See https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html The lab is part of the Earl Stadtman Investigator program for high-risk, high-impact research at the NIH intramural program consisting of 1100 labs. The well-supported lab has dedicated access to complete suites of state-of-the-art equipment in structural biology (Mosquito, Dragonfly, Rock Imager, Akta Pures, FSEC, etc. for X-ray crystallography; new Titan Krios for single-particle Cryo-EM; SAXS, AFM, etc), efficient biochemistry, biophysics (ITC, DSC, SPR, BLI, AUC, DLS, SEC-MALS, CD, fluorescence, thermophoresis, etc), fermentation, genomics, and proteomics core facilities with hands-on training or service by PhD-level staff scientists. The NIH, NIDDK, and LMB are committed to the continued education and career development of trainees through numerous courses and workshops offered by OITE and FAES. We apply innovative technologies to study RNA and RNP structure/function, including RNA cryo-EM, time-resolved XFEL, picosecond SAXS/WAXS, etc. Ongoing research include structural and mechanistic elucidations of how the T-box riboswitches (in bacteria) and Gcn2 kinase (in eukaryotes) recognize the structure and aminoacylation state of tRNA, and couple this readout of nutrient availability with initiating cellular starvation response. A second project addresses how viral and cellular RNA structures differentially manipulate immune response protein activities such as dsRNA-binding PKR. We are delineating the structural hallmarks of self vs. non-self RNA, which are deterministic for activation or suppression of immune protein activity. The lab also works closely with the Center for HIV RNA Studies (CRNA) as a core lab. https://sites.google.com/a/umich.edu/the-center-for-hiv-rna-studies/faculty-cores. Incoming fellows are also encouraged to bring your own ideas that you could develop into research programs that you can take to your independent positions. Requirements: Postdoctoral candidates must have received (or be expecting) a Ph.D. or M.D. within the past five years in molecular or structural biology, biochemistry, or biophysics, and be strongly self-motivated to lead innovative and rigorous research projects. Technician or Postbac candidates should have a BS or MS degree in similar disciplines and extensive laboratory experiences. Strong background in protein expression and purification, enzyme kinetics, RNA, or structural biology is desirable. To apply: Please email a preferred start date, CV, a brief summary of research interests, accomplishments, and career goals, and names and contact information for at least three references to: Dr. Jinwei Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse community and DHHS/NIH is an Equal Opportunity Employer.
[ccp4bb] Postdoctoral Position Available to Study Structure and Mechanisms of Gene-regulatory Noncoding RNAs and Highly Structured Viral RNAs
A fully funded postdoctoral position (up to 5 years) is available in the Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab addresses a widening gap between the accelerated discovery and functional description of the noncoding transcriptome, and a paucity of 3D structures and mechanistic understanding of complex noncoding RNAs. We seek a new member to join our diverse group to deepen current work on gene-regulatory riboswitches, highly structured viral RNAs, circular and other structured long noncoding RNAs. https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html Current manuscripts and recent publications: 1. Li et al., & Zhang (2017) Structural basis of amino acid sensing on the tRNA by a T-box riboswitch. In preparation. 2. Bahmanjah et al., & Zhang (2017) Structural basis of functional repurposing of an aminoacyl-tRNA synthetase in stress response. In preparation. 3. Hood et al., & Zhang (2017) Structural mimicry of codon-anticodon interactions by a viral noncoding RNA. In preparation. 4. Zhang & Ferré-D'Amaré (2014) Dramatic improvement of crystals of large RNA by cation replacement and dehydration. Structure 22, 1363-1371. 5. Zhang & Ferré-D'Amaré (2014) Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Molecular Cell 55, 148-155. 6. Zhang & Ferré-D'Amaré (2013) Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363-7. The lab is part of the Earl Stadtman Investigator program for high-risk, high-impact research at the NIH intramural program consisting of 1100 labs. The well-supported lab has dedicated access to state-of-the-art equipment in structural biology (Mosquito, Dragonfly, Rock Imager, Akta Pures, FSEC, for X-ray crystallography; new Titan Krios for single-particle Cryo-EM; SAXS, AFM, etc), efficient biochemistry, biophysics (ITC, DSC, SPR, BLI, AUC, DLS, SEC-MALS, CD, fluorescence, thermophoresis, etc), fermentation, genomics, and proteomics core facilities with hands-on training or service by PhD-level staff scientists. The NIH, NIDDK, and LMB are committed to the continued education and career development of trainees through numerous courses and workshops offered by NIH OITE and FAES. Requirements: Interested candidates must have received (or be expecting) a Ph.D. or M.D. within the past five years in molecular or structural biology, biochemistry, or biophysics, and be strongly self-motivated to lead innovative and rigorous research projects. Strong background in protein expression and purification, enzyme kinetics, and structural biology is desirable. To apply: Please email a preferred start date, CV, a brief summary of research interests, accomplishments, and career goals, and names and contact information for at least three references to: Dr. Jinwei Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse community and DHHS/NIH is an Equal Opportunity Employer.
[ccp4bb] Postdoctoral fellowship to study structure and mechanism of noncoding RNAs and ribonucleoproteins at the Laboratory of Molecular Biology, NIDDK, NIH
Dear Colleagues, I am looking for a talented young scientist to join my new group at the Laboratory of Molecular Biology at NIDDK, in NIH’s main campus in Bethesda, MD, USA. Set in an exciting and burgeoning field, the lab will explore the emerging roles of large noncoding RNAs (lncRNAs, HIV and other viral RNAs, tRNAs, etc) in bacterial and eukaryotic gene regulation, stress response, and signal transduction, using multidisciplinary tools such as X-ray crystallography, high-resolution Cryo-EM, small-angle X-ray scattering, fluorescence spectroscopy, chemical biology, and other biochemical and biophysical tools. If you are interested or know of a suitable candidate, please contact me at jinwei.zh...@nih.gov. Thank you, -Jinwei Postdoctoral Position Available to Study Structure and Mechanisms of Gene-regulatory Noncoding RNAs and Ribonucleoprotein Complexes. A postdoctoral position is available starting in the Fall of 2015 in Dr. Jinwei Zhang’s group as part of the Laboratory of Molecular Biology (LMB) at the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), in the National Institutes of Health’s vibrant main campus in Bethesda, MD just outside of Washington DC. More details will become available at http://www-mslmb.niddk.nih.gov/ and http://www.niddk.nih.gov/research-funding/at-niddk/labs-branches/LMB/joining-soon/Pages/dr-jinwei-zhang-phd.aspx The laboratory aims to address a widening gap between the exponential growth of genome-wide discovery and functional description of the noncoding transcriptome, and a significant lack of three-dimensional structural information and mechanistic understanding of such complex noncoding RNAs. Initial projects include gene-regulatory riboswitches, stress-sensing Gcn2 kinase system, HIV and other viral RNA and RNPs. The laboratory is established under the Earl Stadtman Investigator program, designed to facilitate high-risk, high-impact research (http://irp.nih.gov/careers/trans-nih-scientific-recruitments/stadtman-tenure-track-investigators). The research of the group is supported by the collaborative and interdisciplinary NIH intramural program consisting of more than 1100 labs and state-of-the-art equipment in structural biology (X-ray crystallography, Cryo-EM, SAXS, etc), biochemistry and biophysics core facilities with hands-on training provided by PhD-level support staff, genomics (RNA-seq), proteomics, and bioinformatics cores, flow cytometry and microscopy, etc. The NIH, NIDDK, and LMB are committed to the continued education and career development of trainees in many aspects such as numerous courses and workshops offered by NIH Office of Intramural Training Education (OITE) and Foundation for Advanced Education in the Sciences (FAES), as well as intramural career transition funding (K grants) opportunities. Requirements: Interested candidates must have received (or be expecting) a Ph.D. or M.D. within the past five years in molecular biology, structural biology, biochemistry, cell biology, or a related discipline and be strongly self-motivated to participate in and design innovative and rigorous research programs. To apply: Please email a cover letter indicating preferred start date, CV, a brief summary of research interests, accomplishments, and career goals, and names and contact information for at least three references to: Dr. Jinwei Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse community in its training and employment programs. DHHS/NIH is an Equal Opportunity Employer.
