Re: [ccp4bb] Helix forming proteins crystallizing as rings
Hi Joern, have a look at these two papers (and probably KK is reading this too and can chime in with the right set of coordinates), Korotkov et al. Secretins: dynamic channels for protein transport across membranes. Trends Biochem Sci (2011) vol. 36 (8) pp. 433-43 Reichow et al. Structure of the cholera toxin secretion channel in its closed state. Nat Struct Mol Biol (2010) vol. 17 (10) pp. 1226-32 I recall in one of the structures an "open continuos helix" with 12 molecules forming a spiral in the crystal lattice. The EM reconstruction showed 12fold symmetry and when you "flatten" the ring from the crystal structure it fitted well into the EM structure. Don't recall details at this point, but I think this is what you are looking for. Jürgen On Jun 5, 2013, at 7:44 AM, Joern Krausze wrote: > Dear Tim, > > the rings I mean are similar to the one in 4FC4 but to my understanding > FocA does not form helices under physiological conditions. > > I am sorry if I was not specific enough. I will give you more details. I > am working on two proteins which are dimers in solution. > > The first of them crystallizes as flat rings consisting of four or five > dimers (the rings showing D4 and D5 point group symmetry, respectively), > depending on the crystal form. We got three different crystal forms, one > of which contains the D4 ring, two of which contain the D5 ring. > > The second protein is homologous to the first and crstallizes in space > group P1. Through the translational symmetry, the dimers form > pseudo-infinite fibers. The crystal contacts are realized by residues > homologous to the residues that form the interfaces in the rings of the > first protein. These residues are conserved and hence seem to be of > importance. > > We now think that these proteins form helices under particular > physiological conditions. We have (weak) biochemical data which support > this assumption and it also makes sense mechanistically. We interpreted > the crystal structures accordingly. We think that these helices are of the > same width as the D4 or D5 rings but with a helical symmetry along the > four- or fivefold axis instead of the purely rotational symmetry. We deem > the rings of the first protein and the fiber of the second protein special > cases of the helix: the rings are helices with a pitch of zero and the > fiber would be a helix with zero turns (or a flat curvature). > > A reviewer now does not really follow our argumentation and asked us to > provide him with examples of proteins showing a similar behavior, i.e. > normally forming helices but forming rings (or fibers) in the crystal. > > Thanks to everyone for their help. > > Best regards, > > Joern > > ** > Address: > > Joern Krausze > Molecular Structural Biology > Helmholtz Centre for Infection Research > Inhoffenstrasse 7 > 38124 Braunschweig > Germany > > Email: joern.krau...@helmholtz-hzi.de > Phone: +49 (0)531 6181 7023 (office) > +49 (0)531 6181 7020 (lab) > ** > > On Wed, 5 Jun 2013, Tim Gruene wrote: > >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Joern, >> >> I am not sure this is what you have in mind: just yesterday I heard a >> talk from Oliver Einsle about FocA ion channels - look at PDB ID 4FC4, >> for example forming a (flat) pentamer, and let us know if this is what >> you mean. >> >> Best, >> Tim >> >> On 06/04/2013 05:24 PM, Joern Krausze wrote: >>> Dear all, >>> >>> can anyone provide me with examples for proteins that form a >>> helical oligomer under physiological conditions and flat rings >>> (basically a helix with a pitch of 0) in the crystal? I only know >>> examples of the other way around. >>> >>> Thank you in advance. >>> >>> Joern >>> >>> ** Address: >>> >>> Joern Krausze Molecular Structural Biology Helmholtz Centre for >>> Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany >>> >>> Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 >>> (office) +49 (0)531 6181 7020 (lab) >>> ** >>> >>> >>> >>> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 >>> | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 >>> zertifiziertes Mitglied im "audit berufundfamilie" >>> >>> Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, >>> Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger >>> Eichel, Abteilungsleiter Niedersächsisches Ministerium für >>> Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf >>> Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der >>> Gesellschaft: Braunschweig Handelsregister: Amtsgericht >>> Braunschweig, HRB 477 >>> >> >> - -- >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID =
Re: [ccp4bb] Helix forming proteins crystallizing as rings
Dear Tim, the rings I mean are similar to the one in 4FC4 but to my understanding FocA does not form helices under physiological conditions. I am sorry if I was not specific enough. I will give you more details. I am working on two proteins which are dimers in solution. The first of them crystallizes as flat rings consisting of four or five dimers (the rings showing D4 and D5 point group symmetry, respectively), depending on the crystal form. We got three different crystal forms, one of which contains the D4 ring, two of which contain the D5 ring. The second protein is homologous to the first and crstallizes in space group P1. Through the translational symmetry, the dimers form pseudo-infinite fibers. The crystal contacts are realized by residues homologous to the residues that form the interfaces in the rings of the first protein. These residues are conserved and hence seem to be of importance. We now think that these proteins form helices under particular physiological conditions. We have (weak) biochemical data which support this assumption and it also makes sense mechanistically. We interpreted the crystal structures accordingly. We think that these helices are of the same width as the D4 or D5 rings but with a helical symmetry along the four- or fivefold axis instead of the purely rotational symmetry. We deem the rings of the first protein and the fiber of the second protein special cases of the helix: the rings are helices with a pitch of zero and the fiber would be a helix with zero turns (or a flat curvature). A reviewer now does not really follow our argumentation and asked us to provide him with examples of proteins showing a similar behavior, i.e. normally forming helices but forming rings (or fibers) in the crystal. Thanks to everyone for their help. Best regards, Joern ** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ** On Wed, 5 Jun 2013, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Joern, I am not sure this is what you have in mind: just yesterday I heard a talk from Oliver Einsle about FocA ion channels - look at PDB ID 4FC4, for example forming a (flat) pentamer, and let us know if this is what you mean. Best, Tim On 06/04/2013 05:24 PM, Joern Krausze wrote: Dear all, can anyone provide me with examples for proteins that form a helical oligomer under physiological conditions and flat rings (basically a helix with a pitch of 0) in the crystal? I only know examples of the other way around. Thank you in advance. Joern ** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ** Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRrxUKUxlJ7aRr7hoRAqDgAJ0TGztRVpkcLPGlxNm8S9ogPy+5BACg0nVK mnWE5qBeTHzVUx81jlZb7mA= =6Ji9 -END PGP SIGNATURE- Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] Helix forming proteins crystallizing as rings
I too am not sure what is being asked but do the TMV helix and disk structures count? See for example slide 3 in http://users.ipfw.edu/blumenth/Virology/Assembly.PDF Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: 05 June 2013 11:38 To: ccp4bb Subject: Re: [ccp4bb] Helix forming proteins crystallizing as rings -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Joern, I am not sure this is what you have in mind: just yesterday I heard a talk from Oliver Einsle about FocA ion channels - look at PDB ID 4FC4, for example forming a (flat) pentamer, and let us know if this is what you mean. Best, Tim On 06/04/2013 05:24 PM, Joern Krausze wrote: > Dear all, > > can anyone provide me with examples for proteins that form a helical > oligomer under physiological conditions and flat rings (basically a > helix with a pitch of 0) in the crystal? I only know examples of the > other way around. > > Thank you in advance. > > Joern > > ** Address: > > Joern Krausze Molecular Structural Biology Helmholtz Centre for > Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany > > Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 > (office) +49 (0)531 6181 7020 (lab) > ** > > > > Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 > | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 > zertifiziertes Mitglied im "audit berufundfamilie" > > Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, > Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger > Eichel, Abteilungsleiter Niedersächsisches Ministerium für > Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf > Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der > Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, > HRB 477 > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRrxUKUxlJ7aRr7hoRAqDgAJ0TGztRVpkcLPGlxNm8S9ogPy+5BACg0nVK mnWE5qBeTHzVUx81jlZb7mA= =6Ji9 -END PGP SIGNATURE-
Re: [ccp4bb] Helix forming proteins crystallizing as rings
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Joern, I am not sure this is what you have in mind: just yesterday I heard a talk from Oliver Einsle about FocA ion channels - look at PDB ID 4FC4, for example forming a (flat) pentamer, and let us know if this is what you mean. Best, Tim On 06/04/2013 05:24 PM, Joern Krausze wrote: > Dear all, > > can anyone provide me with examples for proteins that form a > helical oligomer under physiological conditions and flat rings > (basically a helix with a pitch of 0) in the crystal? I only know > examples of the other way around. > > Thank you in advance. > > Joern > > ** Address: > > Joern Krausze Molecular Structural Biology Helmholtz Centre for > Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany > > Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 > (office) +49 (0)531 6181 7020 (lab) > ** > > > > Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 > | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 > zertifiziertes Mitglied im "audit berufundfamilie" > > Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, > Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger > Eichel, Abteilungsleiter Niedersächsisches Ministerium für > Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf > Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der > Gesellschaft: Braunschweig Handelsregister: Amtsgericht > Braunschweig, HRB 477 > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRrxUKUxlJ7aRr7hoRAqDgAJ0TGztRVpkcLPGlxNm8S9ogPy+5BACg0nVK mnWE5qBeTHzVUx81jlZb7mA= =6Ji9 -END PGP SIGNATURE-
[ccp4bb] Helix forming proteins crystallizing as rings
Dear all, can anyone provide me with examples for proteins that form a helical oligomer under physiological conditions and flat rings (basically a helix with a pitch of 0) in the crystal? I only know examples of the other way around. Thank you in advance. Joern ** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ** Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
