6GX7 | pdb_00006gx7

Tubulin-CopN-alphaRep complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.210 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6GX7

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Insight into microtubule nucleation from tubulin-capping proteins.

Campanacci, V.Urvoas, A.Cantos-Fernandes, S.Aumont-Nicaise, M.Arteni, A.A.Velours, C.Valerio-Lepiniec, M.Dreier, B.Pluckthun, A.Pilon, A.Pous, C.Minard, P.Gigant, B.

(2019) Proc Natl Acad Sci U S A 116: 9859-9864

  • DOI: https://doi.org/10.1073/pnas.1813559116
  • Primary Citation Related Structures: 
    6GVM, 6GVN, 6GX7

  • PubMed Abstract: 

    Nucleation is one of the least understood steps of microtubule dynamics. It is a kinetically unfavorable process that is templated in the cell by the γ-tubulin ring complex or by preexisting microtubules; it also occurs in vitro from pure tubulin. Here we study the nucleation inhibition potency of natural or artificial proteins in connection with their binding mode to the longitudinal surface of α- or β-tubulin. The structure of tubulin-bound CopN, a Chlamydia protein that delays nucleation, suggests that this protein may interfere with two protofilaments at the (+) end of a nucleus. Designed ankyrin repeat proteins that share a binding mode similar to that of CopN also impede nucleation, whereas those that target only one protofilament do not. In addition, an αRep protein predicted to target two protofilaments at the (-) end does not delay nucleation, pointing to different behaviors at both ends of the nucleus. Our results link the interference with protofilaments at the (+) end and the inhibition of nucleation.


  • Organizational Affiliation
    • Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 323.1 kDa 
  • Atom Count: 20,341 
  • Modeled Residue Count: 2,645 
  • Deposited Residue Count: 2,866 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha chain
A, C
451Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWZ0 (Ovis aries)
Explore D0VWZ0 
Go to UniProtKB:  D0VWZ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWZ0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
445Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWY9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
iiiA5 ALPHAREP
E, F
201synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Low calcium response E
G, H
336Chlamydia pneumoniaeMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q9Z8L4 (Chlamydia pneumoniae)
Explore Q9Z8L4 
Go to UniProtKB:  Q9Z8L4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z8L4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
I [auth A],
L [auth B],
Q [auth C],
T [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
N [auth B],
O [auth B],
V [auth D],
W [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
X [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth A],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
P [auth B],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
J [auth A],
M [auth B],
R [auth C],
U [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.210 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.06α = 90
b = 95.85β = 101.49
c = 158.06γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.3: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description