9EOK | pdb_00009eok

Minus end of the vertebrate gamma-tubulin ring complex-capped microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9EOK

This is version 1.1 of the entry. See complete history

Literature

gamma-TuRC asymmetry induces local protofilament mismatch at the RanGTP-stimulated microtubule minus end.

Vermeulen, B.J.Bohler, A.Gao, Q.Neuner, A.Zupa, E.Chu, Z.Wurtz, M.Jakle, U.Gruss, O.J.Pfeffer, S.Schiebel, E.

(2024) EMBO J 43: 2062-2085

  • DOI: https://doi.org/10.1038/s44318-024-00087-4
  • Primary Citation Related Structures: 
    9EOJ, 9EOK

  • PubMed Abstract: 

    The γ-tubulin ring complex (γ-TuRC) is a structural template for de novo microtubule assembly from α/β-tubulin units. The isolated vertebrate γ-TuRC assumes an asymmetric, open structure deviating from microtubule geometry, suggesting that γ-TuRC closure may underlie regulation of microtubule nucleation. Here, we isolate native γ-TuRC-capped microtubules from Xenopus laevis egg extract nucleated through the RanGTP-induced pathway for spindle assembly and determine their cryo-EM structure. Intriguingly, the microtubule minus end-bound γ-TuRC is only partially closed and consequently, the emanating microtubule is locally misaligned with the γ-TuRC and asymmetric. In the partially closed conformation of the γ-TuRC, the actin-containing lumenal bridge is locally destabilised, suggesting lumenal bridge modulation in microtubule nucleation. The microtubule-binding protein CAMSAP2 specifically binds the minus end of γ-TuRC-capped microtubules, indicating that the asymmetric minus end structure may underlie recruitment of microtubule-modulating factors for γ-TuRC release. Collectively, we reveal a surprisingly asymmetric microtubule minus end protofilament organisation diverging from the regular microtubule structure, with direct implications for the kinetics and regulation of nucleation and subsequent modulation of microtubules during spindle assembly.


  • Organizational Affiliation
    • Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 2,137.4 kDa 
  • Atom Count: 143,457 
  • Modeled Residue Count: 17,984 
  • Deposited Residue Count: 18,805 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha chain450Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q5U4V6 (Xenopus laevis)
Explore Q5U4V6 
Go to UniProtKB:  Q5U4V6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U4V6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-4 chain445Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P30883 (Xenopus laevis)
Explore P30883 
Go to UniProtKB:  P30883
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30883
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1

Query on TA1



Download:Ideal Coordinates CCD File
AB [auth F]
BC [auth S]
DC [auth T]
EC [auth U]
HC [auth V]
AB [auth F],
BC [auth S],
DC [auth T],
EC [auth U],
HC [auth V],
JC [auth W],
LC [auth X],
NC [auth Y],
ND [auth o],
PC [auth Z],
PD [auth p],
RC [auth a],
RD [auth q],
TA [auth B],
TC [auth b],
TD [auth r],
VD [auth s],
XB [auth Q],
ZB [auth R]
TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP

Query on GTP



Download:Ideal Coordinates CCD File
AD [auth f]
CB [auth G]
CD [auth g]
EB [auth H]
ED [auth h]
AD [auth f],
CB [auth G],
CD [auth g],
EB [auth H],
ED [auth h],
GB [auth I],
GD [auth i],
IB [auth J],
ID [auth j],
KB [auth K],
KD [auth k],
MB [auth L],
OB [auth M],
QA [auth A],
QB [auth N],
SB [auth O],
UA [auth C],
UB [auth P],
UC [auth c],
WA [auth D],
WC [auth d],
YA [auth E],
YC [auth e]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
AC [auth S]
BB [auth F]
CC [auth T]
FC [auth U]
GC [auth V]
AC [auth S],
BB [auth F],
CC [auth T],
FC [auth U],
GC [auth V],
IC [auth W],
KC [auth X],
MC [auth Y],
MD [auth o],
OC [auth Z],
OD [auth p],
QC [auth a],
QD [auth q],
SA [auth B],
SC [auth b],
SD [auth r],
UD [auth s],
WB [auth Q],
YB [auth R]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BD [auth f]
DB [auth G]
DD [auth g]
FB [auth H]
FD [auth h]
BD [auth f],
DB [auth G],
DD [auth g],
FB [auth H],
FD [auth h],
HB [auth I],
HD [auth i],
JB [auth J],
JD [auth j],
LB [auth K],
LD [auth k],
NB [auth L],
PB [auth M],
RA [auth A],
RB [auth N],
TB [auth O],
VA [auth C],
VB [auth P],
VC [auth c],
XA [auth D],
XC [auth d],
ZA [auth E],
ZC [auth e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyPF 963/1-4
German Research Foundation (DFG)GermanySchi 295/4-4
Other private--
German Research Foundation (DFG)GermanyINST 35/1314-1 FUGG
German Research Foundation (DFG)GermanyINST 35/1503-1 FUGG
German Research Foundation (DFG)GermanyINST 35/1134-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection