7MIZ

Atomic structure of cortical microtubule from Toxoplasma gondii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins.

Wang, X.Fu, Y.Beatty, W.L.Ma, M.Brown, A.David Sibley, L.Zhang, R.

(2021) Nat Commun 12: 3065-3065

  • DOI: https://doi.org/10.1038/s41467-021-23351-1
  • Primary Citation of Related Structures:  
    7MIZ

  • PubMed Abstract: 

    In living cells, microtubules (MTs) play pleiotropic roles, which require very different mechanical properties. Unlike the dynamic MTs found in the cytoplasm of metazoan cells, the specialized cortical MTs from Toxoplasma gondii, a prevalent human pathogen, are extraordinarily stable and resistant to detergent and cold treatments. Using single-particle cryo-EM, we determine their ex vivo structure and identify three proteins (TrxL1, TrxL2 and SPM1) as bona fide microtubule inner proteins (MIPs). These three MIPs form a mesh on the luminal surface and simultaneously stabilize the tubulin lattice in both longitudinal and lateral directions. Consistent with previous observations, deletion of the identified MIPs compromises MT stability and integrity under challenges by chemical treatments. We also visualize a small molecule like density at the Taxol-binding site of β-tubulin. Our results provide the structural basis to understand the stability of cortical MTs and suggest an evolutionarily conserved mechanism of MT stabilization from the inside.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule associated protein SPM1351Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K285 (Toxoplasma gondii)
Explore A0A7J6K285 
Go to UniProtKB:  A0A7J6K285
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J6K285
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chain453Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for P10873 (Toxoplasma gondii)
Explore P10873 
Go to UniProtKB:  P10873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10873
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain449Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for I7BFC9 (Toxoplasma gondii)
Explore I7BFC9 
Go to UniProtKB:  I7BFC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7BFC9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PDI family protein220Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for Q8MPF4 (Toxoplasma gondii)
Explore Q8MPF4 
Go to UniProtKB:  Q8MPF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8MPF4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PDI family proteinGC [auth k],
HC [auth l],
QC [auth w],
RC [auth x]
189Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K232 (Toxoplasma gondii)
Explore A0A7J6K232 
Go to UniProtKB:  A0A7J6K232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J6K232
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AE [auth C0]
BF [auth D8]
CD [auth A4]
DE [auth C2]
EF [auth E0]
AE [auth C0],
BF [auth D8],
CD [auth A4],
DE [auth C2],
EF [auth E0],
FD [auth A6],
GE [auth C4],
HF [auth E2],
ID [auth A8],
JE [auth C6],
KF [auth E4],
LD [auth B0],
ME [auth C8],
NF [auth E6],
OD [auth B2],
PE [auth D0],
QF [auth E8],
RD [auth B4],
SE [auth D2],
TF [auth F0],
UD [auth B6],
VE [auth D4],
WC [auth A0],
XD [auth B8],
YE [auth D6],
ZC [auth A2]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
AF [auth D7]
BD [auth A3]
CE [auth C1]
DF [auth D9]
ED [auth A5]
AF [auth D7],
BD [auth A3],
CE [auth C1],
DF [auth D9],
ED [auth A5],
FE [auth C3],
GF [auth E1],
HD [auth A7],
IE [auth C5],
JF [auth E3],
KD [auth A9],
LE [auth C7],
MF [auth E5],
ND [auth B1],
OE [auth C9],
PF [auth E7],
QD [auth B3],
RE [auth D1],
SF [auth E9],
TD [auth B5],
UE [auth D3],
VF [auth F1],
WD [auth B7],
XE [auth D5],
YC [auth A1],
ZD [auth B9]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth A2]
BE [auth C0]
CF [auth D8]
DD [auth A4]
EE [auth C2]
AD [auth A2],
BE [auth C0],
CF [auth D8],
DD [auth A4],
EE [auth C2],
FF [auth E0],
GD [auth A6],
HE [auth C4],
IF [auth E2],
JD [auth A8],
KE [auth C6],
LF [auth E4],
MD [auth B0],
NE [auth C8],
OF [auth E6],
PD [auth B2],
QE [auth D0],
RF [auth E8],
SD [auth B4],
TE [auth D2],
UF [auth F0],
VD [auth B6],
WE [auth D4],
XC [auth A0],
YD [auth B8],
ZE [auth D6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2-387464
RECONSTRUCTIONRELION3.1
RECONSTRUCTIONcryoSPARC2.15

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI034036

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references