9F3S | pdb_00009f3s

13pf mosaic 20%E254Q - 80% E254N microtubule from recombinant human tubulin decorated with EB3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Hydrolysis-deficient mosaic microtubules as faithful mimics of the GTP cap.

Estevez-Gallego, J.Blum, T.B.Ruhnow, F.Gili, M.Speroni, S.Garcia-Castellanos, R.Steinmetz, M.O.Surrey, T.

(2025) Nat Commun 16: 2396-2396

  • DOI: https://doi.org/10.1038/s41467-025-57555-6
  • Primary Citation of Related Structures:  
    9F3B, 9F3H, 9F3R, 9F3S

  • PubMed Abstract: 

    A critical feature of microtubules is their GTP cap, a stabilizing GTP-tubulin rich region at growing microtubule ends. Microtubules polymerized in the presence of GTP analogs or from GTP hydrolysis-deficient tubulin mutants have been used as GTP-cap mimics for structural and biochemical studies. However, these analogs and mutants generate microtubules with diverse biochemical properties and lattice structures, leaving it unclear what is the most faithful GTP mimic and hence the structure of the GTP cap. Here, we generate a hydrolysis-deficient human tubulin mutant, αE254Q, with the smallest possible modification. We show that αE254Q-microtubules are stable, but still exhibit mild mutation-induced growth abnormalities. However, mixing two GTP hydrolysis-deficient tubulin mutants, αE254Q and αE254N, at an optimized ratio eliminates growth and lattice abnormalities, indicating that these 'mosaic microtubules' are faithful GTP cap mimics. Their cryo-electron microscopy structure reveals that longitudinal lattice expansion, but not protofilament twist, is the primary structural feature distinguishing the GTP-tubulin containing cap from the GDP-tubulin containing microtubule shaft. However, alterations in protofilament twist may be transiently needed to allow lattice compaction and GTP hydrolysis. Together, our results provide insights into the structural origin of GTP cap stability, the pathway of GTP hydrolysis and hence microtubule dynamic instability.


  • Organizational Affiliation

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. juan.estevez-gallego@psi.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated protein RP/EB family member 3A [auth S],
B [auth T]
131Homo sapiensMutation(s): 0 
Gene Names: MAPRE3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPY8 (Homo sapiens)
Explore Q9UPY8 
Go to UniProtKB:  Q9UPY8
PHAROS:  Q9UPY8
GTEx:  ENSG00000084764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPY8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Detyrosinated tubulin alpha-1B chain453Homo sapiensMutation(s): 1 
Gene Names: TUBA1B
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens)
Explore P68363 
Go to UniProtKB:  P68363
PHAROS:  P68363
GTEx:  ENSG00000123416 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68363
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-3 chain456Homo sapiensMutation(s): 0 
Gene Names: TUBB3TUBB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13509 (Homo sapiens)
Explore Q13509 
Go to UniProtKB:  Q13509
PHAROS:  Q13509
GTEx:  ENSG00000258947 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13509
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth I]
CA [auth P]
EA [auth E]
GA [auth F]
IA [auth K]
AA [auth I],
CA [auth P],
EA [auth E],
GA [auth F],
IA [auth K],
KA [auth R],
O [auth A],
Q [auth B],
S [auth G],
U [auth N],
W [auth C],
Y [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth I]
DA [auth P]
FA [auth E]
HA [auth F]
JA [auth K]
BA [auth I],
DA [auth P],
FA [auth E],
HA [auth F],
JA [auth K],
LA [auth R],
P [auth A],
R [auth B],
T [auth G],
V [auth N],
X [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.21
MODEL REFINEMENTPHENIX1.21

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2019-108415GB-I00
Swiss National Science FoundationSwitzerland310030_192566
Generalitat de CatalunyaSpainIU16-014045 (CRYO-TEM)
European Research Council (ERC)European Union951430
Spanish Ministry of Science, Innovation, and UniversitiesSpainFJC2020-043857-I

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release