9D2B | pdb_00009d2b

Symmetry-expanded reconstruction of augmin T-II bonsai on the microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

How augmin establishes the angle of the microtubule branch site.

Travis, S.M.Kraus, J.McManus, C.T.Golden, K.Zhang, R.Petry, S.

(2025) Nat Commun 16: 9646-9646

  • DOI: https://doi.org/10.1038/s41467-025-64650-1
  • Primary Citation of Related Structures:  
    9D2B, 9OLH

  • PubMed Abstract: 

    How microtubules (MTs) are generated in the proper orientation is essential to understanding how the cytoskeleton organizes a cell and MT-dependent events such as cell division. In the spindle, most MTs are generated through the branching MT nucleation pathway. In this pathway, new MTs are nucleated from the side of existing MTs and oriented at a shallow angle by the branching factor augmin, ensuring that both MTs have the same polarity. Yet, how augmin binds MTs and sets the branch angle has remained unclear. Here, we report the cryo-electron microscopy structure of an augmin subcomplex on the MT. This structure resembles that of NDC80 bound to the MT, with the conserved CH domain of augmin's Haus6 subunit directly proximal to the MT lattice. We find that the Haus6 CH domain is a bona fide MT binding site that increases augmin's affinity for the MT and helps establish branch angle. A second binding site, located in the disordered N-terminus of Haus8, also establishes branch angle,. Thus, we find that augmin regulates MT branching using two domains, each tuned to modulate MT affinity and MT branch angle. This work expands our mechanistic understanding of branching MT nucleation and thus spindle formation.


  • Organizational Affiliation
    • Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA [auth C],
C [auth A]
451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
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Go to UniProtKB:  P81947
Entity Groups  
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UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chain445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
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Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HAUS augmin like complex subunit 6 L homeolog isoform X1D [auth F]289Xenopus laevisMutation(s): 0 
Gene Names: haus6.Lhaus6
UniProt
Find proteins for A0A8J1MAE8 (Xenopus laevis)
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UniProt GroupA0A8J1MAE8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HAUS augmin like complex subunit 7 S homeologE [auth G]282Xenopus laevisMutation(s): 0 
Gene Names: haus7.Shaus7LOC100158301uchl5ipuip1
UniProt
Find proteins for B1H1T5 (Xenopus laevis)
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UniProt GroupB1H1T5
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
HAUS augmin-like complex subunit 8F [auth H]260Xenopus laevisMutation(s): 0 
Gene Names: haus8hice1
UniProt
Find proteins for Q0IHJ3 (Xenopus laevis)
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UniProt GroupQ0IHJ3
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth C],
K [auth A]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
G2P
Query on G2P

Download Ideal Coordinates CCD File 
I [auth B]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth C],
J [auth B],
L [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTCoot0.9.8.93
MODEL REFINEMENTPHENIX1.17.1-3660

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32 GM142149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99 GM152794
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01 GM138854
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01 GM141100

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references