9B27 | pdb_00009b27

Dia1 at the Barbed End of F-Actin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9B27

This is version 1.3 of the entry. See complete history

Literature

Mechanisms of actin filament severing and elongation by formins.

Palmer, N.J.Barrie, K.R.Dominguez, R.

(2024) Nature 632: 437-442

  • DOI: https://doi.org/10.1038/s41586-024-07637-0
  • Primary Citation Related Structures: 
    9AZ4, 9AZP, 9AZQ, 9B03, 9B0K, 9B27, 9B3D

  • PubMed Abstract: 

    Humans express fifteen formins, playing crucial roles in actin-based processes, such as cytokinesis, cell motility, and mechanotransduction 1,2 . However, the lack of structures bound to the actin filament (F-actin) has been a major impediment to understanding formin function. While formins are known for their ability to nucleate and elongate F-actin 3-7 , some formins can additionally depolymerize, sever, or bundle F-actin. Two mammalian formins, inverted formin-2 (INF2) and diaphanous-1 (Dia1), exemplify this diversity. INF2 displays potent severing activity but elongates weakly 8-11 , whereas Dia1 has potent elongation activity but does not sever 4,8 . Using cryo-electron microscopy (cryo-EM), we reveal five structural states of INF2 and two of Dia1 bound to the middle and barbed end of F-actin. INF2 and Dia1 bind differently to these sites, consistent with their distinct activities. The FH2 and WH2 domains of INF2 are positioned to sever F-actin, whereas Dia1 appears unsuited for severing. Structures also show how profilin-actin is delivered to the fast-growing barbed end, and how this is followed by a transition of the incoming monomer into the F-actin conformation and the release of profilin. Combined, the seven structures presented here provide step-by-step visualization of the mechanisms of F-actin severing and elongation by formins.


  • Organizational Affiliation
    • Department of Physiology and Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.

Macromolecule Content 

  • Total Structure Weight: 349.41 kDa 
  • Atom Count: 23,828 
  • Modeled Residue Count: 2,991 
  • Deposited Residue Count: 3,070 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle
A, B, C, D, E
A, B, C, D, E, F
371Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein diaphanous homolog 1
G, H
422Mus musculusMutation(s): 0 
Gene Names: Diaph1Diap1
UniProt & NIH Common Fund Data Resources
Find proteins for O08808 (Mus musculus)
Explore O08808 
Go to UniProtKB:  O08808
IMPC:  MGI:1194490
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08808
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC7 H11 N3 O2HIS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references
  • Version 1.3: 2024-08-21
    Changes: Data collection, Database references