9TG8 | pdb_00009tg8

Drebrin actin binding domain 1 conformation A (ABD1a) bound to F-actin

PDB DOI: https://doi.org/10.2210/pdb9TG8/pdb
EM Map EMD-55893: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, Oryctolagus cuniculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-11-28 Released: 2026-09-02
Deposition Author(s): Zhao, W., Abis, G., Oozeer, F., Mulvaney, T., Nagar, N., Topf, M., Gordon-Weeks, P.R., Conte, M.R., Atherton, J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), UK Research and Innovation (UKRI), Leverhulme Trust, Wellcome Trust, British Heart Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.37 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural mechanisms of drebrin-mediated F-actin network modulation.

Zhao, W., Chu, L.Y., Abis, G., Oozeer, F., Mulvaney, T., Nagar, N., Topf, M., Gordon-Weeks, P.R., Conte, M.R., Atherton, J.

(2026) Nat Commun 17

PubMed: 42337253 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-74543-6
Primary Citation Related Structures:
9TG8, 9TG9, 9TGA

PubMed Abstract:
Drebrin modulates F-actin networks and links them to other intracellular components, regulating crucial processes including neuritogenesis, synaptic plasticity, virus internalisation and cancer invasion. Using single-particle cryo-EM we characterise drebrin's interaction with F-actin through two separate conserved actin binding domains (ABD1 and ABD2), revealing structural bases for its F-actin-modulating properties. We describe a multimodal interaction where drebrin's ABD1 can adopt two conformations and a long flexible loop connecting to ABD2 allows the two ABDs to occupy multiple relative positions along F-actin. The flexible loop connecting the two ABDs also confers some propensity to loosely bundle F-actin. Drebrin's ABDs bind across multiple actin protomers and their subdomains and modify the longitudinal inter-protomer interface, explaining its F-actin stabilising properties. Furthermore, we show drebrin's binding site on F-actin is shared with other critical actin-binding and regulatory proteins, explaining their competitive displacement.

Organizational Affiliation

Randall Centre for Cell and Molecular Biophysics, King's College London - New Hunt's House, Guy's Campus, London, UK.

Macromolecule Content

Total Structure Weight: 111.31 kDa
Atom Count: 6,701
Modeled Residue Count: 805
Deposited Residue Count: 975
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Drebrin	A	221	Homo sapiens	Mutation(s): 0 Gene Names: DBN1, D0S117E
UniProt & NIH Common Fund Data Resources
Find proteins for Q16643 (Homo sapiens) Explore Q16643 Go to UniProtKB: Q16643
PHAROS: Q16643 GTEx: ENSG00000113758
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16643
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	B, C [auth D]	377	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth D] MOL2 format, chain D [auth B] MOL2 format, chain F [auth D] mmCIF format, chain D [auth B] mmCIF format, chain F [auth D]	D [auth B], F [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth B] Focus chain F [auth D] Interactions & Density Focus chain D [auth B] Focus chain F [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth D] MOL2 format, chain E [auth B] MOL2 format, chain G [auth D] mmCIF format, chain E [auth B] mmCIF format, chain G [auth D]	E [auth B], G [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain G [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	B, C [auth D]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.37 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V006568/1
UK Research and Innovation (UKRI)	United Kingdom	UKRI2979
Leverhulme Trust	United Kingdom	RPG-2020264
Wellcome Trust	United Kingdom	209250/Z/17/ Z
Wellcome Trust	United Kingdom	206175/Z/17/Z
Wellcome Trust	United Kingdom	202767/Z/16/Z
Leverhulme Trust	United Kingdom	EM-2022-038-2
British Heart Foundation	United Kingdom	IG/16/2/32273