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- EMDB-55895: Drebrin actin binding domain 2 bound to F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-55895
TitleDrebrin actin binding domain 2 bound to F-actin
Map dataDrebrin ABD2 bound to F-actin, unsharpened map.
Sample
  • Complex: Drebrin actin binding domain 2 (ABD2) binding F-actin
    • Complex: Drebrin (isoform E, residues 135-355)
      • Protein or peptide: Drebrin
    • Complex: Actin (rabbit skeletal muscle alpha actin)
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsF-actin binding protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


positive regulation of receptor localization to synapse / regulation of dendrite development / profilin binding / positive regulation of dendritic spine morphogenesis / actomyosin / positive regulation of synaptic plasticity / gap junction / RHOD GTPase cycle / neural precursor cell proliferation / RHOBTB1 GTPase cycle ...positive regulation of receptor localization to synapse / regulation of dendrite development / profilin binding / positive regulation of dendritic spine morphogenesis / actomyosin / positive regulation of synaptic plasticity / gap junction / RHOD GTPase cycle / neural precursor cell proliferation / RHOBTB1 GTPase cycle / cytoskeletal motor activator activity / generation of neurons / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / cortical cytoskeleton / regulation of neuronal synaptic plasticity / skeletal muscle myofibril / striated muscle thin filament / RHOH GTPase cycle / actin filament bundle assembly / skeletal muscle thin filament assembly / actin monomer binding / postsynaptic cytosol / RHOBTB2 GTPase cycle / skeletal muscle fiber development / actin filament polymerization / stress fiber / titin binding / actin filament organization / filopodium / actin filament / protein sequestering activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin cytoskeleton / lamellipodium / growth cone / actin binding / cell body / cytoskeleton / postsynaptic membrane / postsynaptic density / cadherin binding / protein domain specific binding / hydrolase activity / positive regulation of gene expression / calcium ion binding / dendrite / glutamatergic synapse / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Drebrin
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsZhao W / Abis G / Oozeer F / Mulvaney T / Nagar N / Topf M / Gordon-Weeks PR / Conte MR / Atherton J
Funding support United Kingdom, 8 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006568/1 United Kingdom
UK Research and Innovation (UKRI)UKRI2979 United Kingdom
Leverhulme TrustRPG-2020264 United Kingdom
Wellcome Trust209250/Z/17/ Z United Kingdom
Wellcome Trust206175/Z/17/Z United Kingdom
Wellcome Trust202767/Z/16/Z United Kingdom
Leverhulme TrustEM-2022-038-2 United Kingdom
British Heart FoundationIG/16/2/32273 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural mechanisms of drebrin-mediated F-actin network modulation.
Authors: W Zhao / L Y Chu / G Abis / F Oozeer / T Mulvaney / N Nagar / M Topf / P R Gordon-Weeks / M R Conte / J Atherton /
Abstract: Drebrin modulates F-actin networks and links them to other intracellular components, regulating crucial processes including neuritogenesis, synaptic plasticity, virus internalisation and cancer ...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.
History
DepositionNov 28, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55895.png

Downloads & links

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Map

FileDownload / File: emd_55895.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrebrin ABD2 bound to F-actin, unsharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 448 pix.
= 417.088 Å		0.93 Å/pix.
x 448 pix.
= 417.088 Å		0.93 Å/pix.
x 448 pix.
= 417.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.931 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.015244818 - 0.057794012
Average (Standard dev.)-0.0000013354634 (±0.0012552089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 417.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55895_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Drebrin ABD2 bound to F-actin, local resolution sharpened map.

Fileemd_55895_additional_1.map
AnnotationDrebrin ABD2 bound to F-actin, local resolution sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Drebrin ABD1a bound to F-actin, sharpened by DeepEMhancer.

Fileemd_55895_additional_2.map
AnnotationDrebrin ABD1a bound to F-actin, sharpened by DeepEMhancer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Drebrin ABD2 bound to F-actin, half map 2.

Fileemd_55895_half_map_1.map
AnnotationDrebrin ABD2 bound to F-actin, half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Drebrin ABD2 bound to F-actin, half map 1.

Fileemd_55895_half_map_2.map
AnnotationDrebrin ABD2 bound to F-actin, half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Drebrin actin binding domain 2 (ABD2) binding F-actin

EntireName: Drebrin actin binding domain 2 (ABD2) binding F-actin
Components
  • Complex: Drebrin actin binding domain 2 (ABD2) binding F-actin
    • Complex: Drebrin (isoform E, residues 135-355)
      • Protein or peptide: Drebrin
    • Complex: Actin (rabbit skeletal muscle alpha actin)
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Drebrin actin binding domain 2 (ABD2) binding F-actin

SupramoleculeName: Drebrin actin binding domain 2 (ABD2) binding F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Drebrin (isoform E, residues 135-355)

SupramoleculeName: Drebrin (isoform E, residues 135-355) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Actin (rabbit skeletal muscle alpha actin)

SupramoleculeName: Actin (rabbit skeletal muscle alpha actin) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Drebrin

MacromoleculeName: Drebrin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.188834 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NGLARLSSPV LHRLRLREDE NAEPVGTTYQ KTDAAVEMKR INREQFWEQA KKEEELRKEE ERKKALDERL RFEQERMEQE RQEQEERER RYREREQQIE EHRRKQQTLE AEEAKRRLKE QSIFGDHRDE EEETHMKKSE SEVEEAAAII AQRPDNPREF F KQQERVAS ...String:
NGLARLSSPV LHRLRLREDE NAEPVGTTYQ KTDAAVEMKR INREQFWEQA KKEEELRKEE ERKKALDERL RFEQERMEQE RQEQEERER RYREREQQIE EHRRKQQTLE AEEAKRRLKE QSIFGDHRDE EEETHMKKSE SEVEEAAAII AQRPDNPREF F KQQERVAS ASAGSCDVPS PFNHRPGSHL DSHRRMAPTP IPTRSPSDSS TASTPVAEQI ERA

UniProtKB: Drebrin

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 352 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
50.0 mMKClpotassium chloride
1.0 mMMgCl2magnesium chloride
1.0 mMC14H24N2O10EGTA
2.0 mM(CH(OH)CH2SH)2DTT
GridModel: Au-flat 1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7bt7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 149259
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9tga:
Drebrin actin binding domain 2 bound to F-actin

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