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- PDB-9tg8: Drebrin actin binding domain 1 conformation A (ABD1a) bound to F-actin -

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Basic information

Entry
Database: PDB / ID: 9tg8
TitleDrebrin actin binding domain 1 conformation A (ABD1a) bound to F-actin
Components
  • Actin, alpha skeletal muscle
  • Drebrin
KeywordsSTRUCTURAL PROTEIN / F-actin binding 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
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Drebrin
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZhao, W. / Abis, G. / Oozeer, F. / Mulvaney, T. / Nagar, N. / Topf, M. / Gordon-Weeks, P.R. / Conte, M.R. / Atherton, J.
Funding support United Kingdom, 8items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Drebrin
B: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3127
Polymers110,4093
Non-polymers9034
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Drebrin / Developmentally-regulated brain protein


Mass: 26188.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBN1, D0S117E / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16643
#2: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Drebrin actin binding domain 1 conformation A (ABD1a) binding F-actinCOMPLEX#1-#20RECOMBINANT
2Drebrin(isoform E, residues 135-355)COMPLEX#11RECOMBINANT
3Actin (rabbit skeletal muscle alpha actin)COMPLEX#21NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
250 mMpotassium chlorideKCl1
31 mMmagnesium chlorideMgCl21
41 mMEGTAC14H24N2O101
52 mMDTT(CH(OH)CH2SH)21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Au-flat 1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6.2particle selectionFilament Tracer
4CTFFIND4.1.14CTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
11RELION5final Euler assignment
13RELION53D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102155 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementHighest resolution: 2.37 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036568
ELECTRON MICROSCOPYf_angle_d0.5538888
ELECTRON MICROSCOPYf_dihedral_angle_d11.525910
ELECTRON MICROSCOPYf_chiral_restr0.043969
ELECTRON MICROSCOPYf_plane_restr0.0041146

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