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- PDB-9zzi: Cryo-EM structure of F-actin in the ADP state -

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Basic information

Entry
Database: PDB / ID: 9zzi
TitleCryo-EM structure of F-actin in the ADP state
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin / F-actin
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / protein domain specific binding / hydrolase activity / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsBrotzman, S.B. / Palmer, N.J. / Dominguez, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM161161 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5T32AR053461-20 United States
CitationJournal: To Be Published
Title: Mechanism of Actin Thin Filament Pointed-End Elongation by Leiomodin
Authors: Brotzman, S.B. / Palmer, N.J. / Boczkowska, M. / Dominguez, R.
History
DepositionJan 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,63615
Polymers209,3785
Non-polymers2,25810
Water3,693205
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
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: helical reconstruction

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Sample preparation

ComponentName: F-actin in the ADP state / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.5 kDa/nmYES
211.5 kDa/nmYES
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
250 mMPotassium acetateKAc1
31 mMEGTAC14H24N2O101
41 mMmagnesium chlorideMgCl21
50.2 mMadenosine triphosphateATP1
61 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 48.49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategoryImage processing-ID
1cryoSPARCparticle selection1
2EPUimage acquisition
7Cootmodel fitting
12PHENIX3D reconstruction1
13cryoSPARCparticle selection2
18PHENIX3D reconstruction2
19PHENIXmodel refinement
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11NONE
22NONE
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11-166.627.6C1
21166.627.6C1
32-166.627.6C1
42-166.627.6C1
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.06FSC 0.143 CUT-OFF371137219ZZIHELICAL
22.06FSC 0.143 CUT-OFF371137219ZZIHELICAL
32.06FSC 0.143 CUT-OFF371137229ZZIHELICAL
42.06FSC 0.143 CUT-OFF371137229ZZIHELICAL
Atomic model buildingPDB-ID: 8F8P

8f8p


Accession code: 8F8P / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00714960
ELECTRON MICROSCOPYf_angle_d1.28220305
ELECTRON MICROSCOPYf_dihedral_angle_d15.6455565
ELECTRON MICROSCOPYf_chiral_restr0.0742255
ELECTRON MICROSCOPYf_plane_restr0.022595

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