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- PDB-9xye: Two CAP-1 Bound to the Pointed End of F-actin -

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Basic information

Entry
Database: PDB / ID: 9xye
TitleTwo CAP-1 Bound to the Pointed End of F-actin
Components
  • Actin, alpha skeletal muscle
  • Adenylyl cyclase-associated protein 1
KeywordsPROTEIN FIBRIL / Cytoskeleton / Actin / Filament / Helical
Function / homology
Function and homology information


ameboidal-type cell migration / modification of postsynaptic actin cytoskeleton / Role of ABL in ROBO-SLIT signaling / : / cytoskeletal motor activator activity / myosin heavy chain binding / cortical actin cytoskeleton / tropomyosin binding / actin filament bundle / troponin I binding ...ameboidal-type cell migration / modification of postsynaptic actin cytoskeleton / Role of ABL in ROBO-SLIT signaling / : / cytoskeletal motor activator activity / myosin heavy chain binding / cortical actin cytoskeleton / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / establishment or maintenance of cell polarity / skeletal muscle myofibril / adenylate cyclase binding / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / activation of adenylate cyclase activity / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / receptor-mediated endocytosis / actin filament organization / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / calcium-dependent protein binding / azurophil granule lumen / Platelet degranulation / lamellipodium / presynapse / actin binding / cell body / postsynapse / protein domain specific binding / hydrolase activity / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / glutamatergic synapse / magnesium ion binding / signal transduction / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP ...Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / 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 / Adenylyl cyclase-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsPalmer, N.J. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Mechanisms of Actin Filament Depolymerization by Cyclase Associated Protein-1 and Cofilin-2
Authors: Palmer, N.J. / Boczkowska, M. / Rebowski, G. / Dominguze, R.
History
DepositionAug 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 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
W: Adenylyl cyclase-associated protein 1
X: Adenylyl cyclase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,08817
Polymers313,8307
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41978.773 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Adenylyl cyclase-associated protein 1 / CAP 1


Mass: 51968.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAP1, CAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q01518
#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
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
1Complex of the Cyclase Associated Protein-1 bound to F-actinCOMPLEX#1-#20MULTIPLE SOURCES
2Cyclase Associated Protein-1COMPLEX#21RECOMBINANT
3Actin, alpha skeletal muscleCOMPLEX#11NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Oryctolagus cuniculus (rabbit)9986
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 89000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARC4.7CTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARC4.7final Euler assignment
13cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41864 / Symmetry type: POINT
RefinementHighest resolution: 3.18 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00717738
ELECTRON MICROSCOPYf_angle_d1.29524065
ELECTRON MICROSCOPYf_dihedral_angle_d11.2622449
ELECTRON MICROSCOPYf_chiral_restr0.0722673
ELECTRON MICROSCOPYf_plane_restr0.013067

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