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- EMDB-72313: One CAP-1 Bound to the Pointed End of F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-72313
TitleOne CAP-1 Bound to the Pointed End of F-actin
Map data
Sample
  • Complex: Complex of the Cyclase Associated Protein-1 bound to F-actin
    • Complex: Cyclase Associated Protein-1
      • Protein or peptide: Adenylyl cyclase-associated protein 1
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCytoskeleton / Actin / Filament / Helical / PROTEIN FIBRIL
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
Actin, alpha skeletal muscle / Adenylyl cyclase-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsPalmer NJ / Dominguez R
Funding support United States, 1 items
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 NJ / Boczkowska M / Rebowski G / Dominguze R
History
DepositionAug 24, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72313.png

Downloads & links

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Map

FileDownload / File: emd_72313.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 416 pix.
= 344.448 Å		0.83 Å/pix.
x 416 pix.
= 344.448 Å		0.83 Å/pix.
x 416 pix.
= 344.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375
Minimum - Maximum-0.048854247 - 0.19410267
Average (Standard dev.)0.00094494864 (±0.0051253736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 344.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of the Cyclase Associated Protein-1 bound to F-actin

EntireName: Complex of the Cyclase Associated Protein-1 bound to F-actin
Components
  • Complex: Complex of the Cyclase Associated Protein-1 bound to F-actin
    • Complex: Cyclase Associated Protein-1
      • Protein or peptide: Adenylyl cyclase-associated protein 1
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of the Cyclase Associated Protein-1 bound to F-actin

SupramoleculeName: Complex of the Cyclase Associated Protein-1 bound to F-actin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Cyclase Associated Protein-1

SupramoleculeName: Cyclase Associated Protein-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Actin, alpha skeletal muscle

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

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.978773 KDa
SequenceString: CDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GI ITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDS GD GVTHNVPIYE ...String:
CDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GI ITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDS GD GVTHNVPIYE GYALPHAIMR LDLAGRDLTD YLMKILTERG YSFVTTAERE IVRDIKEKLC YVALDFENEM ATAASSSS L EKSYELPDGQ VITIGNERFR CPETLFQPSF IGMESAGIHE TTYNSIMKCD IDIRKDLYAN NVMSGGTTMY PGIADRMQK EITALAPSTM KIKIIAPPER KYSVWIGGSI LASLSTFQQM WITKQEYDEA GPSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Adenylyl cyclase-associated protein 1

MacromoleculeName: Adenylyl cyclase-associated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.968309 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADMQNLVER LERAVGRLEA VSHTSDMHRG YADSPSKAGA APYVQAFDSL LAGPVAEYLK ISKEIGGDVQ KHAEMVHTGL KLERALLVT ASQCQQPAEN KLSDLLAPIS EQIKEVITFR EKNRGSKLFN HLSAVSESIQ ALGWVAMAPK PGPYVKEMND A AMFYTNRV ...String:
MADMQNLVER LERAVGRLEA VSHTSDMHRG YADSPSKAGA APYVQAFDSL LAGPVAEYLK ISKEIGGDVQ KHAEMVHTGL KLERALLVT ASQCQQPAEN KLSDLLAPIS EQIKEVITFR EKNRGSKLFN HLSAVSESIQ ALGWVAMAPK PGPYVKEMND A AMFYTNRV LKEYKDVDKK HVDWVKAYLS IWTELQAYIK EFHTTGLAWS KTGPVAKELS GLPSGPSAGS CPPPPPPCPP PP PVSTISC SYESASRSSL FAQINQGESI THALKHVSDD MKTHKNPALK AQSGPVRSGP KPFSAPKPQT SPSPKRATKK EPA VLELEG KKWRVENQEN VSNLVIEDTE LKQVAYIYKC VNTTLQIKGK INSITVDNCK KLGLVFDDVV GIVEIINSKD VKVQ VMGKV PTISINKTDG CHAYLSKNSL DCEIVSAKSS EMNVLIPTEG GDFNEFPVPE QFKTLWNGQK LVTTVTEIAG

UniProtKB: Adenylyl cyclase-associated protein 1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / 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: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 89000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 75614
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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