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- EMDB-72311: One CAP-1 Bound to the Pointed End of F-actin, HFD Local Refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-72311
TitleOne CAP-1 Bound to the Pointed End of F-actin, HFD Local Refinement
Map data
Sample
  • Complex: Complex of the Cyclase Associated Protein-1 bound to F-actin
    • Complex: Cyclase Associated Protein-1
      • Protein or peptide: Cyclase associated protein-1
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
KeywordsCytoskeleton / Actin / Filament / Helical / CYTOSOLIC PROTEIN
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
Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 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 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72311.png

Downloads & links

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Map

FileDownload / File: emd_72311.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: 0.0393
Minimum - Maximum-0.06787451 - 0.1791306
Average (Standard dev.)0.00014699076 (±0.0039160913)
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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Mask #1

Fileemd_72311_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72311_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72311_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Cyclase associated protein-1
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle

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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: all

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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 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: CDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GIITNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV THNVPIYEGY ...String:
CDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GIITNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV THNVPIYEGY ALPHAIMRLD LAGRDLTDYL MKILTERGYS FVTTAEREIV RDIKEKLCYV ALDFENEMAT AASSSSLEKS YELPDGQVIT IGNERFRCPE TLFQPSFIGM ESAGIHETTY NSIMKCDIDI RKDLYANNVM SGGTTMYPGI ADRMQKEITA LAPSTMKIKI IAPPERKYSV WIGGSILASL STFQQMWITK QEYDEAGPSI VHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Cyclase associated protein-1

MacromoleculeName: Cyclase associated protein-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADMQNLVER LERAVGRLEA VSHTSDMHRG YADSPSKAGA APYVQAFDSL LAGPVAEYLK ISKEIGGDVQ KHAEMVHTGL KLERALLVTA SQCQQPAENK LSDLLAPISE QIKEVITFRE KNRGSKLFNH LSAVSESIQA LGWVAMAPKP GPYVKEMNDA AMFYTNRVLK ...String:
MADMQNLVER LERAVGRLEA VSHTSDMHRG YADSPSKAGA APYVQAFDSL LAGPVAEYLK ISKEIGGDVQ KHAEMVHTGL KLERALLVTA SQCQQPAENK LSDLLAPISE QIKEVITFRE KNRGSKLFNH LSAVSESIQA LGWVAMAPKP GPYVKEMNDA AMFYTNRVLK EYKDVDKKHV DWVKAYLSIW TELQAYIKEF HTTGLAWSKT GPVAKELSGL PSGPSAGSCP PPPPPCPPPP PVSTISCSYE SASRSSLFAQ INQGESITHA LKHVSDDMKT HKNPALKAQS GPVRSGPKPF SAPKPQTSPS PKRATKKEPA VLELEGKKWR VENQENVSNL VIEDTELKQV AYIYKCVNTT LQIKGKINSI TVDNCKKLGL VFDDVVGIVE IINSKDVKVQ VMGKVPTISI NKTDGCHAYL SKNSLDCEIV SAKSSEMNVL IPTEGGDFNE FPVPEQFKTL WNGQKLVTTV TEIAG

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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
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: 3.51 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)
FSC plot (resolution estimation)

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