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- PDB-9ec0: Structure of the CARMIL dimer bound to Capping Protein -

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Basic information

Entry
Database: PDB / ID: 9ec0
TitleStructure of the CARMIL dimer bound to Capping Protein
Components
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta
  • F-actin-uncapping protein LRRC16A
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / membrane / cell motility
Function / homology
Function and homology information


barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / macropinosome / actin filament network formation / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / macropinocytosis / regulation of Arp2/3 complex-mediated actin nucleation ...barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / macropinosome / actin filament network formation / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / macropinocytosis / regulation of Arp2/3 complex-mediated actin nucleation / urate metabolic process / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / ruffle organization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / Sensory processing of sound by inner hair cells of the cochlea / lamellipodium assembly / filamentous actin / cortical cytoskeleton / positive regulation of actin filament polymerization / cell leading edge / brush border / Advanced glycosylation endproduct receptor signaling / COPI-mediated anterograde transport / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / actin filament organization / hippocampal mossy fiber to CA3 synapse / sarcomere / Schaffer collateral - CA1 synapse / actin filament binding / cell migration / actin cytoskeleton / lamellipodium / Factors involved in megakaryocyte development and platelet production / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoskeleton / postsynaptic density / nuclear speck / positive regulation of cell migration / cadherin binding / protein-containing complex binding / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. ...CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / F-actin-uncapping protein LRRC16A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBarrie, K.R. / Dominguez, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM073791 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM152412 United States
CitationJournal: To Be Published
Title: Structural basis for regulation of Capping Protein by the CARMIL dimer
Authors: Barrie, K.R. / Dominguez, R.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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

Downloads & links

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Assembly

Deposited unit
A: F-actin-uncapping protein LRRC16A
B: F-actin-uncapping protein LRRC16A
C: F-actin-capping protein subunit alpha-1
D: F-actin-capping protein subunit beta
E: F-actin-capping protein subunit alpha-1
F: F-actin-capping protein subunit beta


Theoretical massNumber of molelcules
Total (without water)365,7986
Polymers365,7986
Non-polymers00
Water00
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 F-actin-uncapping protein LRRC16A / CARMIL homolog / Capping protein regulator and myosin 1 linker protein 1 / Capping protein / Arp2/3 ...CARMIL homolog / Capping protein regulator and myosin 1 linker protein 1 / Capping protein / Arp2/3 and myosin-I linker homolog 1 / Arp2/3 and myosin-I linker protein 1 / Leucine-rich repeat-containing protein 16A


Mass: 118676.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARMIL1, CARMIL, LRRC16, LRRC16A / Production host: Homo sapiens (human) / References: UniProt: Q5VZK9
#2: Protein F-actin-capping protein subunit alpha-1 / CapZ alpha-1


Mass: 32964.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPZA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52907
#3: Protein F-actin-capping protein subunit beta / CapZ beta


Mass: 31258.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPZB / Production host: Escherichia coli (E. coli) / References: UniProt: P47756
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of the CARMIL dimer bound to Capping Protein / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.37 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 690592
Details: Please note that this is a composite map (used for model building and refinement) and therefore does not have a single particle number or resolution associated with it. Instead, the map was ...Details: Please note that this is a composite map (used for model building and refinement) and therefore does not have a single particle number or resolution associated with it. Instead, the map was obtained by combining multiple different maps (already deposited as separate EMDB entries) each at different resolutions and with different numbers of particles. Since the number of particles and resolution are required, the values included here reflect the consensus map (EMD-47891). Thank you.
Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00523766
ELECTRON MICROSCOPYf_angle_d1.14432094
ELECTRON MICROSCOPYf_dihedral_angle_d6.0213176
ELECTRON MICROSCOPYf_chiral_restr0.063684
ELECTRON MICROSCOPYf_plane_restr0.0074138

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