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- PDB-3aa0: Crystal structure of Actin Capping Protein in complex with the Cp... -

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Basic information

Entry
Database: PDB / ID: 3aa0
TitleCrystal structure of Actin Capping Protein in complex with the Cp-binding motif derived from CARMIL
Components
  • 21mer peptide from Leucine-rich repeat-containing protein 16A
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1 and 2
KeywordsPROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END REGULATION / CARMIL FAMILY PROTEIN / CONFORMATIONAL CHANGE / CELL MOTILITY / Actin capping / Actin-binding / Cytoskeleton / Isopeptide bond / Leucine-rich repeat
Function / homology
Function and homology information


barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / macropinosome / Factors involved in megakaryocyte development and platelet production ...barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / macropinosome / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly / actin filament network formation / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / macropinocytosis / Factors involved in megakaryocyte development and platelet production / urate metabolic process / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / ruffle organization / regulation of lamellipodium assembly / intermediate filament cytoskeleton / regulation of cell morphogenesis / lamellipodium assembly / cortical cytoskeleton / positive regulation of actin filament polymerization / filamentous actin / establishment or maintenance of cell polarity / brush border / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / hippocampal mossy fiber to CA3 synapse / Schaffer collateral - CA1 synapse / Z disc / cell morphogenesis / actin filament binding / cell migration / lamellipodium / actin cytoskeleton organization / postsynaptic density / nuclear speck / positive regulation of cell migration / protein-containing complex binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site ...CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / 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 / Ribosomal protein S3 C-terminal domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Aspartate Aminotransferase, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / PH-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / F-actin-uncapping protein LRRC16A
Similarity search - Component
Biological speciesGallus gallus (chicken)
mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTakeda, S. / Minakata, S. / Narita, A. / Kitazawa, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y.
CitationJournal: Plos Biol. / Year: 2010
Title: Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition
Authors: Takeda, S. / Minakata, S. / Koike, R. / Kawahata, I. / Narita, A. / Kitazawa, M. / Ota, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y.
History
DepositionNov 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
C: 21mer peptide from Leucine-rich repeat-containing protein 16A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1484
Polymers63,0883
Non-polymers601
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-48 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.814, 67.921, 137.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ORIGOMETRIC STATE OF THE ACTIN CAPPING PROTEIN IS A HETERO DIMER COMPOSE OF SUBUNIT A (CHAIN A) AND SUBUNIT B (CHAIN B) IN VIVO AND IN VITRO.

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Components

#1: Protein F-actin-capping protein subunit alpha-1 / CapZ 36/32 / Beta-actinin subunit I


Mass: 33001.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3) / References: UniProt: P13127
#2: Protein F-actin-capping protein subunit beta isoforms 1 and 2 / CapZ B1 and B2 / CapZ 36/32 / Beta-actinin subunit II


Mass: 27473.070 Da / Num. of mol.: 1 / Mutation: residues 244-277 deletion mutation
Source method: isolated from a genetically manipulated source
Details: BETA TENTACLE DELETION / Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3) / References: UniProt: P14315
#3: Protein/peptide 21mer peptide from Leucine-rich repeat-containing protein 16A / CARMIL / CAPPING PROTEIN ARP2/3 MYOSIN I LINKER / CARMIL homolog


Mass: 2613.070 Da / Num. of mol.: 1 / Fragment: CP-BINDING MOTIF, recidues 985-1005 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) mus musculus (house mouse) / References: UniProt: Q6EDY6
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% PEG 400, 40MM BACL2, 100MM MES-NAOH, PH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 12, 2009 / Details: mirrors
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 55697 / % possible obs: 97.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.32
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.03 / Num. unique all: 4405 / % possible all: 78.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IZN

1izn


Resolution: 1.7→42.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.382 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23919 2822 5.1 %RANDOM
Rwork0.19149 ---
obs0.19391 52798 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.7→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 4 438 4723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224494
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.956106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96324.655232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.815814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3441532
X-RAY DIFFRACTIONr_chiral_restr0.1210.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213471
X-RAY DIFFRACTIONr_mcbond_it1.0761.52720
X-RAY DIFFRACTIONr_mcangle_it1.96824421
X-RAY DIFFRACTIONr_scbond_it2.85431774
X-RAY DIFFRACTIONr_scangle_it4.7374.51667
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 168 -
Rwork0.304 2906 -
obs--73.97 %

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