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- PDB-4xei: Orthorhombic isomorph of bovine Arp2/3 complex -

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Basic information

Entry
Database: PDB / ID: 4xei
TitleOrthorhombic isomorph of bovine Arp2/3 complex
Components(Actin-related protein ...) x 7
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly ...EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of lamellipodium assembly / actin filament polymerization / cell projection / structural constituent of cytoskeleton / actin filament binding / cell migration / site of double-strand break / actin binding / neuron projection / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 ...Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 16 kDa subunit (p16-Arc) / ARP2/3 complex 20 kDa subunit (ARPC4) / Yope Regulator; Chain: A, / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / YVTN repeat-like/Quinoprotein amine dehydrogenase / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Actin / Actin family / Actin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Roll / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Actin-related protein 2 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.874 Å
AuthorsJurgenson, C.J. / Pollard, T.P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites.
Authors: Jurgenson, C.T. / Pollard, T.D.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 3
B: Actin-related protein 2
C: Actin-related protein 2/3 complex subunit 1B
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5


Theoretical massNumber of molelcules
Total (without water)224,2317
Polymers224,2317
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-92 kcal/mol
Surface area76730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.574, 156.981, 178.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Actin-related protein ... , 7 types, 7 molecules ABCDEFG

#1: Protein Actin-related protein 3 / Actin-2 / Actin-like protein 3


Mass: 47428.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: thymus / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: P61157
#2: Protein Actin-related protein 2 / Actin-like protein 2


Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: A7MB62
#3: Protein Actin-related protein 2/3 complex subunit 1B / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41016.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q58CQ2
#4: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3MHR7
#5: Protein Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3T035
#6: Protein Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa subunit / p20-ARC


Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q148J6
#7: Protein Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


Mass: 16295.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3SYX9

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Non-polymers , 1 types, 48 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: Ethanol 10%, 1,4-butanediol 15%, 100 mM Tris 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.874→50 Å / Num. obs: 26925 / % possible obs: 97.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K8K

1k8k


Resolution: 3.874→45.408 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3285 1343 4.99 %RANDOM
Rwork0.279 ---
obs0.2815 26925 95.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.874→45.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13685 0 0 48 13733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713983
X-RAY DIFFRACTIONf_angle_d1.5118907
X-RAY DIFFRACTIONf_dihedral_angle_d16.1875183
X-RAY DIFFRACTIONf_chiral_restr0.0652085
X-RAY DIFFRACTIONf_plane_restr0.0072428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8743-4.01270.39521210.34812346X-RAY DIFFRACTION90
4.0127-4.17330.39421320.31892593X-RAY DIFFRACTION98
4.1733-4.36310.29411410.29992569X-RAY DIFFRACTION98
4.3631-4.59290.34241200.28792619X-RAY DIFFRACTION98
4.5929-4.88030.33871210.27512567X-RAY DIFFRACTION97
4.8803-5.25660.32921650.27792558X-RAY DIFFRACTION97
5.2566-5.78470.30271460.29082584X-RAY DIFFRACTION97
5.7847-6.61950.34071460.29472577X-RAY DIFFRACTION96
6.6195-8.33150.32961170.27232592X-RAY DIFFRACTION95
8.3315-45.41070.30171340.23532577X-RAY DIFFRACTION90

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