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- PDB-1k8k: Crystal Structure of Arp2/3 Complex -

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Basic information

Entry
Database: PDB / ID: 1k8k
TitleCrystal Structure of Arp2/3 Complex
Components
  • (ACTIN-LIKE PROTEIN ...) x 2
  • (ARP2/3 COMPLEX ...) x 5
KeywordsSTRUCTURAL PROTEIN / beta-propeller
Function / homology
Function and homology information


muscle cell projection membrane / 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 actin filament polymerization ...muscle cell projection membrane / 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 actin filament polymerization / cilium assembly / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / cell projection / structural constituent of cytoskeleton / actin filament binding / synaptic vesicle membrane / cell migration / lamellipodium / site of double-strand break / actin binding / cell cortex / postsynapse / endosome / neuron projection / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Yope Regulator; Chain: A, / 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 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 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Yope Regulator; Chain: A, / 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 20 kDa subunit (ARPC4) / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / ATPase, nucleotide binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Nucleotidyltransferase; domain 5 / Alpha Horseshoe / WD domain, G-beta repeat / Roll / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsRobinson, R.C. / Turbedsky, K. / Kaiser, D.A. / Higgs, H.N. / Marchand, J.-B. / Choe, S. / Pollard, T.D.
Citation
#1: Journal: Biochemistry / Year: 1999
Title: Influence of the Wiskott-Aldrich syndrome protein (WASp) C terminus and Arp2/3 complex on actin polymerization
Authors: Higgs, H.N. / Blanchoin, L. / Pollard, T.D.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1999
Title: Structure and function of the Arp2/3 complex
Authors: Mullins, R.D. / Pollard, T.D.
#3: Journal: Annu.Rev.Biophys.Biomol.Struct. / Year: 2000
Title: Biophysics of actin filament dynamics in nonmuscle cells
Authors: Pollard, T.D. / Blanchoin, L. / Mullins, R.D.
History
DepositionOct 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-LIKE PROTEIN 3
B: ACTIN-LIKE PROTEIN 2
C: ARP2/3 COMPLEX 41 KDA SUBUNIT
D: ARP2/3 COMPLEX 34 KDA SUBUNIT
E: ARP2/3 COMPLEX 21 KDA SUBUNIT
F: ARP2/3 COMPLEX 20 KDA SUBUNIT
G: ARP2/3 COMPLEX 16 KDA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)224,2317
Polymers224,2317
Non-polymers00
Water30,8061710
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19740 Å2
ΔGint-91 kcal/mol
Surface area72890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.710, 130.400, 204.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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ACTIN-LIKE PROTEIN ... , 2 types, 2 molecules AB

#1: Protein ACTIN-LIKE PROTEIN 3 / ARP3 / ACTIN-RELATED PROTEIN 3 / ACTIN-2


Mass: 47428.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: P61157
#2: Protein ACTIN-LIKE PROTEIN 2 / ARP2 / ACTIN-RELATED PROTEIN 2


Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: A7MB62

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ARP2/3 COMPLEX ... , 5 types, 5 molecules CDEFG

#3: Protein ARP2/3 COMPLEX 41 KDA SUBUNIT / p40 / P41-ARC / ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1B


Mass: 41016.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: Q58CQ2
#4: Protein ARP2/3 COMPLEX 34 KDA SUBUNIT / p34 / P34-ARC / ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2


Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: Q3MHR7
#5: Protein ARP2/3 COMPLEX 21 KDA SUBUNIT / p21 / P21-ARC / ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3


Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: Q3T035
#6: Protein ARP2/3 COMPLEX 20 KDA SUBUNIT / p20 / P20-ARC / ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 4


Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: Q148J6
#7: Protein ARP2/3 COMPLEX 16 KDA SUBUNIT / p16 / P16-ARC / ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5


Mass: 16295.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (domestic cattle) / Organ: thymus / References: UniProt: Q3SYX9

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Non-polymers , 1 types, 1710 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1710 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, KSCN, Hepes at pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris1droppH8.0
3100 mM1dropNaCl
41 mMEGTA1drop
51 mM1dropMgCl2
61 mMdithiothreitol1drop
76 %PEG80001reservoir
80.1 MKSCN1reservoir
90.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2001 / Details: double crystal monochromator
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 196866 / Num. obs: 185141 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.064 / Net I/σ(I): 8.6
Reflection
*PLUS
Highest resolution: 2.01 Å / Lowest resolution: 20 Å / Num. obs: 183319 / % possible obs: 92.8 % / Num. measured all: 852046 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 -random
Rwork0.216 --
all-185141 -
obs-183284 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13616 0 0 1710 15326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.285
X-RAY DIFFRACTIONp_angle_deg1.285
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d_na
X-RAY DIFFRACTIONp_dihedral_angle_d_prot
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_d_na
X-RAY DIFFRACTIONp_improper_angle_d_prot
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.01 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.353

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