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- PDB-4xf2: Tetragonal structure of Arp2/3 complex -

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Basic information

Entry
Database: PDB / ID: 4xf2
TitleTetragonal structure of 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 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 ...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) / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / 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
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 / MIR / Resolution: 5 Å
AuthorsJurgenson, C.T. / 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 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag

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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
T: Actin-related protein 3
U: Actin-related protein 2
V: Actin-related protein 2/3 complex subunit 1B
W: Actin-related protein 2/3 complex subunit 2
X: Actin-related protein 2/3 complex subunit 3
Y: Actin-related protein 2/3 complex subunit 4
Z: Actin-related protein 2/3 complex subunit 5


Theoretical massNumber of molelcules
Total (without water)448,46114
Polymers448,46114
Non-polymers00
Water0
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20760 Å2
ΔGint-98 kcal/mol
Surface area81750 Å2
MethodPISA
2
T: Actin-related protein 3
U: Actin-related protein 2
V: Actin-related protein 2/3 complex subunit 1B
W: Actin-related protein 2/3 complex subunit 2
X: Actin-related protein 2/3 complex subunit 3
Y: Actin-related protein 2/3 complex subunit 4
Z: Actin-related protein 2/3 complex subunit 5


Theoretical massNumber of molelcules
Total (without water)224,2317
Polymers224,2317
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20760 Å2
ΔGint-104 kcal/mol
Surface area81950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.930, 149.930, 265.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Actin-related protein ... , 7 types, 14 molecules ATBUCVDWEXFYGZ

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


Mass: 47428.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3SYX9

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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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris 7.0, 15% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5→50 Å / Num. obs: 24560 / % possible obs: 96.8 % / Redundancy: 6.4 % / Rsym value: 0.09 / Net I/σ(I): 20.3
Reflection shellResolution: 5→50 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.469 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: 1U2V with the calcium and ADP ligands removed

1u2v


Resolution: 5→47.536 Å / SU ML: 0.81 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3031 1216 4.97 %
Rwork0.2748 --
obs0.2762 24450 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5→47.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27564 0 0 0 27564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128247
X-RAY DIFFRACTIONf_angle_d2.36538197
X-RAY DIFFRACTIONf_dihedral_angle_d17.24310481
X-RAY DIFFRACTIONf_chiral_restr0.1034214
X-RAY DIFFRACTIONf_plane_restr0.0124923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.0001-5.20010.44011170.38052255X-RAY DIFFRACTION85
5.2001-5.43640.35721430.33862400X-RAY DIFFRACTION91
5.4364-5.72260.37091290.34642568X-RAY DIFFRACTION96
5.7226-6.08050.35151150.3412691X-RAY DIFFRACTION99
6.0805-6.54880.37461450.33112652X-RAY DIFFRACTION100
6.5488-7.20580.35261310.31982670X-RAY DIFFRACTION100
7.2058-8.24380.35991480.26742684X-RAY DIFFRACTION100
8.2438-10.36860.25191430.22712656X-RAY DIFFRACTION100
10.3686-47.53850.25181450.24412658X-RAY DIFFRACTION98

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