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- PDB-3rse: Structural and biochemical characterization of two binding sites ... -

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Basic information

Entry
Database: PDB / ID: 3rse
TitleStructural and biochemical characterization of two binding sites for nucleation promoting factor WASp-VCA on Arp2/3 complex
Components
  • (Actin-related protein ...) x 7
  • CA fragment of Bos taurus N-WASP
KeywordsSTRUCTURAL PROTEIN / Heteroheptamer / Heptameric heterocomplex / F-actin branch initiation / actin / cytosol
Function / homology
Function and homology information


NOSTRIN mediated eNOS trafficking / Nephrin family interactions / DCC mediated attractive signaling / : / protein-containing complex localization => GO:0031503 / negative regulation of membrane tubulation / spindle localization / positive regulation of Arp2/3 complex-mediated actin nucleation / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation ...NOSTRIN mediated eNOS trafficking / Nephrin family interactions / DCC mediated attractive signaling / : / protein-containing complex localization => GO:0031503 / negative regulation of membrane tubulation / spindle localization / positive regulation of Arp2/3 complex-mediated actin nucleation / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / negative regulation of lymphocyte migration / Arp2/3 complex-mediated actin nucleation / actin cap / actin filament-based movement / regulation of actin filament polymerization / Clathrin-mediated endocytosis / dendritic spine morphogenesis / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of lamellipodium assembly / actin filament polymerization / cell projection / actin filament / response to bacterium / structural constituent of cytoskeleton / regulation of protein localization / actin filament binding / cell migration / lamellipodium / site of double-strand break / actin binding / neuron projection / cell division / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Actin nucleation-promoting factor WASL / Actin-related protein 2/3 complex subunit 3 / Actin nucleation-promoting factor WAS, C-terminal / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / WASP family, EVH1 domain / 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 nucleation-promoting factor WASL / Actin-related protein 2/3 complex subunit 3 / Actin nucleation-promoting factor WAS, C-terminal / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / WASP family, EVH1 domain / 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) / WH2 motif / Wiskott Aldrich syndrome homology region 2 / Yope Regulator; Chain: A, / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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 / PH-like domain superfamily / 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 / Neural Wiskott-Aldrich syndrome protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPollard, T.D. / Jurgenson, C.T. / Ti, S. / Nolen, B.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural and biochemical characterization of two binding sites for nucleation-promoting factor WASp-VCA on Arp2/3 complex.
Authors: Ti, S.C. / Jurgenson, C.T. / Nolen, B.J. / Pollard, T.D.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 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
Z: CA fragment of Bos taurus N-WASP


Theoretical massNumber of molelcules
Total (without water)224,6638
Polymers224,6638
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.443, 129.340, 204.559
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 / Source: (natural) Bos taurus (cattle) / 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) / References: UniProt: A7MB62
#3: Protein Actin-related protein 2/3 complex subunit 1B / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41030.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / 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) / 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) / 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) / References: UniProt: Q148J6
#7: Protein Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


Mass: 16251.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYX9

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Protein/peptide / Non-polymers , 2 types, 209 molecules Z

#8: Protein/peptide CA fragment of Bos taurus N-WASP


Mass: 462.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: Q95107*PLUS
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES 7.5, 8% PEG 8000, 200 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Aug 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 87036 / Num. obs: 87036 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 23.9
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1 / Num. unique all: 8474

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P9S

2p9s


Resolution: 2.65→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 4355 random
Rwork0.213 --
obs0.215 87036 -
all-87036 -
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13599 0 0 208 13807
LS refinement shellResolution: 2.65→2.71 Å
RfactorNum. reflection
Rfree0.355 300
Rwork0.292 -
obs-5660

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