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- PDB-6dec: Crystal structure of Bos taurus Arp2/3 complex binding with C-ter... -

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Basic information

Entry
Database: PDB / ID: 6dec
TitleCrystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90
Components
  • (Actin-related protein ...) x 7
  • (unidentified) x 2
  • NCK-interacting protein with SH3 domain
KeywordsENDOCYTOSIS / SPIN90 Arp2-3 complex / actin filament binding interface / linear filament nucleation activation
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 / Arp2/3 complex binding / regulation of actin filament polymerization / Clathrin-mediated endocytosis / intermediate filament / Neutrophil degranulation ...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 / Arp2/3 complex binding / regulation of actin filament polymerization / Clathrin-mediated endocytosis / intermediate filament / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / cytoskeleton organization / actin filament polymerization / cytoskeletal protein binding / cell projection / FCGR3A-mediated phagocytosis / structural constituent of cytoskeleton / positive regulation of neuron projection development / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / endocytosis / 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
SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / 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 ...SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / 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 / SH3 domain / ATPase, nucleotide binding domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 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
ADENOSINE-5'-TRIPHOSPHATE / 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 / NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
AuthorsNolen, B.J. / Luan, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)R01GM092917 United States
CitationJournal: EMBO J. / Year: 2018
Title: Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex.
Authors: Luan, Q. / Liu, S.L. / Helgeson, L.A. / Nolen, B.J.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
M: NCK-interacting protein with SH3 domain
H: Actin-related protein 3
I: Actin-related protein 2
J: Actin-related protein 2/3 complex subunit 1B
K: Actin-related protein 2/3 complex subunit 2
L: Actin-related protein 2/3 complex subunit 3
N: Actin-related protein 2/3 complex subunit 4
O: Actin-related protein 2/3 complex subunit 5
P: NCK-interacting protein with SH3 domain
Q: unidentified
R: unidentified
hetero molecules


Theoretical massNumber of molelcules
Total (without water)553,20026
Polymers551,01018
Non-polymers2,1898
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
M: NCK-interacting protein with SH3 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,94312
Polymers274,8498
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Actin-related protein 3
I: Actin-related protein 2
J: Actin-related protein 2/3 complex subunit 1B
K: Actin-related protein 2/3 complex subunit 2
L: Actin-related protein 2/3 complex subunit 3
N: Actin-related protein 2/3 complex subunit 4
O: Actin-related protein 2/3 complex subunit 5
P: NCK-interacting protein with SH3 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,94312
Polymers274,8498
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
Q: unidentified


  • defined by author
  • 529 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5291
Polymers5291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
R: unidentified


  • defined by author
  • 784 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7841
Polymers7841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.840, 197.381, 202.067
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, 14 molecules AHBICJDKELFNGO

#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: 41030.766 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: 16251.308 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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Protein , 1 types, 2 molecules MP

#8: Protein NCK-interacting protein with SH3 domain / 54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein ...54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein interacting with Nck / AF3p21 / Dia-interacting protein 1 / DIP-1 / Diaphanous protein-interacting protein / SH3 adapter protein SPIN90 / WASP-interacting SH3-domain protein / WISH / Wiskott-Aldrich syndrome protein-interacting protein


Mass: 50648.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKIPSD, AF3P21, SPIN90 / Plasmid: pGv67
Details (production host): N-terminal GST-fusion vector with TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9NZQ3

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Protein/peptide , 2 types, 2 molecules QR

#9: Protein/peptide unidentified


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#10: Protein/peptide unidentified


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 2 types, 8 molecules

#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#12: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 3.25 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES, pH 7.5, 5% PEG3350, 50 mM L-Proline, 0.5 mM ATP, 0.5 mM calcium chloride, 1 mM DTT
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2014 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 39413 / % possible obs: 93.9 % / Redundancy: 5.4 % / Rpim(I) all: 0.073 / Rsym value: 0.119 / Χ2: 1.148 / Net I/σ(I): 11.8
Reflection shellResolution: 4.6→4.68 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1921 / CC1/2: 0.591 / Rpim(I) all: 0.671 / Χ2: 0.963 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-30002.3.6data reduction
HKL-30002.3.6data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JD2

4jd2


Resolution: 4.6→48.939 Å / SU ML: 0.95 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.05
RfactorNum. reflection% reflectionSelection details
Rfree0.3141 1908 5 %random selection
Rwork0.2747 ---
obs0.2767 38150 94.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.6→48.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20436 0 128 0 20564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220537
X-RAY DIFFRACTIONf_angle_d0.47828512
X-RAY DIFFRACTIONf_dihedral_angle_d5.7564161
X-RAY DIFFRACTIONf_chiral_restr0.0163875
X-RAY DIFFRACTIONf_plane_restr0.0014041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6001-4.7150.42851320.31522501X-RAY DIFFRACTION92
4.715-4.84240.41021170.32192543X-RAY DIFFRACTION93
4.8424-4.98480.45461410.33042533X-RAY DIFFRACTION94
4.9848-5.14550.34711190.3212569X-RAY DIFFRACTION94
5.1455-5.32920.41381590.32482553X-RAY DIFFRACTION94
5.3292-5.54230.37081360.3222559X-RAY DIFFRACTION94
5.5423-5.79420.42621410.34532576X-RAY DIFFRACTION95
5.7942-6.09910.38191320.33632604X-RAY DIFFRACTION95
6.0991-6.48040.3631250.32772628X-RAY DIFFRACTION95
6.4804-6.97950.39811310.30692649X-RAY DIFFRACTION96
6.9795-7.67940.3811290.27312634X-RAY DIFFRACTION95
7.6794-8.78510.26761480.22742642X-RAY DIFFRACTION95
8.7851-11.04730.19881560.19052604X-RAY DIFFRACTION94
11.0473-48.94210.28381420.27982647X-RAY DIFFRACTION90

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