[English] 日本語
Yorodumi
- PDB-6dec: Crystal structure of Bos taurus Arp2/3 complex binding with C-ter... -

+
Open data


ID or keywords:

Loading...

-
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 complex binding / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / intermediate filament ...EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 complex binding / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / intermediate filament / regulation of postsynapse assembly / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / cytoskeletal protein binding / actin filament polymerization / cytoskeleton organization / cell projection / FCGR3A-mediated phagocytosis / positive regulation of neuron projection development / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / endocytosis / actin filament binding / cell migration / site of double-strand break / actin binding / cell cortex / postsynapse / neuron projection / synapse / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / plasma membrane / 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 / ARP2/3 complex 16 kDa subunit (p16-Arc) / 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 ...SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / 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/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / SH3 domain / Src homology 3 domains / ATPase, nucleotide binding domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / WD domain, G-beta repeat / 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
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 (domestic 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

-
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 (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic cattle) / Organ: Thymus / References: UniProt: Q3SYX9

-
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

-
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)

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more