[English] 日本語
Yorodumi
- PDB-3wps: crystal structure of the GAP domain of MgcRacGAP(S387D) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wps
Titlecrystal structure of the GAP domain of MgcRacGAP(S387D)
ComponentsRac GTPase-activating protein 1
KeywordsSIGNALING PROTEIN / GTPase activation / small G-proteins
Function / homology
Function and homology information


centralspindlin complex / actomyosin contractile ring assembly / sulfate transport / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / RHOD GTPase cycle / Kinesins / Flemming body / regulation of small GTPase mediated signal transduction ...centralspindlin complex / actomyosin contractile ring assembly / sulfate transport / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / RHOD GTPase cycle / Kinesins / Flemming body / regulation of small GTPase mediated signal transduction / COPI-dependent Golgi-to-ER retrograde traffic / RHOB GTPase cycle / beta-tubulin binding / RHOC GTPase cycle / positive regulation of cytokinesis / cleavage furrow / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of embryonic development / CDC42 GTPase cycle / Rho protein signal transduction / mitotic cytokinesis / alpha-tubulin binding / RHOA GTPase cycle / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / monoatomic ion transport / RAC1 GTPase cycle / MHC class II antigen presentation / erythrocyte differentiation / GTPase activator activity / acrosomal vesicle / mitotic spindle / cytoplasmic side of plasma membrane / spindle / protein-macromolecule adaptor activity / midbody / spermatogenesis / microtubule binding / microtubule / protein kinase binding / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMurayama, K. / Kato-murayama, M. / Shirouzu, M. / Kitamura, T. / Yokoyama, S.
CitationJournal: To be Published
Title: crystal structure of the GAP domain of MgcRacGAP
Authors: Murayama, K. / Kato-Murayama, M. / Shirouzu, M. / Kitamura, T. / Yokoyama, S.
History
DepositionJan 15, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rac GTPase-activating protein 1
B: Rac GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4784
Polymers47,2862
Non-polymers1922
Water1,67593
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-9 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.321, 77.321, 108.744
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Rac GTPase-activating protein 1 / Male germ cell RacGap / MgcRacGAP / Protein CYK4 homolog / CYK4 / HsCYK-4


Mass: 23642.951 Da / Num. of mol.: 2 / Fragment: UNP residues 346-546 / Mutation: S387D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PLASMID pCR2.1 / Gene: RACGAP1, KIAA1478, MGCRACGAP / Production host: cell-free protein synthesis (unknown) / References: UniProt: Q9H0H5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ACCESSION NUMBER BAA90247.1 IN THE GENEBANK.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0M magnesium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19881 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.129 / Net I/σ(I): 13.7
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.613 / % possible all: 100

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OVJ

2ovj


Resolution: 2.7→38.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1238223.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 960 4.8 %RANDOM
Rwork0.21 ---
obs0.21 19856 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.867 Å2 / ksol: 0.327308 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.29 Å210.6 Å20 Å2
2--7.29 Å20 Å2
3----14.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 10 93 3279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 160 5 %
Rwork0.338 3069 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

+
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://pdbjlvh1.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