[English] 日本語
Yorodumi
- PDB-4b6d: Structure of the atypical C1 domain of MgcRacGAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b6d
TitleStructure of the atypical C1 domain of MgcRacGAP
ComponentsRAC GTPASE-ACTIVATING PROTEIN 1
KeywordsSIGNALING PROTEIN / CYTOKINESIS / PLASMA MEMBRANE / PHOSPHOLIPIDS / CENTRALSPINDLIN / SPINDLE MIDZONE / CENTRAL SPINDLE / MIDBODY
Function / homology
Function and homology information


centralspindlin complex / actomyosin contractile ring assembly / mitotic spindle midzone assembly / sulfate transmembrane transport / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / RHOD GTPase cycle / Flemming body / Kinesins / regulation of small GTPase mediated signal transduction ...centralspindlin complex / actomyosin contractile ring assembly / mitotic spindle midzone assembly / sulfate transmembrane transport / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / RHOD GTPase cycle / Flemming body / Kinesins / regulation of small GTPase mediated signal transduction / COPI-dependent Golgi-to-ER retrograde traffic / RHOB GTPase cycle / positive regulation of cytokinesis / spindle midzone / RHOC GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / mitotic cytokinesis / CDC42 GTPase cycle / regulation of embryonic development / RHOA GTPase cycle / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / alpha-tubulin binding / beta-tubulin binding / Rho protein signal transduction / monoatomic ion transport / RAC1 GTPase cycle / MHC class II antigen presentation / acrosomal vesicle / GTPase activator activity / erythrocyte differentiation / spindle / cytoplasmic side of plasma membrane / mitotic spindle / midbody / spermatogenesis / protein-macromolecule adaptor activity / microtubule binding / microtubule / protein kinase binding / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Rho GTPase activation protein / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Rho GTPase activation protein / Phorbol esters/diacylglycerol binding domain (C1 domain) / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPye, V.E. / Lekomtsev, S. / Petronczki, M. / Cherepanov, P.
CitationJournal: Nature / Year: 2012
Title: Centralspindlin Links the Mitotic Spindle to the Plasma Membrane During Cytokinesis.
Authors: Lekomtsev, S. / Su, K. / Pye, V.E. / Blight, K. / Sundaramoorthy, S. / Takaki, T. / Collinson, L.M. / Cherepanov, P. / Divecha, N. / Petronczki, M.
History
DepositionAug 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAC GTPASE-ACTIVATING PROTEIN 1
B: RAC GTPASE-ACTIVATING PROTEIN 1
C: RAC GTPASE-ACTIVATING PROTEIN 1
D: RAC GTPASE-ACTIVATING PROTEIN 1
E: RAC GTPASE-ACTIVATING PROTEIN 1
F: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,81719
Polymers40,9406
Non-polymers87713
Water2,936163
1
A: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0464
Polymers6,8231
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9543
Polymers6,8231
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9543
Polymers6,8231
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9543
Polymers6,8231
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9543
Polymers6,8231
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: RAC GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9543
Polymers6,8231
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.850, 133.850, 56.682
Angle α, β, γ (deg.)90.00, 109.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1), (-0.6003, -0.0626, 0.7974), (-0.7712, 0.3097, -0.5562)-20.48, -28.43
2given(1, -0.002775, -0.008213), (0.003114, 0.9991, 0.04146), (0.008091, -0.04148, 0.9991)18.12, 0.1996, -1.067
3given(0.999, 0.01697, -0.04098), (0.01695, -0.9999, -0.000998), (-0.04099, 0.000303, -0.9992)-18.59
4given(-0.2326, 0.9395, 0.2515), (-0.6027, 0.0637, -0.7954), (-0.7633, -0.3365, 0.5514)-15.42, -10.03, -14.19
5given(0.9993, 0.01422, -0.03586), (0.01323, -0.9995, -0.0278), (-0.03623, 0.0273, -0.999)-0.3703, -1.429, -1.879

-
Components

#1: Protein
RAC GTPASE-ACTIVATING PROTEIN 1 / MALE GERM CELL RACGAP / MGCRACGAP / PROTEIN CYK4 HOMOLG / CYK4 / HSCYK-4


Mass: 6823.265 Da / Num. of mol.: 6 / Fragment: C1 DOMAIN, RESIDUES 284-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-C1WT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CODON PLUS RIL / References: UniProt: Q9H0H5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 284-338 WITH AN N-TERMINAL EXTENSION SEQUENCE EXTENSION SEQUENCE GPLGS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 % / Description: NONE
Crystal growpH: 7.1
Details: 1.3 M SODIUM CITRATE, PH 7.1 AND 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: H,-K,-H-L / Fraction: 0.5
ReflectionResolution: 2.2→66.93 Å / Num. obs: 26140 / % possible obs: 99.4 % / Observed criterion σ(I): 2.6 / Redundancy: 9.7 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.6 / % possible all: 98.8

-
Processing

Software
NameClassification
MOLREPmodel building
SCALAdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
MOLREPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1PTQ

1ptq


Resolution: 2.2→66.925 Å / σ(F): 1.14 / Phase error: 28.33 / Stereochemistry target values: TWIN_LSQ_F / Details: CHAINS A, B, C, D, E AND F ARE RELATED BY NCS.
RfactorNum. reflection% reflection
Rfree0.2355 1308 5 %
Rwork0.2103 --
obs0.2125 24803 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 56.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→66.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 18 163 2915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072866
X-RAY DIFFRACTIONf_angle_d1.1283859
X-RAY DIFFRACTIONf_dihedral_angle_d15.1231156
X-RAY DIFFRACTIONf_chiral_restr0.056424
X-RAY DIFFRACTIONf_plane_restr0.008483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.24270.29631430.31062677X-RAY DIFFRACTION95
2.2427-2.28850.32241420.28762695X-RAY DIFFRACTION93
2.2885-2.33830.28711480.29082696X-RAY DIFFRACTION93
2.3383-2.39270.26781400.26772696X-RAY DIFFRACTION95
2.3927-2.45250.35651490.27232758X-RAY DIFFRACTION93
2.4525-2.51880.26691360.26372657X-RAY DIFFRACTION95
2.5188-2.59290.31321420.27112779X-RAY DIFFRACTION94
2.5929-2.67660.28851430.26552659X-RAY DIFFRACTION93
2.6766-2.77230.28531370.25062700X-RAY DIFFRACTION95
2.7723-2.88330.27251450.26142720X-RAY DIFFRACTION94
2.8833-3.01450.24681500.2312735X-RAY DIFFRACTION95
3.0145-3.17340.30051410.24022740X-RAY DIFFRACTION94
3.1734-3.37220.20281520.21772739X-RAY DIFFRACTION94
3.3722-3.63250.28291390.18942692X-RAY DIFFRACTION95
3.6325-3.9980.19431490.16722711X-RAY DIFFRACTION94
3.998-4.57620.13091440.15072715X-RAY DIFFRACTION94
4.5762-5.76450.171400.16092705X-RAY DIFFRACTION94
5.7645-53.59850.24851320.19552733X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.91760.79930.26283.73841.25831.4284-0.0927-0.2174-0.12710.0732-0.0554-0.1565-0.00510.06020.06070.4772-0.0259-0.12950.51340.0230.168-8.9325-15.2364-1.8697
20.788-0.4397-0.04572.98841.28741.61760.1623-0.0958-0.1760.184-0.13330.07440.2337-0.0027-0.00590.50240.00520.02870.57810.0520.1981-13.8265-19.3937-6.2764
33.0537-0.95320.00772.41551.49334.1937-0.19670.75440.3878-0.15430.4148-0.0342-0.26170.3555-0.27150.73170.01540.16770.65640.09130.3021-18.86360.3443-14.5935
47.2746-2.0317-0.48191.90661.41851.40260.10050.6396-0.0166-0.2801-0.2872-0.3197-0.05540.05850.04690.60170.01270.01530.6830.11260.2548-22.2038-1.1616-13.0768
52.4729-0.2866-0.12997.57762.53064.45070.1196-0.0752-0.41850.3129-0.0194-0.23690.1056-0.3394-0.07050.34230.023-0.00620.28590.05680.4058-30.4092-19.6691-3.5496
62.1669-0.0858-0.13534.33952.40831.3360.26250.1011-0.1254-0.25680.1736-0.34420.08060.3062-0.18250.4992-0.0360.06130.7870.10840.0857-30.7043-12.3957-4.4243
70.4120.49810.46932.0113-0.11470.8154-0.03310.56730.3872-0.1829-0.2098-0.1810.04780.1125-0.23960.3923-0.16670.01310.13420.04291.31066.811515.12823.9593
81.13680.38270.85398.98461.94651.7129-0.1051-0.0341-0.08450.0416-0.18820.1447-0.01640.16570.15610.3862-0.06750.04370.30940.07361.0255.78817.46385.1073
94.13350.26820.08352.61550.86874.0081-0.2162-0.9829-0.46860.82830.15580.03130.27950.4292-0.04950.62040.011-0.04420.50480.0570.2654-0.1366-1.072114.4789
102.282.64441.2443.19861.821.86050.0929-0.4510.14890.4336-0.0048-0.1523-0.2366-0.142-0.07550.5651-0.00240.05650.47250.09890.3457-5.3793-1.146410.7572
110.62241.64960.8927.83521.13691.64140.08320.24470.3672-0.3131-0.0032-0.09120.05330.0147-0.18620.4127-0.0678-0.00730.24890.1260.9822-12.352217.45433.6482
121.95171.3270.57042.50062.52663.06540.1110.0165-0.2718-0.07410.04780.26890.160.1467-0.03030.4517-0.0294-0.03630.27580.06831.1607-11.815515.31523.3197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 279:297)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 298:338)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 282:309)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 310:338)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 279:325)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 326:338)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 279:305)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 306:338)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 282:316)
10X-RAY DIFFRACTION10(CHAIN E AND RESID 317:338)
11X-RAY DIFFRACTION11(CHAIN F AND RESID 279:310)
12X-RAY DIFFRACTION12(CHAIN F AND RESID 311:338)

+
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