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- PDB-4b6d: Structure of the atypical C1 domain of MgcRacGAP -

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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 / sulfate transport / actomyosin contractile ring assembly / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / Kinesins / RHOD GTPase cycle / Flemming body / regulation of small GTPase mediated signal transduction ...centralspindlin complex / sulfate transport / actomyosin contractile ring assembly / mitotic spindle midzone assembly / regulation of attachment of spindle microtubules to kinetochore / gamma-tubulin binding / Kinesins / RHOD GTPase cycle / 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 / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / regulation of embryonic development / alpha-tubulin binding / CDC42 GTPase cycle / mitotic cytokinesis / Rho protein signal transduction / neuroblast proliferation / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / spindle midzone / monoatomic ion transport / RAC1 GTPase cycle / MHC class II antigen presentation / GTPase activator activity / erythrocyte differentiation / acrosomal vesicle / cytoplasmic side of plasma membrane / mitotic spindle / spindle / midbody / microtubule binding / spermatogenesis / microtubule / protein kinase binding / extracellular exosome / nucleoplasm / metal ion binding / 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 / 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. ...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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Glycerol


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 / 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

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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: 3.35 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

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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

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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)

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