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- PDB-3c5h: Crystal structure of the Ras homolog domain of human GRLF1 (p190R... -

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Basic information

Entry
Database: PDB / ID: 3c5h
TitleCrystal structure of the Ras homolog domain of human GRLF1 (p190RhoGAP)
ComponentsGlucocorticoid receptor DNA-binding factor 1
KeywordsSIGNALING PROTEIN / ras / gtpase / glucorticoid receptor / Structural Genomics Consortium / SGC / Alternative splicing / Anti-oncogene / Cell cycle / Cytoplasm / DNA-binding / GTPase activation / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


neuron projection guidance / central nervous system neuron axonogenesis / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / : / positive regulation of cilium assembly / mammary gland development / camera-type eye development / RHOD GTPase cycle / negative regulation of vascular permeability ...neuron projection guidance / central nervous system neuron axonogenesis / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / : / positive regulation of cilium assembly / mammary gland development / camera-type eye development / RHOD GTPase cycle / negative regulation of vascular permeability / axonal fasciculation / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / wound healing, spreading of cells / RND2 GTPase cycle / RND3 GTPase cycle / negative regulation of Rho protein signal transduction / regulation of cell size / RHOB GTPase cycle / regulation of axonogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / forebrain development / RAC1 GTPase cycle / GTPase activator activity / ciliary basal body / neural tube closure / axon guidance / regulation of actin cytoskeleton organization / phospholipid binding / positive regulation of neuron projection development / cell migration / actin cytoskeleton / regulation of cell shape / GTPase activity / protein-containing complex binding / GTP binding / DNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain / FF domain superfamily ...Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Small GTPase / Ras family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rho GTPase-activating protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / mad / Resolution: 1.8 Å
AuthorsShen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the Ras homolog domain of human GRLF1 (p190RhoGAP).
Authors: Shen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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.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_ref_seq_dif.details / _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: Glucocorticoid receptor DNA-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5189
Polymers28,9471
Non-polymers5718
Water1,72996
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.959, 108.959, 51.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Glucocorticoid receptor DNA-binding factor 1 / Glucocorticoid receptor repression factor 1 / GRF-1 / Rho GAP p190A / p190-A


Mass: 28946.740 Da / Num. of mol.: 1 / Fragment: Ras homolog domain: Residues 13-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRLF1, GRF1, KIAA1722 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9NRY4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6353.25
2
Crystal grow
Crystal-IDDetails
1Native crystal, used for model refinement: 26% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride, 0.1mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
2Seleno-methionine derivative crystal, used for MAD phasing: 33% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride, 0.1mM DTT, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K. A ten-fold excess of GppNHp was added to the protein samples prior to crystallization.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.97926
SYNCHROTRONAPS 19-ID20.97931, 0.97945, 0.98166, 0.97243
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 29, 2007
ADSC QUANTUM 3152CCDDec 6, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979311
30.979451
40.981661
50.972431
ReflectionResolution: 1.8→50 Å / Num. obs: 26661 / % possible obs: 95.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.075 / Χ2: 1.527 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.862.70.45616900.94161.8
1.86-1.944.10.38724911.1489.1
1.94-2.036.10.32827961.05398.9
2.03-2.137.30.23827881.184100
2.13-2.277.50.1827971.296100
2.27-2.447.60.1427911.306100
2.44-2.697.60.10327751.331100
2.69-3.087.60.0828111.779100
3.08-3.887.50.05528392.219100
3.88-507.40.04528832.174100

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Phasing

PhasingMethod: mad
Phasing set
ID
1
2
3
4
Phasing MADD res high: 3 Å / D res low: 30 Å / FOM : 0.71 / Reflection: 6679
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
14 wavelength10.97935.56-8.17
14 wavelength20.97943.58-10.47
14 wavelength30.98170.73-6.61
14 wavelength40.97243.09-3.56
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.0520.27700.872
2Se600.7270.4480.3310.707
3Se600.3330.2770.4050.584
Phasing MAD shell
Resolution (Å)FOM Reflection
10.49-300.75329
6.73-10.490.81567
5.29-6.730.8711
4.5-5.290.8825
3.98-4.50.76935
3.61-3.980.721020
3.32-3.610.631116
3.1-3.320.561176
Phasing dmFOM : 0.61 / FOM acentric: 0.61 / FOM centric: 0.62 / Reflection: 10178 / Reflection acentric: 9456 / Reflection centric: 722
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-28.7390.950.950.9644936881
4.6-7.40.930.940.8613891239150
3.7-4.60.920.920.8817091581128
3.3-3.70.820.830.6217291613116
2.8-3.30.440.450.2830262854172
2.6-2.80.120.120.081876180175

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefmac_5.3.0037refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MAR345CCDdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.197 / SU B: 2.936 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Due to considerable non-isomorphism between the phasing and refinement data sets, a preliminary model obtained by the program 'resolve' based on the phasing data was used in molecular ...Details: Due to considerable non-isomorphism between the phasing and refinement data sets, a preliminary model obtained by the program 'resolve' based on the phasing data was used in molecular replacement with the higher resolution refinement data and the program 'phaser'. Following density modification with 'DM', 'ARP/wARP' was used for autotracing of the higher resolution model. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS during final refinement. Programs, ARP/wARP, coot, molprobity have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1352 5.1 %RANDOM
Rwork0.205 ---
obs0.207 26626 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 39 96 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221869
X-RAY DIFFRACTIONr_bond_other_d0.0010.021193
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9732549
X-RAY DIFFRACTIONr_angle_other_deg0.95432938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33125.30981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.159155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined0.2110.2352
X-RAY DIFFRACTIONr_nbd_other0.1860.21235
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2916
X-RAY DIFFRACTIONr_nbtor_other0.0810.2915
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.294
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.27
X-RAY DIFFRACTIONr_mcbond_it2.7221291
X-RAY DIFFRACTIONr_mcbond_other0.7022477
X-RAY DIFFRACTIONr_mcangle_it3.60131876
X-RAY DIFFRACTIONr_scbond_it2.8612785
X-RAY DIFFRACTIONr_scangle_it3.8993668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8480.391610.2851152208958.066
1.848-1.8980.298750.2671501195280.738
1.898-1.9520.344950.2491718192394.28
1.952-2.0120.277790.2311779187599.093
2.012-2.0770.302940.2261772186799.946
2.077-2.1490.2371080.20816531761100
2.149-2.2290.292830.2116151698100
2.229-2.3190.24900.2031567165999.879
2.319-2.420.257840.21114821566100
2.42-2.5360.222760.20514521528100
2.536-2.6710.237790.20713481427100
2.671-2.8290.217770.20912731350100
2.829-3.020.339550.2081240129699.923
3.02-3.2550.239660.20211451211100
3.255-3.5560.242450.1961058110499.909
3.556-3.9590.246530.1869481001100
3.959-4.540.193430.16870913100
4.54-5.4840.196380.177726764100
5.484-7.4590.229260.244602628100
7.459-19.2630.245250.21437339999.749

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