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- PDB-3brw: Structure of the Rap-RapGAP complex -

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Basic information

Entry
Database: PDB / ID: 3brw
TitleStructure of the Rap-RapGAP complex
Components
  • Rap1 GTPase-activating protein 1
  • Ras-related protein Rap-1b
KeywordsGTP BINDING PROTEIN / GAP / G PROTEINS / GTPASE / RAP / GTPASE ACTIVATION / GTP-BINDING
Function / homology
Function and homology information


negative regulation of microvillus assembly / negative regulation of thyroid gland epithelial cell proliferation / cellular response to glial cell derived neurotrophic factor / Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis ...negative regulation of microvillus assembly / negative regulation of thyroid gland epithelial cell proliferation / cellular response to glial cell derived neurotrophic factor / Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / regulation of small GTPase mediated signal transduction / azurophil granule membrane / regulation of GTPase activity / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / RET signaling / negative regulation of neuron differentiation / cellular response to cAMP / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / lipid droplet / Integrin signaling / small monomeric GTPase / G protein activity / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / small GTPase binding / positive regulation of GTPase activity / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / cell population proliferation / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / early endosome / axon / Golgi membrane / GTPase activity / dendrite / neuronal cell body / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / signal transduction / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arylsulfatase, C-terminal domain - #160 / Rap/Ran-GAP / Rap/Ran-GAP protein dimerization domain / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / GoLoco motif / Ras-related protein Rap1 / GoLoco motif ...Arylsulfatase, C-terminal domain - #160 / Rap/Ran-GAP / Rap/Ran-GAP protein dimerization domain / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / GoLoco motif / Ras-related protein Rap1 / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Arylsulfatase, C-terminal domain / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / Rap1 GTPase-activating protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsScrima, A. / Thomas, C. / Deaconescu, D. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2008
Title: The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues
Authors: Scrima, A. / Thomas, C. / Deaconescu, D. / Wittinghofer, A.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rap1 GTPase-activating protein 1
B: Rap1 GTPase-activating protein 1
C: Rap1 GTPase-activating protein 1
D: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2587
Polymers135,7244
Non-polymers5343
Water18010
1
A: Rap1 GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)38,9011
Polymers38,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rap1 GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)38,9011
Polymers38,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rap1 GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)38,9011
Polymers38,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5544
Polymers19,0211
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.723, 209.723, 108.217
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Rap1 GTPase-activating protein 1 / Rap1GAP1 / Rap1GAP


Mass: 38901.250 Da / Num. of mol.: 3 / Fragment: Rap1GAP, UNP residues 75-415 / Mutation: Q204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1GAP / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P47736
#2: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19020.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B / Plasmid: ptac / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P61224

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Non-polymers , 4 types, 13 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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

CrystalDensity Matthews: 5.061804 Å3/Da / Density % sol: 75.700363 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3.4→182.57 Å / Num. all: 37639 / Num. obs: 37639 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 15.48
Reflection shellResolution: 3.4→3.5 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.6 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SRQ for Rap1GAP

1srq


Resolution: 3.4→48.08 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.885 / SU B: 26.796 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Molecules B and D, representing the Rap1GAP-Rap1B complex, are well defined with average B-factors of 82 and 76. Rap1GAP molecules A and C ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Molecules B and D, representing the Rap1GAP-Rap1B complex, are well defined with average B-factors of 82 and 76. Rap1GAP molecules A and C are partially highly flexible and ill defined resulting in B-factors of 100 and 120, respectively.
RfactorNum. reflection% reflectionSelection details
Rfree0.28043 1878 5 %RANDOM
Rwork0.23389 ---
obs0.23624 35759 99.16 %-
all-37637 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.485 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å22.1 Å20 Å2
2--4.21 Å20 Å2
3----6.31 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9422 0 33 10 9465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.96313094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00751167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00924.232482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.627151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5891554
X-RAY DIFFRACTIONr_chiral_restr0.0770.21432
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027398
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.24102
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26475
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4391.55961
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79829442
X-RAY DIFFRACTIONr_scbond_it0.48534107
X-RAY DIFFRACTIONr_scangle_it0.844.53652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 128 -
Rwork0.333 2637 -
obs--98.5 %

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