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- PDB-3x1x: Ras-related protein Rap1B with GppNHp -

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Basic information

Entry
Database: PDB / ID: 3x1x
TitleRas-related protein Rap1B with GppNHp
ComponentsRas-related protein Rap-1b
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates RAP1 and RAC1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Rap1 signalling / cellular response to gonadotropin-releasing hormone / Rap protein signal transduction / modification of postsynaptic structure / MAP2K and MAPK activation / regulation of cell junction assembly ...GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates RAP1 and RAC1 / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Rap1 signalling / cellular response to gonadotropin-releasing hormone / Rap protein signal transduction / modification of postsynaptic structure / MAP2K and MAPK activation / 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 / response to carbohydrate / establishment of endothelial barrier / regulation of establishment of cell polarity / Neutrophil degranulation / small GTPase-mediated signal transduction / cellular response to organic cyclic compound / cellular response to cAMP / lipid droplet / small monomeric GTPase / G protein activity / establishment of localization in cell / GDP binding / cell-cell junction / cellular response to xenobiotic stimulus / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / glutamatergic synapse / protein-containing complex binding / GTP binding / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rap1 / 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 ...Ras-related protein Rap1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsNoguchi, H. / Ikegami, T. / Park, S.Y. / Tame, J.R.H. / Unzai, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: The structure and conformational switching of Rap1B
Authors: Noguchi, H. / Ikegami, T. / Nagadoi, A. / Kamatari, Y.O. / Park, S.Y. / Tame, J.R. / Unzai, S.
History
DepositionDec 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_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.ptnr1_label_seq_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.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_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: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6524
Polymers18,9931
Non-polymers6593
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.722, 52.460, 60.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 18993.484 Da / Num. of mol.: 1 / Fragment: RAS-RELATED PROTEIN RAP1B, UNP residues 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rap1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62636
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 12%(w/v) PEG3350, 5mM Cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. all: 421896 / Num. obs: 421896 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.3
Reflection shellResolution: 1→1.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 5.1 / % possible all: 92.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
MOLREPphasing
PHENIX(phenix.refine: dev_1394)refinement
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→18.902 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 3623 5.06 %
Rwork0.1959 --
obs0.1966 71626 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→18.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 34 152 1504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061368
X-RAY DIFFRACTIONf_angle_d1.2651851
X-RAY DIFFRACTIONf_dihedral_angle_d14.531520
X-RAY DIFFRACTIONf_chiral_restr0.078207
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.9997-1.01280.23221690.2154252592
1.0128-1.02670.22491460.211255994
1.0267-1.04140.22451570.2026253392
1.0414-1.05690.21891480.2015254294
1.0569-1.07340.19721270.1892259393
1.0734-1.0910.18591430.1717257994
1.091-1.10990.17761310.1637259294
1.1099-1.130.15531420.161262395
1.13-1.15180.18031440.1576259594
1.1518-1.17530.17571460.1574261495
1.1753-1.20080.21121220.1564266696
1.2008-1.22880.16131440.163261095
1.2288-1.25950.1751750.1636262696
1.2595-1.29350.22111270.1697269496
1.2935-1.33160.19031320.1713268597
1.3316-1.37450.21221380.1699268797
1.3745-1.42370.19711360.183270897
1.4237-1.48060.20651270.1809273798
1.4806-1.5480.19161350.1819272298
1.548-1.62960.19891220.1852275398
1.6296-1.73160.21891360.1937275999
1.7316-1.86520.21141420.1997278999
1.8652-2.05270.22751480.195277899
2.0527-2.34920.2151540.2015276698
2.3492-2.9580.21021560.2258263993
2.958-18.90560.3068760.2759162954

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