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- PDB-3x1z: Ras-related protein Rap1B(T65A) with GppNHp -

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Basic information

Entry
Database: PDB / ID: 3x1z
TitleRas-related protein Rap1B(T65A) 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: 1.25 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_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.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_asym_id / _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_asym_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: Ras-related protein Rap-1b
B: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1127
Polymers37,9272
Non-polymers1,1855
Water6,377354
1
A: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6024
Polymers18,9631
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5103
Polymers18,9631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.420, 59.040, 68.070
Angle α, β, γ (deg.)90.00, 93.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18963.459 Da / Num. of mol.: 2 / Fragment: RAS-RELATED PROTEIN RAP1B, UNP residues 1-167 / Mutation: T65A
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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Lithium sulfate, 0.1M bis-tris pH5.5, 25%(w/v) PEG3350, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→33.96 Å / Num. obs: 78079 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3 / % possible all: 92.7

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: dev_1839)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→33.96 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 4059 5.2 %
Rwork0.1455 --
obs0.1469 78048 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 72 354 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072829
X-RAY DIFFRACTIONf_angle_d1.243829
X-RAY DIFFRACTIONf_dihedral_angle_d14.4041094
X-RAY DIFFRACTIONf_chiral_restr0.044434
X-RAY DIFFRACTIONf_plane_restr0.005488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.25-1.26470.19741290.1963240392
1.2647-1.28010.2181260.1886249293
1.2801-1.29630.20061580.1822245693
1.2963-1.31340.1981410.1794248093
1.3134-1.33140.21131480.1688245293
1.3314-1.35040.19951150.1655251593
1.3504-1.37060.19821510.158246693
1.3706-1.3920.20121210.1552253294
1.392-1.41480.18761340.1454248494
1.4148-1.43920.18011350.1404252894
1.4392-1.46540.18851380.1404251695
1.4654-1.49360.17531240.1307253994
1.4936-1.5240.16321440.1305252095
1.524-1.55720.17781210.1281258195
1.5572-1.59340.14971200.1262253495
1.5934-1.63330.1671380.1264255996
1.6333-1.67740.15911270.13253996
1.6774-1.72680.17161540.1308253896
1.7268-1.78250.16481410.1366260396
1.7825-1.84620.17731210.1333260396
1.8462-1.92010.13681270.131256497
1.9201-2.00750.16281410.1377259697
2.0075-2.11330.17231630.1366259397
2.1133-2.24570.16781650.1398257998
2.2457-2.41910.17091600.1457263198
2.4191-2.66240.16911370.1576265898
2.6624-3.04750.1781540.1625263199
3.0475-3.83860.15771500.1423267499
3.8386-33.97740.1751760.1486272399

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