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- PDB-3dz8: Crystal structure of human Rab3B GTPase bound with GDP -

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Basic information

Entry
Database: PDB / ID: 3dz8
TitleCrystal structure of human Rab3B GTPase bound with GDP
ComponentsRas-related protein Rab-3B
KeywordsPROTEIN TRANSPORT / ras / gdp / gtpase / structural genomics consortium / sgc / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Prenylation / Transport
Function / homology
Function and homology information


positive regulation of dopamine uptake involved in synaptic transmission / regulation of vesicle size / dopaminergic synapse / regulation of synaptic vesicle cycle / RAB geranylgeranylation / regulation of exocytosis / myosin V binding / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion ...positive regulation of dopamine uptake involved in synaptic transmission / regulation of vesicle size / dopaminergic synapse / regulation of synaptic vesicle cycle / RAB geranylgeranylation / regulation of exocytosis / myosin V binding / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / synaptic vesicle membrane / GDP binding / synaptic vesicle / vesicle / endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Rab3 / small GTPase Rab1 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 ...Rab3 / small GTPase Rab1 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsShen, Y. / Tong, Y. / Sukumar, D. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. ...Shen, Y. / Tong, Y. / Sukumar, D. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Rab3B GTPase bound with GDP
Authors: Shen, Y. / Tong, Y. / Sukumar, D. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6268
Polymers22,1831
Non-polymers4437
Water54030
1
A: Ras-related protein Rab-3B
hetero molecules

A: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,25216
Polymers44,3662
Non-polymers88614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3890 Å2
ΔGint-19 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.969, 50.875, 73.553
Angle α, β, γ (deg.)90.000, 110.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ras-related protein Rab-3B


Mass: 22182.936 Da / Num. of mol.: 1 / Fragment: UNP residues 18-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3B / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-V2R / References: UniProt: P20337
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M ammonium sulfate, 0.2M sodium acetate, 0.1M HEPES, 5% MPD, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 15627 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.061 / Χ2: 1.518
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.30.60915001.374197.9
1.97-2.0550.47115691.403199.6
2.05-2.147.10.3715431.515199.7
2.14-2.257.20.30215631.4881100
2.25-2.397.20.21815611.5071100
2.39-2.587.30.15615551.5321100
2.58-2.847.40.10815701.541100
2.84-3.257.50.05915701.4971100
3.25-4.097.40.03315821.5061100
4.09-257.40.0316141.6761100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.005data extraction
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GF9
Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.204 / SU B: 8.566 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 763 4.903 %RANDOM
Rwork0.211 ---
obs0.213 15562 99.724 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.646 Å2
Baniso -1Baniso -2Baniso -3
1--1.208 Å20 Å2-1.59 Å2
2--1.537 Å20 Å2
3----1.464 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 34 30 1454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221456
X-RAY DIFFRACTIONr_bond_other_d0.0020.02962
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9551976
X-RAY DIFFRACTIONr_angle_other_deg0.86232330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19223.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06615240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.515159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
X-RAY DIFFRACTIONr_mcbond_it1.4032884
X-RAY DIFFRACTIONr_mcbond_other0.4152364
X-RAY DIFFRACTIONr_mcangle_it2.13431419
X-RAY DIFFRACTIONr_scbond_it1.6842572
X-RAY DIFFRACTIONr_scangle_it2.3683556
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 (%)
1.9-1.9490.368470.3271037111297.482
1.949-2.0020.295570.2941053111799.373
2.002-2.0590.289520.2311003105999.622
2.059-2.1220.249670.1931020108999.816
2.122-2.1910.22460.215947993100
2.191-2.2670.287450.21693798499.797
2.267-2.3510.219410.196919960100
2.351-2.4460.196390.169879918100
2.446-2.5530.236460.189851897100
2.553-2.6750.236470.205768815100
2.675-2.8170.216370.209775812100
2.817-2.9840.229240.203746770100
2.984-3.1850.261380.218692730100
3.185-3.4330.205360.213619655100
3.433-3.750.253260.201590616100
3.75-4.1740.163300.182541571100
4.174-4.7850.245280.172481509100
4.785-5.7780.273230.227401424100
5.778-7.8510.377220.287326348100
7.851-200.423120.239214226100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2491-0.28791.09670.9063-0.23673.94170.01170.59530.0624-0.1411-0.0209-0.16740.10750.29520.00910.0998-0.00170.01180.1620.01340.122214.06357.949519.0319
22.6703-0.53621.53286.81775.696410.17640.08010.1975-0.16970.1134-0.27030.44930.2552-0.63680.19020.0583-0.0124-0.03130.1148-0.00850.07260.18346.345616.9318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 18711 - 188
2X-RAY DIFFRACTION2AB201

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