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- PDB-6y7g: Structure of the human RAB3C in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 6y7g
TitleStructure of the human RAB3C in complex with GDP
ComponentsRas-related protein Rab-3C
KeywordsSTRUCTURAL GENOMICS / RAB3C / human Ras-related protein Rab-3C / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / GTP-dependent protein binding / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis / protein secretion / antigen processing and presentation / protein localization to plasma membrane / synaptic vesicle ...: / GTP-dependent protein binding / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis / protein secretion / antigen processing and presentation / protein localization to plasma membrane / synaptic vesicle / vesicle / endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / plasma membrane / cytosol
Similarity search - Function
Rab3 / small GTPase Rab1 family profile. / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsDiaz-Saez, L. / Jung, S. / Raux, B. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative
CitationJournal: To Be Published
Title: Structure of the human RAB3C in complex with GDP
Authors: Diaz-Saez, L. / Jung, S. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M.
History
DepositionFeb 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3148
Polymers51,9602
Non-polymers1,3536
Water1,47782
1
A: Ras-related protein Rab-3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6574
Polymers25,9801
Non-polymers6773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6574
Polymers25,9801
Non-polymers6773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.190, 40.434, 66.362
Angle α, β, γ (deg.)86.020, 74.160, 66.450
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25980.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3C / Plasmid: pET28a-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96E17
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1M BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→63.78 Å / Num. obs: 16096 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 9.5 / Num. measured all: 57285 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.383.60.573571715690.7890.3490.6721.697.8
8.91-63.783.70.02610452820.9960.0170.03135.598.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å63.78 Å
Translation2.8 Å63.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZBD

1zbd


Resolution: 2.3→63.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.867 / SU B: 10.34 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 792 4.9 %RANDOM
Rwork0.1999 ---
obs0.2041 15301 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.42 Å2 / Biso mean: 43.127 Å2 / Biso min: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.31 Å20.15 Å2
2--1.66 Å2-2.27 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 2.3→63.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 86 82 2823
Biso mean--47.71 46.71 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132797
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182478
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6773782
X-RAY DIFFRACTIONr_angle_other_deg1.2041.5965761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17523.938160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06415489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2581513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 57 -
Rwork0.276 1146 -
all-1203 -
obs--97.65 %

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