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- PDB-2e9s: human neuronal Rab6B in three intermediate forms -

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Basic information

Entry
Database: PDB / ID: 2e9s
Titlehuman neuronal Rab6B in three intermediate forms
ComponentsRas-related protein Rab-6B
KeywordsPROTEIN TRANSPORT / human neuron / Rab6B / GDP MG NO3 complex / GDP MG complex / GDP complex
Function / homology
Function and homology information


protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / intra-Golgi vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs ...protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / intra-Golgi vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endomembrane system / small monomeric GTPase / intracellular protein transport / neuron projection development / presynapse / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / cytosol
Similarity search - Function
: / 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 ...: / 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 / NITRATE ION / Ras-related protein Rab-6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsVellieux, F.M. / Tcherniuk, S. / Garcia-Saez, I. / Kozielski, F.
Citation
Journal: To be Published
Title: 3D structure of human neuronal Rab6B in three intermediate forms
Authors: Vellieux, F.M. / Tcherniuk, S. / Garcia-Saez, I. / Kozielski, F.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: The structure of human neuronal Rab6B in the active and inactive form
Authors: Garcia-Saez, I. / Tcherniuk, S. / Kozielski, F.
History
DepositionJan 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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-6B
B: Ras-related protein Rab-6B
C: Ras-related protein Rab-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8219
Polymers59,3803
Non-polymers1,4406
Water6,485360
1
A: Ras-related protein Rab-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3234
Polymers19,7931
Non-polymers5303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2613
Polymers19,7931
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras-related protein Rab-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2372
Polymers19,7931
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.808, 65.185, 108.672
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 Rab-6B / Rab6B


Mass: 19793.441 Da / Num. of mol.: 3 / Fragment: residues in database 13-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6B / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NRW1
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 1.81 Å3/Da / Density % sol: 32.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2M ammonium nitrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.78→19.74 Å / Num. obs: 42010 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.7
Reflection shellResolution: 1.78→1.9 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 9.8 / Num. unique all: 7141 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2FE4

2fe4


Resolution: 1.78→19.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2088564.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2099 5 %RANDOM
Rwork0.199 ---
obs0.199 41978 99.6 %-
all-41978 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2543 Å2 / ksol: 0.39709 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2---2.07 Å20 Å2
3---0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.78→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 90 360 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d4.14
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 342 5 %
Rwork0.212 6493 -
obs-6493 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4no3.paramno3.top
X-RAY DIFFRACTION5gdp.paramgdp.top

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