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- PDB-1s8f: Crystal structure of Rab9 complexed to GDP reveals a dimer with a... -

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Basic information

Entry
Database: PDB / ID: 1s8f
TitleCrystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II
ComponentsRas-related protein Rab-9A
KeywordsPROTEIN TRANSPORT / intracellular transport / vesicular trafficking / hemihedral twinning
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / RAB GEFs exchange GTP for GDP on RABs / negative regulation by host of symbiont catalytic activity => GO:0052403 / RAB geranylgeranylation / Rab protein signal transduction / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / phagocytic vesicle membrane / GDP binding ...Retrograde transport at the Trans-Golgi-Network / RAB GEFs exchange GTP for GDP on RABs / negative regulation by host of symbiont catalytic activity => GO:0052403 / RAB geranylgeranylation / Rab protein signal transduction / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / phagocytic vesicle membrane / GDP binding / regulation of protein localization / melanosome / protein transport / late endosome / lysosome / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Rab9 / small GTPase Rab1 family profile. / Small GTPase / Ras family / 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
BENZOIC ACID / GUANOSINE-5'-DIPHOSPHATE / STRONTIUM ION / Ras-related protein Rab-9A
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWittmann, J.G. / Rudolph, M.G.
CitationJournal: Febs Lett. / Year: 2004
Title: Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II.
Authors: Wittmann, J.G. / Rudolph, M.G.
History
DepositionFeb 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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-9A
B: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,68512
Polymers40,0752
Non-polymers1,61010
Water4,161231
1
A: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9356
Polymers20,0371
Non-polymers8975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7506
Polymers20,0371
Non-polymers7135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ras-related protein Rab-9A
B: Ras-related protein Rab-9A
hetero molecules

A: Ras-related protein Rab-9A
B: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,36924
Polymers80,1504
Non-polymers3,22020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area12070 Å2
ΔGint-222 kcal/mol
Surface area28900 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-81 kcal/mol
Surface area15770 Å2
MethodPISA
5
B: Ras-related protein Rab-9A
hetero molecules

B: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,50012
Polymers40,0752
Non-polymers1,42510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area3640 Å2
ΔGint-91 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.245, 98.245, 79.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-2001-

SR

21A-9012-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ras-related protein Rab-9A / Rab-9 / RAB9 GTPASE


Mass: 20037.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal truncation / Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: RAB9A, RAB9 / Production host: Escherichia coli (E. coli) / References: UniProt: P24408

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Non-polymers , 6 types, 241 molecules

#2: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: 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 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.17 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG8000, Na-benzoate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0091 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0091 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. obs: 37662 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.053 / Net I/σ(I): 24.8
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3752 / Rsym value: 0.0691 / % possible all: 99.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ky3

1ky3


Resolution: 1.77→30 Å / Num. parameters: 12164 / Num. restraintsaints: 11650 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined against data from a hemihedrally twinned crystal. The twin fraction is 0.253, the twin operator is (k,h,-l).
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 1825 5 %keep twin-related reflection in same set
Rwork0.1646 ---
all-35770 --
obs-35770 99.9 %-
Displacement parametersBiso mean: 30 Å2
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 2550 / Occupancy sum non hydrogen: 3027.5
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 96 231 3039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0255
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0

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