[English] 日本語
Yorodumi
- PDB-1s8f: Crystal structure of Rab9 complexed to GDP reveals a dimer with a... -

+
Open data


ID or keywords:

Loading...

-
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 / RHOBTB3 ATPase cycle / RAB geranylgeranylation / Rab protein signal transduction / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / receptor-mediated endocytosis / small monomeric GTPase ...Retrograde transport at the Trans-Golgi-Network / RAB GEFs exchange GTP for GDP on RABs / RHOBTB3 ATPase cycle / RAB geranylgeranylation / Rab protein signal transduction / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / receptor-mediated endocytosis / small monomeric GTPase / phagocytic vesicle membrane / GDP binding / melanosome / late endosome / protein transport / regulation of protein localization / G protein activity / lysosome / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Rab9 / Small GTPase Rab domain 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 ...Rab9 / Small GTPase Rab domain 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 6 types, 241 molecules

#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-GDP / GUANOSINE-5'-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


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


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


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more