[English] 日本語
Yorodumi
- PDB-1oiv: X-ray structure of the small G protein Rab11a in complex with GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oiv
TitleX-ray structure of the small G protein Rab11a in complex with GDP
ComponentsRAS-RELATED PROTEIN RAB-11A
KeywordsPROTEIN TRANSPORT / SMALL G PROTEIN / INTRACELLULAR TRAFFICKING / GTP-BINDING / LIPOPROTEIN
Function / homology
Function and homology information


Anchoring of the basal body to the plasma membrane / VxPx cargo-targeting to cilium / RAB geranylgeranylation / regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / kinetochore microtubule / exosomal secretion ...Anchoring of the basal body to the plasma membrane / VxPx cargo-targeting to cilium / RAB geranylgeranylation / regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / kinetochore microtubule / exosomal secretion / melanosome transport / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / amyloid-beta clearance by transcytosis / exocytic vesicle / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / multivesicular body assembly / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / mitotic metaphase plate congression / syntaxin binding / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / mitotic spindle assembly / positive regulation of axon extension / centriolar satellite / Vasopressin regulates renal water homeostasis via Aquaporins / phagocytic vesicle / G protein activity / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / small monomeric GTPase / multivesicular body / vesicle-mediated transport / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / regulation of cytokinesis / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / spindle pole / recycling endosome membrane / neuron projection development / microtubule binding / cytoplasmic vesicle / vesicle / endosome / axon / centrosome / GTPase activity / glutamatergic synapse / intracellular membrane-bounded organelle / protein domain specific binding / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras family / Small GTPase / 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
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structural Gdp/GTP Cycle of Rab11 Reveals a Novel Interface Involved in the Dynamics of Recycling Endosomes
Authors: Pasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J.
History
DepositionJun 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-11A
B: RAS-RELATED PROTEIN RAB-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1256
Polymers43,0802
Non-polymers1,0454
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.349, 69.701, 108.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.31774, -0.90002, 0.29833), (-0.89605, 0.18213, -0.40487), (0.31005, -0.39596, -0.86434)
Vector: 2.64872, 5.48818, 10.76037)
DetailsTHIS MAY BE RESULT OF CRYSTAL PACKING

-
Components

#1: Protein RAS-RELATED PROTEIN RAB-11A / RAB-11 / 24KG / YL8 / RAB11A


Mass: 21540.230 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-173
Source method: isolated from a genetically manipulated source
Details: DELETION MUTANT LACKING THE 43 C-TERMINAL RESIDUES / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24410, UniProt: P62491*PLUS
#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 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growpH: 8
Details: 1.7M (NH4)2SO4,5%PEG400,8% 1,3 BUTANEDIOL,0.1M TRIS-HCL PH8.0, pH 8.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 8.5 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.6-1.8 Mammonium sulfate1reservoir
33-6 %PEG4001reservoir
43-10 %1,3-butanediol1reservoir
5100 mMTris-HCl1reservoirpH8-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Nov 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 26143 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.393 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. obs: 26100 / Num. measured all: 233617 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.8

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G16
Resolution: 1.98→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1189171.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAP, AS WELL AS THE FIRST 5 RESIDUES OF RAB11A. ASP6 WAS MODELLED AS ALANINE BECAUSE ...Details: RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAP, AS WELL AS THE FIRST 5 RESIDUES OF RAB11A. ASP6 WAS MODELLED AS ALANINE BECAUSE ITS SIDE CHAIN WAS NOT VISIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1702 6.8 %RANDOM
Rwork0.21 ---
obs0.21 24954 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.7544 Å2 / ksol: 0.399156 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--3.31 Å20 Å2
3----3.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.98→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 65 191 2926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.12
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it4.262.5
LS refinement shellResolution: 1.98→2.03 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.272 103 6.2 %
Rwork0.239 1556 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP_XPLOR_PAR.TXTGDP_XPLOR_TOP.TXT
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EDO_XPLOR_PAR.TXTEDO_XPLOR_TOP.TXT
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

+
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