[English] 日本語
Yorodumi
- PDB-6iy1: Structure of human Ras-related protein Rab11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iy1
TitleStructure of human Ras-related protein Rab11
Components(Ras-related protein Rab-11A) x 3
KeywordsTRANSPORT PROTEIN / Complex / transport / GTPase
Function / homology
Function and homology information


regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / exosomal secretion / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / amyloid-beta clearance by transcytosis ...regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / exosomal secretion / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / amyloid-beta clearance by transcytosis / neurotransmitter receptor transport, endosome to postsynaptic membrane / 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 / cleavage furrow / exocytosis / mitotic spindle assembly / centriolar satellite / phagocytic vesicle / Vasopressin regulates renal water homeostasis via Aquaporins / G protein activity / transport vesicle / Anchoring of the basal body to the plasma membrane / small monomeric GTPase / positive regulation of G2/M transition of mitotic cell cycle / multivesicular body / centriole / vesicle-mediated transport / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of cytokinesis / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / spindle pole / recycling endosome membrane / neuron projection development / microtubule binding / cytoplasmic vesicle / vesicle / endosome / axon / GTPase activity / centrosome / glutamatergic synapse / intracellular membrane-bounded organelle / GTP binding / 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 / 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
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMa, P. / Li, S. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31500632 China
CitationJournal: To Be Published
Title: Structure of human Ras-related protein Rab11
Authors: Ma, P. / Li, S. / Li, J.
History
DepositionDec 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein Rab-11A
B: Ras-related protein Rab-11A
C: Ras-related protein Rab-11A
D: Ras-related protein Rab-11A
E: Ras-related protein Rab-11A
F: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,64012
Polymers111,9816
Non-polymers2,6596
Water3,855214
1
A: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area8570 Å2
MethodPISA
2
B: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-8 kcal/mol
Surface area8580 Å2
MethodPISA
3
C: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area8560 Å2
MethodPISA
4
D: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2822
Polymers18,8391
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area8640 Å2
MethodPISA
5
E: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-7 kcal/mol
Surface area8550 Å2
MethodPISA
6
F: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3972
Polymers18,9541
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.606, 150.762, 60.125
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 18546.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#2: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 18839.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#3: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 18954.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GDP / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15M Li2SO4, 0.1M Glycine, 0.8M NaH2PO4 1.2M Na2HPO4

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48648 / % possible obs: 91.2 % / Redundancy: 2.5 % / CC1/2: 0.945 / Rpim(I) all: 0.063 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 2190 / CC1/2: 0.945 / Rpim(I) all: 0.248

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OIV
Resolution: 2.11→46.73 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.26108 2421 5 %RANDOM
Rwork0.21938 ---
obs0.22148 46212 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.154 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.11→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 0 214 8223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.66711054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94621.518448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4491566
X-RAY DIFFRACTIONr_chiral_restr0.0950.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7742.5273943
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9693.7754913
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2572.8354203
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.88434.37912711
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.107→2.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 154 -
Rwork0.342 3073 -
obs--82.2 %

+
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