[English] 日本語
Yorodumi
- PDB-1x3s: Crystal structure of human Rab18 in complex with Gppnhp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x3s
TitleCrystal structure of human Rab18 in complex with Gppnhp
ComponentsRas-related protein Rab-18
KeywordsENDOCYTOSIS/EXOCYTOSIS / GTPase / Rab / GNP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


endoplasmic reticulum tubular network organization / endoplasmic reticulum tubular network / neutrophil degranulation / eye development / RAB geranylgeranylation / lipid droplet organization / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / small GTPase-mediated signal transduction / endomembrane system ...endoplasmic reticulum tubular network organization / endoplasmic reticulum tubular network / neutrophil degranulation / eye development / RAB geranylgeranylation / lipid droplet organization / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / small GTPase-mediated signal transduction / endomembrane system / viral process / lipid droplet / secretory granule membrane / intracellular protein transport / brain development / GDP binding / apical plasma membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Sigma-54 interaction domain, ATP-binding site 1 / small GTPase Rab1 family profile. / Small GTPase / Ras family / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.32 Å
AuthorsKukimoto-Niino, M. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of human Rab18 in complex with Gppnhp
Authors: Kukimoto-Niino, M. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: 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-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3053
Polymers21,7591
Non-polymers5472
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.889, 65.182, 40.710
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ras-related protein Rab-18 / GTP-binding protein Rab18


Mass: 21758.973 Da / Num. of mol.: 1 / Fragment: GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis system / References: UniProt: Q9NP72
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97931, 0.97917, 0.96860
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979171
30.96861
ReflectionResolution: 1.32→50 Å / Num. obs: 44016 / % possible obs: 87.2 % / Observed criterion σ(I): -3 / Redundancy: 5.38303 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.057 / Net I/σ(I): 32.5881
Reflection shellResolution: 1.32→1.37 Å / Mean I/σ(I) obs: 7.49867 / Rsym value: 0.171 / % possible all: 69.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.32→14.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 596602.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 4425 10.1 %RANDOM
Rwork0.185 ---
obs0.185 40584 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8389 Å2 / ksol: 0.419208 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20.52 Å2
2---2.28 Å20 Å2
3----1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.32→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 33 230 1668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.36
LS refinement shellResolution: 1.32→1.4 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 659 10.6 %
Rwork0.214 5567 -
obs--80.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gnp_paramgnp_xplor_top

+
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://pdbjlvh1.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