[English] 日本語
Yorodumi
- PDB-6hdu: Crystal structure of human Rab38 in complex with GTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hdu
TitleCrystal structure of human Rab38 in complex with GTP
ComponentsRas-related protein Rab-38
KeywordsSIGNALING PROTEIN / Rab small GTPase / membrane trafficking / cellular dynamics
Function / homology
Function and homology information


BLOC-2 complex binding / AP-3 adaptor complex binding / phagosome acidification / positive regulation of phosphatidylcholine biosynthetic process / AP-1 adaptor complex binding / endosome to melanosome transport / platelet dense granule organization / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / positive regulation of melanin biosynthetic process ...BLOC-2 complex binding / AP-3 adaptor complex binding / phagosome acidification / positive regulation of phosphatidylcholine biosynthetic process / AP-1 adaptor complex binding / endosome to melanosome transport / platelet dense granule organization / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / positive regulation of melanin biosynthetic process / GTP-dependent protein binding / melanosome membrane / RAB geranylgeranylation / melanosome organization / RAB GEFs exchange GTP for GDP on RABs / protein localization to membrane / positive regulation of protein localization to cell periphery / small GTPase-mediated signal transduction / vesicle-mediated transport / phagocytic vesicle / mitochondrion organization / intracellular protein transport / trans-Golgi network / phagocytic vesicle membrane / melanosome / protein transport / cell body / lysosome / early endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rab29/Rab38/Rab32 / 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'-TRIPHOSPHATE / Ras-related protein Rab-38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.793 Å
AuthorsMcGrath, E. / Waschbusch, D. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/1A/1239 Ireland
CitationJournal: Small GTPases / Year: 2019
Title: LRRK2 binds to the Rab32 subfamily in a GTP-dependent mannerviaits armadillo domain.
Authors: McGrath, E. / Waschbusch, D. / Baker, B.M. / Khan, A.R.
History
DepositionAug 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein Rab-38
B: Ras-related protein Rab-38
C: Ras-related protein Rab-38
D: Ras-related protein Rab-38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,75412
Polymers83,5644
Non-polymers2,1908
Water12,611700
1
A: Ras-related protein Rab-38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4393
Polymers20,8911
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4393
Polymers20,8911
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras-related protein Rab-38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4393
Polymers20,8911
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rab-38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4393
Polymers20,8911
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.045, 70.993, 74.487
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ras-related protein Rab-38 / Melanoma antigen NY-MEL-1


Mass: 20891.076 Da / Num. of mol.: 4 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB38 / Production host: Escherichia coli (E. coli) / References: UniProt: P57729
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 43.22 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Morpheus A9 10% PEG 20000 20% PEG 550 MME 0.02M divalent cations 0.1M bicine/Trizma base pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→49.28 Å / Num. obs: 66651 / % possible obs: 98.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.082 / Net I/σ(I): 12.9
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.652 / Rrim(I) all: 0.718

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ff8

6ff8


Resolution: 1.793→49.28 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.84 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2123 3358 5.05 %
Rwork0.1884 --
obs0.1897 66457 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.793→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 132 700 6349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055867
X-RAY DIFFRACTIONf_angle_d0.7967978
X-RAY DIFFRACTIONf_dihedral_angle_d10.4914433
X-RAY DIFFRACTIONf_chiral_restr0.054867
X-RAY DIFFRACTIONf_plane_restr0.005988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7926-1.81820.2706910.27282333X-RAY DIFFRACTION86
1.8182-1.84530.27961210.25522629X-RAY DIFFRACTION100
1.8453-1.87410.31671210.25022656X-RAY DIFFRACTION100
1.8741-1.90490.26721540.22962616X-RAY DIFFRACTION100
1.9049-1.93770.24651270.22792649X-RAY DIFFRACTION100
1.9377-1.9730.24111250.22032629X-RAY DIFFRACTION100
1.973-2.01090.26361480.22182659X-RAY DIFFRACTION99
2.0109-2.05190.23931590.20192589X-RAY DIFFRACTION100
2.0519-2.09660.24931360.18732631X-RAY DIFFRACTION99
2.0966-2.14530.22041450.18562631X-RAY DIFFRACTION100
2.1453-2.1990.23661440.18832636X-RAY DIFFRACTION100
2.199-2.25840.21561550.17852635X-RAY DIFFRACTION100
2.2584-2.32490.22171390.18352637X-RAY DIFFRACTION100
2.3249-2.39990.21521390.18652623X-RAY DIFFRACTION100
2.3999-2.48570.22941470.19022630X-RAY DIFFRACTION100
2.4857-2.58520.21591290.19292654X-RAY DIFFRACTION100
2.5852-2.70290.22111390.18832657X-RAY DIFFRACTION100
2.7029-2.84540.19821670.19012630X-RAY DIFFRACTION100
2.8454-3.02360.20381320.1872668X-RAY DIFFRACTION100
3.0236-3.2570.19261390.1792648X-RAY DIFFRACTION100
3.257-3.58470.18721430.16832656X-RAY DIFFRACTION100
3.5847-4.10320.18321580.16412645X-RAY DIFFRACTION100
4.1032-5.16870.17641600.15852663X-RAY DIFFRACTION100
5.1687-49.29870.22211400.20842695X-RAY DIFFRACTION98

+
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