[English] 日本語
Yorodumi
- PDB-6hh2: Rab29 small GTPase bound to GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hh2
TitleRab29 small GTPase bound to GDP
ComponentsRas-related protein Rab-7L1
KeywordsSIGNALING PROTEIN / Rab GTPase / membrane trafficking
Function / homology
Function and homology information


protein localization to ciliary membrane / regulation of retrograde transport, endosome to Golgi / modulation by host of viral process / positive regulation of intracellular protein transport / RAB geranylgeranylation / melanosome organization / cis-Golgi network / vacuole / retrograde transport, endosome to Golgi / protein localization to membrane ...protein localization to ciliary membrane / regulation of retrograde transport, endosome to Golgi / modulation by host of viral process / positive regulation of intracellular protein transport / RAB geranylgeranylation / melanosome organization / cis-Golgi network / vacuole / retrograde transport, endosome to Golgi / protein localization to membrane / cellular detoxification / positive regulation of receptor recycling / intracellular vesicle / dynein complex binding / Golgi organization / positive regulation of T cell receptor signaling pathway / kinesin binding / synapse assembly / endomembrane system / T cell activation / mitochondrion organization / intracellular protein transport / response to bacterium / trans-Golgi network / recycling endosome / small GTPase binding / GDP binding / melanosome / negative regulation of neuron projection development / nuclear membrane / cell differentiation / cytoskeleton / early endosome / Golgi membrane / GTPase activity / intracellular membrane-bounded organelle / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / mitochondrion / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ras-related protein Rab29/Rab38/Rab32 / small GTPase Rab1 family 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 ...Ras-related protein Rab29/Rab38/Rab32 / small GTPase Rab1 family 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
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-7L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsKhan, A.R. / McGrath, E. / Waschbusch, D.
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 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein Rab-7L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9553
Polymers20,4871
Non-polymers4682
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-14 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.960, 71.960, 86.348
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Ras-related protein Rab-7L1 / Rab-7-like protein 1 / Ras-related protein Rab-29


Mass: 20487.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB29, RAB7L1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14966
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 2M NaCl 0.1M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.449→86.35 Å / Num. obs: 46405 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.017 / Rrim(I) all: 0.055 / Net I/σ(I): 27.4
Reflection shellResolution: 1.449→1.47 Å / Rmerge(I) obs: 1.631 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.68 / Rpim(I) all: 0.585 / Rsym value: 1.736

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hdu

6hdu


Resolution: 1.449→62.319 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 18.88
RfactorNum. reflection% reflection
Rfree0.1843 2383 5.15 %
Rwork0.1651 --
obs0.1661 46316 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.449→62.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 29 194 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171511
X-RAY DIFFRACTIONf_angle_d1.6292064
X-RAY DIFFRACTIONf_dihedral_angle_d15.721574
X-RAY DIFFRACTIONf_chiral_restr0.147232
X-RAY DIFFRACTIONf_plane_restr0.008257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.47860.27051300.28492474X-RAY DIFFRACTION97
1.4786-1.51070.32521400.25852537X-RAY DIFFRACTION100
1.5107-1.54590.25781500.23562548X-RAY DIFFRACTION100
1.5459-1.58450.24961410.21692568X-RAY DIFFRACTION100
1.5845-1.62740.19821570.2042564X-RAY DIFFRACTION100
1.6274-1.67520.21831360.18622555X-RAY DIFFRACTION100
1.6752-1.72930.20981090.18652611X-RAY DIFFRACTION100
1.7293-1.79110.22011380.17992527X-RAY DIFFRACTION100
1.7911-1.86290.15521430.17392566X-RAY DIFFRACTION100
1.8629-1.94760.20331480.17212608X-RAY DIFFRACTION100
1.9476-2.05030.18311340.16562583X-RAY DIFFRACTION100
2.0503-2.17880.18571320.15812594X-RAY DIFFRACTION100
2.1788-2.3470.17361390.1522578X-RAY DIFFRACTION100
2.347-2.58320.19081270.16492620X-RAY DIFFRACTION100
2.5832-2.9570.19011440.16922626X-RAY DIFFRACTION100
2.957-3.72550.16731650.14962621X-RAY DIFFRACTION100
3.7255-62.37660.17121500.15342753X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 37.5723 Å / Origin y: 16.2535 Å / Origin z: 32.9528 Å
111213212223313233
T0.173 Å2-0.0269 Å2-0.0046 Å2-0.1614 Å2-0.0076 Å2--0.1582 Å2
L1.0889 °2-0.4119 °20.0468 °2-2.1746 °20.2797 °2--1.8491 °2
S0.0025 Å °-0.002 Å °0.0209 Å °0.0115 Å °0.0245 Å °-0.091 Å °-0.0473 Å °-0.0101 Å °-0.0304 Å °
Refinement TLS groupSelection details: all

+
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