[English] 日本語
Yorodumi
- PDB-5z2m: Structure of Orp1L/Rab7 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z2m
TitleStructure of Orp1L/Rab7 complex
Components
  • Oxysterol-binding protein-related protein 1
  • Ras-related protein Rab-7a
KeywordsENDOCYTOSIS / GTPase / Effector / Complex
Function / homology
Function and homology information


: / : / small GTPase binding => GO:0031267 / lipophagy / epidermal growth factor catabolic process / TBC/RABGAPs / positive regulation of viral process / phagosome acidification / protein to membrane docking / RAB geranylgeranylation ...: / : / small GTPase binding => GO:0031267 / lipophagy / epidermal growth factor catabolic process / TBC/RABGAPs / positive regulation of viral process / phagosome acidification / protein to membrane docking / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / organelle membrane contact site / Synthesis of bile acids and bile salts / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / : / retromer complex binding / sterol binding / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / early endosome to late endosome transport / positive regulation of exosomal secretion / MHC class II antigen presentation / retrograde transport, endosome to Golgi / cholesterol binding / endosome to lysosome transport / autophagosome membrane / autophagosome assembly / viral release from host cell / lipid catabolic process / phagocytic vesicle / bone resorption / Neutrophil degranulation / lipid droplet / intracellular protein transport / phagocytic vesicle membrane / GDP binding / positive regulation of protein catabolic process / late endosome / late endosome membrane / cytoplasmic vesicle / lysosome / endosome membrane / endosome / intracellular membrane-bounded organelle / GTPase activity / GTP binding / Golgi apparatus / membrane / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeats (many copies) / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / PH domain profile. / Pleckstrin homology domain. ...Ankyrin repeats (many copies) / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-7a / Oxysterol-binding protein-related protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.142 Å
AuthorsMa, X.L. / Liu, K. / Li, J. / Li, H.H. / Li, J. / Yang, C.L. / Liang, H.H.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A non-canonical GTPase interaction enables ORP1L-Rab7-RILP complex formation and late endosome positioning.
Authors: Ma, X. / Liu, K. / Li, J. / Li, H. / Li, J. / Liu, Y. / Yang, C. / Liang, H.
History
DepositionJan 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Oxysterol-binding protein-related protein 1
A: Ras-related protein Rab-7a
C: Ras-related protein Rab-7a
D: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5697
Polymers70,4994
Non-polymers1,0713
Water6,233346
1
B: Oxysterol-binding protein-related protein 1
A: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7974
Polymers35,2492
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-7a
D: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7723
Polymers35,2492
Non-polymers5231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.222, 109.626, 77.811
Angle α, β, γ (deg.)90.00, 99.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Oxysterol-binding protein-related protein 1 / OSBP-related protein 1


Mass: 15250.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Osbpl1a, Orp1, Orp1a, Orp1l / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q91XL9
#2: Protein Ras-related protein Rab-7a


Mass: 19998.902 Da / Num. of mol.: 2 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab7a, Rab7 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P51150
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 4% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 38402 / % possible obs: 98.2 % / Redundancy: 7.4 % / Net I/σ(I): 22.9
Reflection shellResolution: 2.14→2.18 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T91

1t91


Resolution: 2.142→25.586 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91
RfactorNum. reflection% reflection
Rfree0.2093 1995 5.2 %
Rwork0.1815 --
obs0.183 38402 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.142→25.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 65 346 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084967
X-RAY DIFFRACTIONf_angle_d1.0026718
X-RAY DIFFRACTIONf_dihedral_angle_d14.8453004
X-RAY DIFFRACTIONf_chiral_restr0.056756
X-RAY DIFFRACTIONf_plane_restr0.008858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1419-2.19540.2911360.2332497X-RAY DIFFRACTION95
2.1954-2.25470.31351400.21372574X-RAY DIFFRACTION97
2.2547-2.3210.28511410.21362558X-RAY DIFFRACTION97
2.321-2.39590.231430.20412602X-RAY DIFFRACTION97
2.3959-2.48150.21871400.20292550X-RAY DIFFRACTION98
2.4815-2.58070.21231430.19292617X-RAY DIFFRACTION97
2.5807-2.69810.23941420.19972593X-RAY DIFFRACTION98
2.6981-2.84010.23741430.20062600X-RAY DIFFRACTION98
2.8401-3.01780.23871430.20032614X-RAY DIFFRACTION98
3.0178-3.25040.24991440.20412631X-RAY DIFFRACTION99
3.2504-3.57670.2071440.17992628X-RAY DIFFRACTION99
3.5767-4.09250.15711450.16162629X-RAY DIFFRACTION99
4.0925-5.14920.17131440.15742637X-RAY DIFFRACTION99
5.1492-25.58770.18651470.15912677X-RAY DIFFRACTION99

+
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