[English] 日本語
Yorodumi
- PDB-6wcw: Structure of human Rubicon RH domain in complex with GTP-bound Rab7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wcw
TitleStructure of human Rubicon RH domain in complex with GTP-bound Rab7
Components
  • Ras-related protein Rab-7a
  • Run domain Beclin-1-interacting and cysteine-rich domain-containing protein
KeywordsMETAL BINDING PROTEIN / autophagy / rab / gtpase / aging / zinc finger / g protein
Function / homology
Function and homology information


negative regulation of autophagosome maturation / phagosome acidification / lipophagy / protein to membrane docking / phosphatidylinositol 3-kinase inhibitor activity / positive regulation of viral process / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / synaptic vesicle recycling via endosome ...negative regulation of autophagosome maturation / phagosome acidification / lipophagy / protein to membrane docking / phosphatidylinositol 3-kinase inhibitor activity / positive regulation of viral process / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / synaptic vesicle recycling via endosome / negative regulation of intralumenal vesicle formation / Suppression of autophagy / phagosome-lysosome fusion / negative regulation of exosomal secretion / establishment of vesicle localization / phosphatidylinositol phosphate binding / retromer complex binding / phagosome maturation / presynaptic endosome / endosome to plasma membrane protein transport / early endosome to late endosome transport / protein localization to lysosome / multivesicular body sorting pathway / phagophore assembly site membrane / positive regulation of exosomal secretion / RAB geranylgeranylation / melanosome membrane / protein targeting to lysosome / negative regulation of endocytosis / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / TBC/RABGAPs / retrograde transport, endosome to Golgi / RHOF GTPase cycle / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / autophagosome membrane / RHOH GTPase cycle / viral release from host cell / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / immune system process / autophagosome assembly / bone resorption / intracellular transport / phagocytosis / lipid catabolic process / phagocytic vesicle / RAC1 GTPase cycle / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / lipid droplet / secretory granule membrane / negative regulation of autophagy / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / small monomeric GTPase / response to bacterium / autophagy / mitochondrial membrane / small GTPase binding / endocytosis / phagocytic vesicle membrane / positive regulation of protein catabolic process / GDP binding / late endosome / late endosome membrane / protein transport / synaptic vesicle membrane / G protein activity / intracellular membrane-bounded organelle / early endosome / lysosome / endosome membrane / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
: / : / Rubicon, PI3K-binding domain / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily / RUN domain ...: / : / Rubicon, PI3K-binding domain / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Small GTPase Rab domain 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'-TRIPHOSPHATE / Ras-related protein Rab-7a / Run domain Beclin-1-interacting and cysteine-rich domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBhargava, H.K. / Byck, J.M. / Farrell, D.P. / Anishchenko, I. / DiMaio, F. / Im, Y.J. / Hurley, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM123089 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM111730 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Authors: Bhargava, H.K. / Tabata, K. / Byck, J.M. / Hamasaki, M. / Farrell, D.P. / Anishchenko, I. / DiMaio, F. / Im, Y.J. / Yoshimori, T. / Hurley, J.H.
History
DepositionMar 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 5, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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
Revision 1.3Oct 18, 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: Ras-related protein Rab-7a
A: Run domain Beclin-1-interacting and cysteine-rich domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1918
Polymers50,3822
Non-polymers8096
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex tightly associates as a heterodimer on size exclusion chromatography., immunoprecipitation, The Rubicon RH domain is sufficient to pull down GTP-bound Rab7 from cell ...Evidence: gel filtration, Complex tightly associates as a heterodimer on size exclusion chromatography., immunoprecipitation, The Rubicon RH domain is sufficient to pull down GTP-bound Rab7 from cell lysates., microscopy, Rubicon and Rab7 colocalize in human cells.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.040, 45.330, 186.277
Angle α, β, γ (deg.)90.000, 98.507, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein Ras-related protein Rab-7a


Mass: 20840.699 Da / Num. of mol.: 1 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A, RAB7 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P51149
#2: Protein Run domain Beclin-1-interacting and cysteine-rich domain-containing protein / Rubicon / Beclin-1 associated RUN domain containing protein / Baron


Mass: 29541.436 Da / Num. of mol.: 1 / Fragment: RH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUBCN, KIAA0226 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92622
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 6% (w/v) PEG 8000, 100mM Tris-HCl pH 7.4, 15mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.8→92.11 Å / Num. obs: 12498 / % possible obs: 99.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 50.62 Å2 / CC1/2: 0.986 / Net I/σ(I): 6.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1234 / CC1/2: 0.715 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Blu-Icedata collection
ELVESdata processing
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YHN

1yhn


Resolution: 2.8→54.22 Å / SU ML: 0.3844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1988
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 591 4.77 %Random selection
Rwork0.1995 11804 --
obs0.2024 12395 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→54.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 0 0 3447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093512
X-RAY DIFFRACTIONf_angle_d1.05414748
X-RAY DIFFRACTIONf_chiral_restr0.056521
X-RAY DIFFRACTIONf_plane_restr0.0055607
X-RAY DIFFRACTIONf_dihedral_angle_d24.58531320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.39221300.28242923X-RAY DIFFRACTION98.74
3.08-3.530.31021690.24432898X-RAY DIFFRACTION98.55
3.53-4.440.21241370.17492958X-RAY DIFFRACTION99.36
4.44-54.220.23531550.17353025X-RAY DIFFRACTION98.97
Refinement TLS params.Method: refined / Origin x: -3.97387330335 Å / Origin y: 24.7072069095 Å / Origin z: 38.6235448201 Å
111213212223313233
T0.2649171581 Å20.0319573900416 Å2-0.00480449627833 Å2-0.375452392478 Å20.0958277321209 Å2--0.322596506454 Å2
L0.208932859123 °20.225932558673 °2-1.06707365976 °2--0.00725053557181 °2-0.380485090947 °2--2.40464517327 °2
S0.0467383014816 Å °0.0856833581124 Å °0.0240848780564 Å °0.0111097981558 Å °0.0598718620997 Å °0.000128416162956 Å °-0.0455502657974 Å °-0.306900529773 Å °-0.039085844215 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