[English] 日本語
Yorodumi
- PDB-5o74: Crystal structure of human Rab1b covalently bound to the GEF doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o74
TitleCrystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP
Components
  • Multifunctional virulence effector protein DrrA
  • Ras-related protein Rab-1B
KeywordsHYDROLASE / Rab1b / DrrA / exchange factor / Legionella pneumophila
Function / homology
Function and homology information


: / protein guanylylation / positive regulation of glycoprotein metabolic process / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs ...: / protein guanylylation / positive regulation of glycoprotein metabolic process / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / host cell cytoplasmic vesicle / Golgi Cisternae Pericentriolar Stack Reorganization / phosphatidylinositol-4-phosphate binding / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / regulation of GTPase activity / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / host cell cytoplasmic vesicle membrane / intracellular protein transport / small GTPase binding / protein guanylyltransferase activity / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / extracellular region / ATP binding / membrane / cytosol
Similarity search - Function
Ferritin - #70 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / ARF-like small GTPases; ARF, ADP-ribosylation factor ...Ferritin - #70 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ferritin / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Multifunctional virulence effector protein DrrA / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCigler, M. / Mueller, T. / Horn-Ghetko, D. / von Wrisberg, M.K. / Fottner, M. / Goody, R.S. / Itzen, A. / Mueller, M.P. / Lang, K.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB1035, grant B10 Germany
German Research FoundationGRK1721, grant C4 Germany
Center for Integrated Protein Science MunichCIPSM Germany
German Research FoundationSFB 642, grant A4 Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Proximity-Triggered Covalent Stabilization of Low-Affinity Protein Complexes In Vitro and In Vivo.
Authors: Cigler, M. / Muller, T.G. / Horn-Ghetko, D. / von Wrisberg, M.K. / Fottner, M. / Goody, R.S. / Itzen, A. / Muller, M.P. / Lang, K.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 2.0Dec 6, 2017Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity_poly.pdbx_target_identifier
Revision 2.1Jan 17, 2024Group: 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
A: Multifunctional virulence effector protein DrrA
B: Ras-related protein Rab-1B
C: Multifunctional virulence effector protein DrrA
D: Ras-related protein Rab-1B
E: Multifunctional virulence effector protein DrrA
F: Ras-related protein Rab-1B
G: Multifunctional virulence effector protein DrrA
H: Ras-related protein Rab-1B
I: Multifunctional virulence effector protein DrrA
J: Ras-related protein Rab-1B
K: Multifunctional virulence effector protein DrrA
L: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,29718
Polymers255,63812
Non-polymers2,6596
Water0
1
A: Multifunctional virulence effector protein DrrA
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0503
Polymers42,6062
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-16 kcal/mol
Surface area16130 Å2
MethodPISA
2
C: Multifunctional virulence effector protein DrrA
D: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0503
Polymers42,6062
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-18 kcal/mol
Surface area16570 Å2
MethodPISA
3
E: Multifunctional virulence effector protein DrrA
F: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0503
Polymers42,6062
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-19 kcal/mol
Surface area16150 Å2
MethodPISA
4
G: Multifunctional virulence effector protein DrrA
H: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0503
Polymers42,6062
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-19 kcal/mol
Surface area16280 Å2
MethodPISA
5
I: Multifunctional virulence effector protein DrrA
J: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0503
Polymers42,6062
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-20 kcal/mol
Surface area16250 Å2
MethodPISA
6
K: Multifunctional virulence effector protein DrrA
L: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0503
Polymers42,6062
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-18 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.910, 87.450, 93.170
Angle α, β, γ (deg.)114.61, 97.69, 100.74
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Multifunctional virulence effector protein DrrA / Defects in Rab1 recruitment protein A


Mass: 22001.195 Da / Num. of mol.: 6 / Mutation: D512C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: drrA, sidM / Production host: Escherichia coli (E. coli)
References: UniProt: Q29ST3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein
Ras-related protein Rab-1B


Mass: 20605.148 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0U4
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Production host: Escherichia coli (E. coli) / Comment: GDP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.5→46.525 Å / Num. obs: 72360 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rsym value: 0.092 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7978 / Rsym value: 0.596 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jza

3jza


Resolution: 2.5→46.525 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.49
RfactorNum. reflection% reflection
Rfree0.266 3618 5 %
Rwork0.2286 --
obs0.2304 72353 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17004 0 0 0 17004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617283
X-RAY DIFFRACTIONf_angle_d0.95223318
X-RAY DIFFRACTIONf_dihedral_angle_d13.06710525
X-RAY DIFFRACTIONf_chiral_restr0.0932646
X-RAY DIFFRACTIONf_plane_restr0.0052913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53290.4161380.39882626X-RAY DIFFRACTION98
2.5329-2.56760.42451400.3772668X-RAY DIFFRACTION98
2.5676-2.60430.38571360.37162581X-RAY DIFFRACTION98
2.6043-2.64310.35581420.35642688X-RAY DIFFRACTION98
2.6431-2.68440.38281370.35162608X-RAY DIFFRACTION98
2.6844-2.72850.33461390.34662643X-RAY DIFFRACTION98
2.7285-2.77550.37331400.3242659X-RAY DIFFRACTION98
2.7755-2.8260.35751400.32492670X-RAY DIFFRACTION98
2.826-2.88030.29181370.30742595X-RAY DIFFRACTION98
2.8803-2.93910.34011390.28542652X-RAY DIFFRACTION98
2.9391-3.0030.32611410.27342664X-RAY DIFFRACTION98
3.003-3.07280.31571380.26112634X-RAY DIFFRACTION98
3.0728-3.14970.3181410.27272663X-RAY DIFFRACTION98
3.1497-3.23480.29691390.26262652X-RAY DIFFRACTION98
3.2348-3.330.28411390.26332640X-RAY DIFFRACTION98
3.33-3.43740.30351380.24492627X-RAY DIFFRACTION98
3.4374-3.56020.27231400.23032656X-RAY DIFFRACTION98
3.5602-3.70270.25081380.23282629X-RAY DIFFRACTION98
3.7027-3.87110.27621390.21522637X-RAY DIFFRACTION98
3.8711-4.07510.24921410.20342669X-RAY DIFFRACTION98
4.0751-4.33030.24161390.22651X-RAY DIFFRACTION99
4.3303-4.66430.23181400.16552654X-RAY DIFFRACTION98
4.6643-5.13320.23111390.16932641X-RAY DIFFRACTION98
5.1332-5.87470.2171380.19522629X-RAY DIFFRACTION97
5.8747-7.39670.23131400.19932645X-RAY DIFFRACTION99
7.3967-46.53330.18371400.16482654X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 18.2404 Å / Origin y: -8.8812 Å / Origin z: -48.605 Å
111213212223313233
T0.4865 Å2-0.0048 Å2-0.014 Å2-0.513 Å20.0002 Å2--0.5119 Å2
L-0.0384 °2-0.0112 °2-0.0492 °2-0.0727 °20.0234 °2--0.0356 °2
S-0.0251 Å °0.0645 Å °-0.0242 Å °0.0075 Å °-0.0208 Å °0.028 Å °0.0801 Å °-0.1148 Å °-0 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