[English] 日本語
Yorodumi
- PDB-6yx5: Structure of DrrA from Legionella pneumophilia in complex with hu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yx5
TitleStructure of DrrA from Legionella pneumophilia in complex with human Rab8a
Components
  • Multifunctional virulence effector protein DrrA
  • Ras-related protein Rab-8A
KeywordsCELL INVASION / vesicular trafficking virulence factor
Function / homology
Function and homology information


: / protein guanylylation / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / AMPylase activity / vesicle-mediated transport in synapse / protein adenylyltransferase / regulation of protein transport / protein adenylylation / VxPx cargo-targeting to cilium ...: / protein guanylylation / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / AMPylase activity / vesicle-mediated transport in synapse / protein adenylyltransferase / regulation of protein transport / protein adenylylation / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / non-motile cilium / host cell cytoplasmic vesicle / endocytic recycling / phosphatidylinositol-4-phosphate binding / TBC/RABGAPs / ciliary membrane / ciliary base / regulation of GTPase activity / Golgi organization / protein secretion / cilium assembly / phagocytic vesicle / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / guanyl-nucleotide exchange factor activity / small monomeric GTPase / trans-Golgi network membrane / ciliary basal body / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / host cell cytoplasmic vesicle membrane / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / protein guanylyltransferase activity / synaptic vesicle / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / extracellular exosome / extracellular region / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
alpha-D-glucopyranose / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-LJN / ras-related protein Rab-8A / Ras-related protein Rab-8A / Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSchneider, S. / Du, J. / von Wrisberg, M.K. / Lang, K. / Itzen, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
German Research Foundation (DFG)EXC114 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1.
Authors: Du, J. / Wrisberg, M.V. / Gulen, B. / Stahl, M. / Pett, C. / Hedberg, C. / Lang, K. / Schneider, S. / Itzen, A.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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: Ras-related protein Rab-8A
B: Multifunctional virulence effector protein DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,79913
Polymers58,8792
Non-polymers1,92011
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, ATP analogue used to stabilise weak DrrA-Rab8a complex Validated by mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-75 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.309, 142.309, 76.616
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Ras-related protein Rab-8A


Mass: 20042.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: recombinant / Source: (gene. exp.) Homo sapiens (human) / Gene: Rab8a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U7REJ8, UniProt: P61006*PLUS
#2: Protein Multifunctional virulence effector protein DrrA


Mass: 38837.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residue number 1 disordered L197C / Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q29ST3

-
Sugars , 1 types, 3 molecules

#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 121 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-LJN / [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 352.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N4O8P
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 45 % / Description: hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M bicine, pH 9, 2.4M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.14→48.06 Å / Num. obs: 49091 / % possible obs: 99.7 % / Redundancy: 20 % / Biso Wilson estimate: 43.52 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.206 / Net I/σ(I): 15.57
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 18.3 % / Rmerge(I) obs: 2.43 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 4745 / CC1/2: 0.43 / CC star: 0.775 / Rpim(I) all: 0.57 / Rrim(I) all: 2.5 / % possible all: 96.97

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NKU, 4LHV

3nku

4lhv


Resolution: 2.14→48.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.681 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.159
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2441 5 %RANDOM
Rwork0.2068 ---
obs0.2084 46650 99.63 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 113.26 Å2 / Biso mean: 50.306 Å2 / Biso min: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å2-0 Å2
2---0.07 Å20 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.14→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 116 113 4344
Biso mean--69 43.06 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134313
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174008
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.6665830
X-RAY DIFFRACTIONr_angle_other_deg1.1481.5989336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08723.017232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76915805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7771527
X-RAY DIFFRACTIONr_chiral_restr0.050.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
LS refinement shellResolution: 2.144→2.2 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.358 163 -
Rwork0.35 3308 -
obs--95.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1061-0.5065-0.10953.0705-0.42531.98610.07840.3427-0.1944-0.5316-0.1020.08130.18240.00740.02360.18580.0655-0.03080.1669-0.03110.0239-20.711-71.8810.375
22.3614-1.0380.46670.9877-0.25331.075-0.089-0.05320.22930.05120.0702-0.2037-0.22180.09190.01880.15950.01530.00830.1828-0.03130.0466-11.643-53.47322.761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 175
2X-RAY DIFFRACTION2B14 - 352

+
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