[English] 日本語
Yorodumi
- PDB-5ms2: Crystal structure of the Legionella pneumophila effector protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ms2
TitleCrystal structure of the Legionella pneumophila effector protein RavZ in complex with human LC3B
Components
  • Legionella pneumophila effector protein RavZ
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsHYDROLASE / Autophagy / Host-pathogen interaction
Function / homology
Function and homology information


host intracellular membrane-bounded organelle / protein delipidation / SARS-CoV-2 modulates autophagy / ceramide binding / symbiont-mediated suppression of host autophagy / phosphatidylinositol-3-phosphate binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation ...host intracellular membrane-bounded organelle / protein delipidation / SARS-CoV-2 modulates autophagy / ceramide binding / symbiont-mediated suppression of host autophagy / phosphatidylinositol-3-phosphate binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / cysteine-type peptidase activity / Pexophagy / autophagosome / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / host cell cytoplasmic vesicle membrane / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / ubiquitin protein ligase binding / mitochondrion / proteolysis / extracellular region / membrane / cytosol
Similarity search - Function
: / RavZ C-terminal PI3P-binding domain / RavZ catalytic domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Cysteine protease RavZ / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsPantoom, S. / Vetter, I.R. / Wu, Y.W.
CitationJournal: Elife / Year: 2017
Title: Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins.
Authors: Yang, A. / Pantoom, S. / Wu, Y.W.
History
DepositionDec 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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: Legionella pneumophila effector protein RavZ
B: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)63,1032
Polymers63,1032
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-2 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 69.550, 90.170
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Legionella pneumophila effector protein RavZ


Mass: 48523.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg1683 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5ZUV9
#2: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14579.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9GZQ8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17 M ammonium acetate, 0.085M tri sodium citrate, 25.5% PEG 4000 and 15% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.47→48.08 Å / Num. obs: 22607 / % possible obs: 99.91 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.26 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.51
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.57 / % possible all: 99.42

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQC, 2Z0D

5cqc

2z0d


Resolution: 2.47→48.08 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2384 1131 5 %
Rwork0.1774 --
obs0.1805 22607 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.47→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 0 111 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014251
X-RAY DIFFRACTIONf_angle_d1.4465742
X-RAY DIFFRACTIONf_dihedral_angle_d17.0961608
X-RAY DIFFRACTIONf_chiral_restr0.057648
X-RAY DIFFRACTIONf_plane_restr0.007735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.58240.29861410.24282672X-RAY DIFFRACTION100
2.5824-2.71860.29031390.22832645X-RAY DIFFRACTION100
2.7186-2.88890.29691410.21362679X-RAY DIFFRACTION100
2.8889-3.11190.25871410.1942664X-RAY DIFFRACTION100
3.1119-3.4250.24121400.18022672X-RAY DIFFRACTION100
3.425-3.92040.21851420.15612702X-RAY DIFFRACTION100
3.9204-4.93850.19971410.13932688X-RAY DIFFRACTION100
4.9385-48.0890.22041460.16852754X-RAY DIFFRACTION100
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)
17.9846-4.46412.03285.4453-0.7411.25540.33420.097-0.049-0.1296-0.22440.3378-0.131-0.3121-0.10340.22750.05540.09460.22190.01790.225-22.9077-11.8276-10.7976
21.67340.6268-0.99583.0016-1.08762.70650.01560.041-0.2391-0.1327-0.0488-0.24330.09940.0287-0.00990.10380.0443-0.02210.1428-0.00540.2829-6.0867-33.6655-6.2996
32.7109-1.33940.16143.338-0.01710.21650.0660.24060.4963-0.3571-0.1813-0.3059-0.12150.03750.12110.18690.03090.04190.19740.05780.2678-14.7147-1.583-11.1442
46.34170.15724.74164.3623-3.46658.38340.3934-0.7515-0.51250.46670.57680.45841.3091-1.305-0.85110.7773-0.16650.04190.6313-0.0410.3278-41.48790.9958-54.8847
53.12963.56830.24857.0082-1.1121.45250.1255-2.55330.83050.96590.00161.2581-1.5895-2.6877-0.10160.62820.13180.07741.1194-0.02370.4873-44.789411.6881-55.8763
63.49061.74952.54641.50910.02954.3169-0.53570.95270.8238-0.78120.38710.9266-1.4799-1.23230.16261.72261.0043-0.27562.0267-0.12710.8191-49.708116.8835-44.157
75.3628-0.13012.16596.1679-0.6598.5835-0.1097-0.2987-0.1696-0.1213-0.1410.49170.4015-1.82380.21020.71720.06510.05361.01260.10910.3035-38.95711.1673-41.3482
82.97540.7381-2.73944.7865-2.94033.62910.2567-0.32550.0590.4904-0.20130.21220.3661-0.70080.00991.00050.102-0.08650.9988-0.2229-0.0431-39.12132.3509-32.0359
92.0018-2.02313.223.1721-5.31188.9216-0.1217-0.8386-1.31830.2206-0.3048-0.29951.0105-0.24290.35620.98490.1311-0.04870.87170.23060.9676-33.2285-3.5293-33.1511
108.744-7.1564-7.05059.36067.3536.3994-0.64030.55230.92070.5131-0.0455-1.3452-0.3510.42830.62221.48270.6286-0.25191.1797-0.06520.7807-28.627310.096-37.8026
110.52040.11140.20024.4695.72487.3378-0.0149-0.43060.84380.4474-0.0966-0.3636-1.01440.27310.09551.41410.0449-0.35040.7194-0.00760.7317-34.107215.8791-41.5265
125.6638-2.68082.08976.9268-4.58596.7616-0.6213-0.16340.3861-0.51720.0476-0.11520.322-0.92690.48720.87850.1473-0.02750.6058-0.12480.3086-36.26347.4359-47.3682
134.59374.0211-4.4213.5196-3.87024.2573-0.98060.0633-0.9316-1.95370.2694-2.65251.52472.00660.82231.11220.33530.34331.2140.27621.4652-23.8212-3.51-41.732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 275 )
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 429 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 12 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 70 )
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 83 )
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 114 )
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 119 )

+
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