[English] 日本語
Yorodumi
- PDB-6vhr: Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) sec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vhr
TitleStructure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422
Components
  • ESX-3 secretion-associated protein EspG3
  • PE family immunomodulator PE5
  • PPE family protein PPE4
KeywordsPROTEIN TRANSPORT / chaperone / protein secretion
Function / homology
Function and homology information


: / response to host immune response / cell surface / extracellular region / plasma membrane
Similarity search - Function
PPE-PPW subfamily, C-terminal / PPE-PPW subfamily C-terminal region / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / PPE superfamily / EspG family / EspG family
Similarity search - Domain/homology
Conserved protein / PE family immunomodulator PE5 / PPE family protein PPE4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWilliamson, Z.A. / Korotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI119022 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: PE5-PPE4-EspG3heterotrimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems.
Authors: Williamson, Z.A. / Chaton, C.T. / Ciocca, W.A. / Korotkova, N. / Korotkov, K.V.
History
DepositionJan 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
A: PE family immunomodulator PE5
B: PPE family protein PPE4
C: ESX-3 secretion-associated protein EspG3


Theoretical massNumber of molelcules
Total (without water)58,2043
Polymers58,2043
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-63 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.090, 219.090, 104.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein PE family immunomodulator PE5


Mass: 9228.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PE5, Rv0285, LH57_01560 / Plasmid: pRSF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: L7N695
#2: Protein PPE family protein PPE4


Mass: 18099.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment residues 1-178
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PPE4, Rv0286 / Plasmid: pRSF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: P9WI43
#3: Protein ESX-3 secretion-associated protein EspG3


Mass: 30875.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment residues 5-290
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_0548 / Plasmid: pCDF-21d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: B2HNX0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.38 Å3/Da / Density % sol: 77.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2M sodium chloride, 0.1M BIS-TRIS

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 5, 2018
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→35.727 Å / Num. obs: 19380 / % possible obs: 99.8 % / Redundancy: 10.295 % / Biso Wilson estimate: 125.541 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.091 / Χ2: 1.046 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.399.5332.1821.3113404140614060.5972.308100
3.39-3.4810.961.7921.815289139613950.7791.87999.9
3.48-3.5810.9761.1522.7614445131713160.8871.20899.9
3.58-3.6910.9610.8343.5814238129912990.940.875100
3.69-3.8110.8450.5495.0113751126912680.9730.57699.9
3.81-3.9410.7580.4156.3913125122012200.980.436100
3.94-4.0910.6470.2798.5912691119211920.9910.293100
4.09-4.2610.5410.20111.4811837112511230.9940.21299.8
4.26-4.4510.3150.15314.0911419110711070.9960.161100
4.45-4.6710.0160.12117.8310607105910590.9960.128100
4.67-4.928.9550.09919.6588219899850.9960.10699.6
4.92-5.2210.3480.09821.3298729549540.9970.103100
5.22-5.5810.8480.08724.5195908848840.9980.091100
5.58-6.0210.6880.08127.1590538478470.9980.085100
6.02-6.610.3960.06330.9180577757750.9990.066100
6.6-7.3810.1120.04936.8772207147140.9990.052100
7.38-8.529.3950.04144.1558816266260.9990.044100
8.52-10.448.2820.03446.2944895475420.9990.03699.1
10.44-14.769.1720.03450.3739354304290.9990.03799.8
14.76-35.7277.4980.03745.3317922652390.9990.0490.2

-
Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018 BUILT=20180319data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180319data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2g38, 4l4w

2g38

4l4w


Resolution: 3.3→35.727 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1739 4.77 %
Rwork0.2476 --
obs0.2485 19335 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 330.77 Å2 / Biso mean: 190.6195 Å2 / Biso min: 80.02 Å2
Refinement stepCycle: final / Resolution: 3.3→35.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 0 0 3643
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023729
X-RAY DIFFRACTIONf_angle_d0.5035121
X-RAY DIFFRACTIONf_dihedral_angle_d7.7352176
X-RAY DIFFRACTIONf_chiral_restr0.037604
X-RAY DIFFRACTIONf_plane_restr0.004666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.3970.42731320.4028290999
3.397-3.50650.41491200.3546288799
3.5065-3.63170.36391370.32932904100
3.6317-3.7770.31461610.31832848100
3.777-3.94870.32131490.30682880100
3.9487-4.15660.28531290.2871291799
4.1566-4.41660.25871620.26232888100
4.4166-4.75680.27981560.24562869100
4.7568-5.23420.28221410.26222917100
5.2342-5.98850.26341290.28562889100
5.9885-7.53330.31221450.25032899100
7.5333-35.7270.21411780.1822875100

+
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