[English] 日本語
Yorodumi
- PDB-7bnt: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bnt
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with a predicted ancestral HMA domain of Pik-1 from Oryza spp.
Components
  • AVR-Pik protein
  • Predicted ancestral HMA domain of Pik-1 from Oryza spp.
KeywordsPROTEIN BINDING / RICE BLAST DISEASE / PLANT DISEASE RESISTANCE / EFFECTOR PROTEIN / INTEGRATED HMA DOMAIN
Function / homologyAVR-Pik protein
Function and homology information
Biological speciessynthetic construct (others)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å
AuthorsBialas, A. / Langner, T. / Harant, A. / Contreras, M.P. / Stevenson, C.E.M. / Lawson, D.M. / Sklenar, J. / Kellner, R. / Moscou, M.J. / Terauchi, R. ...Bialas, A. / Langner, T. / Harant, A. / Contreras, M.P. / Stevenson, C.E.M. / Lawson, D.M. / Sklenar, J. / Kellner, R. / Moscou, M.J. / Terauchi, R. / Banfield, M.J. / Kamoun, S.
Funding support Belgium, United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)743165 Belgium
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574/1 United Kingdom
CitationJournal: Elife / Year: 2021
Title: Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain.
Authors: Bialas, A. / Langner, T. / Harant, A. / Contreras, M.P. / Stevenson, C.E. / Lawson, D.M. / Sklenar, J. / Kellner, R. / Moscou, M.J. / Terauchi, R. / Banfield, M.J. / Kamoun, S.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Predicted ancestral HMA domain of Pik-1 from Oryza spp.
B: Predicted ancestral HMA domain of Pik-1 from Oryza spp.
C: AVR-Pik protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5735
Polymers26,4493
Non-polymers1242
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-1 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.486, 119.486, 35.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Predicted ancestral HMA domain of Pik-1 from Oryza spp.


Mass: 7799.269 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Predicted ancestral HMA domain corresponding to residues 186-258 of a Oryza spp. Pik-1 protein. The N-terminal residues GP are left over from affinity tag cleavage.
Source: (gene. exp.) synthetic construct (others) / Plasmid: pOPIN-M / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein / Fragment of Magnaporthe oryzae AVR-PikD


Mass: 10850.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 22-113 of Magnaporthe oryzae AVR-PikD. The N-terminal residues GP are left over from affinity tag cleavage.
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Plasmid: pOPIN-S3C / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: C4B8B8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL / PH range: NULL / Temp details: NULL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.32→59.81 Å / Num. obs: 59464 / % possible obs: 96.3 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.018 / Rrim(I) all: 0.07 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.32-1.3413.92.20128620.730.6052.28594.1
7.23-59.8112.30.0524620.9980.0150.05599.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data reduction
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5A6W

5a6w


Resolution: 1.32→59.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.783 / SU ML: 0.032 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1839 2981 5 %RANDOM
Rwork0.1452 ---
obs0.1472 56338 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.95 Å2 / Biso mean: 21.866 Å2 / Biso min: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.26 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.32→59.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 12 258 2007
Biso mean--36.82 35.45 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131827
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171837
X-RAY DIFFRACTIONr_angle_refined_deg1.591.6322461
X-RAY DIFFRACTIONr_angle_other_deg1.4671.5984247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.6332275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_rigid_bond_restr2.28933664
LS refinement shellResolution: 1.32→1.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 215 -
Rwork0.271 4033 -
all-4248 -
obs--94.46 %

+
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