[English] 日本語
Yorodumi
- PDB-9rsv: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rsv
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-Pia with the HMA domain of OsHPP09 from rice (Oryza sativa)
Components
  • AVR-Pia protein
  • Os03g0111400 protein
KeywordsPLANT PROTEIN / Effector / HMA
Function / homology: / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / metal ion binding / Os03g0111400 protein / AVR-Pia protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMaidment, J.H.R. / Bocquet, A. / Gelin, M. / De Guillen, K. / Cesari, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2019-STG-852482-ii-MAXEuropean Union
CitationJournal: Biorxiv / Year: 2025
Title: The Magnaporthe oryzae MAX effector AVR-Pia binds a novel group of rice HMA domain-containing proteins
Authors: Maidment, J.H. / Saile, S.C. / Bocquet, A. / Thivolle, C. / Bourcet, L. / Planel, L.F. / Gelin, M. / Kroj, T. / Padilla, A. / de Guillen, K. / Cesari, S.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Os03g0111400 protein
B: AVR-Pia protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0624
Polymers15,8692
Non-polymers1922
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-15 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.665, 93.665, 72.873
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

21B-218-

HOH

31B-257-

HOH

-
Components

#1: Protein Os03g0111400 protein / cDNA / clone: J100050C22 / full insert sequence


Mass: 8080.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HMA domain / Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: Os03g0111400, OSNPB_030111400 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3ADD6
#2: Protein AVR-Pia protein


Mass: 7788.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: No signal peptide. / Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: AVR-Pia / Production host: Escherichia coli (E. coli) / References: UniProt: B9WZW9
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.911 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulphate, 20% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.65→46.83 Å / Num. obs: 23168 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.025 / Rrim(I) all: 0.044 / Net I/σ(I): 19.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1125 / CC1/2: 0.837 / Rpim(I) all: 0.592 / Rrim(I) all: 1.059 / % possible all: 100

-
Processing

Software
NameVersionClassification
EDNAdata collection
XDSdata reduction
PHASER2.8.3phasing
Aimless0.7.13data scaling
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.906 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2021 1151 4.974 %
Rwork0.176 21988 -
all0.177 --
obs-23139 99.673 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.032 Å2
Baniso -1Baniso -2Baniso -3
1-0.799 Å20.399 Å2-0 Å2
2--0.799 Å20 Å2
3----2.591 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 10 191 1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121076
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161072
X-RAY DIFFRACTIONr_angle_refined_deg2.2431.8311456
X-RAY DIFFRACTIONr_angle_other_deg0.7681.7882476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.70655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01710200
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.4221041
X-RAY DIFFRACTIONr_chiral_restr0.1180.2174
X-RAY DIFFRACTIONr_chiral_restr_other0.0040.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02210
X-RAY DIFFRACTIONr_nbd_refined0.2320.2173
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.2964
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2532
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.2624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.221
X-RAY DIFFRACTIONr_nbd_other0.3470.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.230
X-RAY DIFFRACTIONr_mcbond_it3.543.043542
X-RAY DIFFRACTIONr_mcbond_other3.5383.043542
X-RAY DIFFRACTIONr_mcangle_it4.8715.421674
X-RAY DIFFRACTIONr_mcangle_other4.8685.42675
X-RAY DIFFRACTIONr_scbond_it6.0013.707534
X-RAY DIFFRACTIONr_scbond_other5.9933.711526
X-RAY DIFFRACTIONr_scangle_it8.6836.425782
X-RAY DIFFRACTIONr_scangle_other8.6646.432771
X-RAY DIFFRACTIONr_lrange_it10.85433.3821233
X-RAY DIFFRACTIONr_lrange_other10.8130.961169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.304780.2911601X-RAY DIFFRACTION100
1.693-1.7390.271800.2731548X-RAY DIFFRACTION100
1.739-1.790.234940.2351489X-RAY DIFFRACTION99.8108
1.79-1.8440.213700.2311485X-RAY DIFFRACTION99.9357
1.844-1.9050.246690.2011427X-RAY DIFFRACTION100
1.905-1.9720.195740.1871384X-RAY DIFFRACTION99.7947
1.972-2.0460.228600.1731352X-RAY DIFFRACTION99.8586
2.046-2.1290.177820.1681270X-RAY DIFFRACTION99.5582
2.129-2.2240.171610.1761249X-RAY DIFFRACTION99.7715
2.224-2.3320.234580.1681181X-RAY DIFFRACTION99.4382
2.332-2.4580.176520.1691141X-RAY DIFFRACTION99.7492
2.458-2.6060.251570.1741080X-RAY DIFFRACTION99.8244
2.606-2.7860.214480.1851022X-RAY DIFFRACTION100
2.786-3.0080.208540.175944X-RAY DIFFRACTION99.3035
3.008-3.2940.239550.181874X-RAY DIFFRACTION98.935
3.294-3.680.148460.172798X-RAY DIFFRACTION99.2941
3.68-4.2450.203310.152733X-RAY DIFFRACTION100
4.245-5.1890.186350.135609X-RAY DIFFRACTION98.6217
5.189-7.2940.198250.178494X-RAY DIFFRACTION98.482
7.294-46.830.176220.191307X-RAY DIFFRACTION98.7988

+
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