[English] 日本語
Yorodumi
- PDB-7b1i: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b1i
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with the HMA domain of OsHIPP19 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • OSIGBa0128P10.9 protein
KeywordsPLANT PROTEIN / complex / effector / HMA domain / rice / rice blast fungus
Function / homologyHeavy metal-associated isoprenylated plant protein 47 / : / AVR-Pik-like, HMA interaction domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / metal ion binding / Avr-Pik / AVR-Pik protein / OSIGBa0128P10.9 protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaidment, J.H.R. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Multiple variants of the fungal effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19, providing a foundation to engineer plant defense.
Authors: Maidment, J.H.R. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Jantasuriyarat, C. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2020
Title: Multiple variants of the blast fungus effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19 with high affinity
Authors: Maidment, J.H.R. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Jantasuriyarat, C. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
History
DepositionNov 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: OSIGBa0128P10.9 protein
C: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)19,1942
Polymers19,1942
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-0 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.783, 53.782, 98.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein OSIGBa0128P10.9 protein / OsHIPP19 protein / OSIGBa0150F01.4 protein


Mass: 8337.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OSIGBa0150F01.4, OSIGBa0128P10.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01IL6
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein


Mass: 10856.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B8, UniProt: A0A219T3Y8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12M Alcohols [0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol], 0.1M Buffer System 3 pH 8.5 [1M Tris (base); BICINE], ...Details: 0.12M Alcohols [0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol], 0.1M Buffer System 3 pH 8.5 [1M Tris (base); BICINE], 50% v/v Precipitant Mix 1 [40% v/v PEG 500* MME; 20% w/v PEG 20000]

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→98.03 Å / Num. obs: 13077 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Net I/σ(I): 12.4 / Num. measured all: 165357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9411.11.12989688110.910.3521.1841.9100
9.11-98.039.60.04715401600.9990.0150.04935.999.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 1.9→98.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.897 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 664 5.1 %RANDOM
Rwork0.1956 ---
obs0.1975 12365 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.19 Å2 / Biso mean: 37.001 Å2 / Biso min: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2---0.23 Å20 Å2
3---3.84 Å2
Refinement stepCycle: final / Resolution: 1.9→98.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 67 1275
Biso mean---37.47 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191256
X-RAY DIFFRACTIONr_bond_other_d0.0020.021189
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9541696
X-RAY DIFFRACTIONr_angle_other_deg0.95632774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45624.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08615229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.728157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 45 -
Rwork0.275 889 -
all-934 -
obs--100 %
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)
14.26572.3048-1.16486.6342-2.28174.2026-0.08380.30470.3013-0.7010.23720.0232-0.59470.1001-0.15340.3542-0.04490.01070.13920.0090.039444.91810.459107.066
26.09070.26321.61154.78061.47382.04190.0856-0.1673-0.31330.0390.01140.0234-0.0754-0.0004-0.0970.0634-0.00490.00310.00610.00860.019141.2840.129121.548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 76
2X-RAY DIFFRACTION2C33 - 113

+
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