[English] 日本語
Yorodumi
- PDB-7a8x: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a8x
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with the HMA domain of Pikh-1 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • NBS-LRR class disease resistance protein
KeywordsANTIFUNGAL PROTEIN / Fungal effector / HMA domain / NLR protein / MAX effector
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA ...: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / : / Leucine-rich repeat region / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NBS-LRR class disease resistance protein / AVR-Pik-like HMA interaction domain-containing protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaidment, J.H.R. / Xiao, G. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M02198X United Kingdom
European Research Council (ERC)743165 United Kingdom
John Innes Foundation United Kingdom
Citation
Journal: Plos Pathog. / Year: 2021
Title: The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface.
Authors: De la Concepcion, J.C. / Maidment, J.H.R. / Longya, A. / Xiao, G. / Franceschetti, M. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2020
Title: The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface
Authors: De la Concepcion, J.C. / Maidment, J.H.R. / Longya, A. / Xiao, G. / Franceschetti, M. / Banfield, M.J.
History
DepositionAug 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
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 / citation / 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 / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NBS-LRR class disease resistance protein
B: NBS-LRR class disease resistance protein
C: AVR-Pik protein
D: NBS-LRR class disease resistance protein
E: NBS-LRR class disease resistance protein
F: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)54,6336
Polymers54,6336
Non-polymers00
Water2,090116
1
A: NBS-LRR class disease resistance protein
B: NBS-LRR class disease resistance protein
C: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)27,3173
Polymers27,3173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-11 kcal/mol
Surface area11340 Å2
MethodPISA
2
D: NBS-LRR class disease resistance protein
E: NBS-LRR class disease resistance protein
F: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)27,3173
Polymers27,3173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-12 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.351, 83.121, 107.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
NBS-LRR class disease resistance protein / NBS-LRR class disease resistance protein Pikh-1


Mass: 8234.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pi-km1, Pikh-1 / Production host: Escherichia coli (E. coli) / References: UniProt: D5L9G5
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein


Mass: 10847.306 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus)
Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_15972 / Production host: Escherichia coli (E. coli) / References: UniProt: G4MXW3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 1 (1 M Imidazole; MES monohydrate ...Details: 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 1 (1 M Imidazole; MES monohydrate (acid)) pH 6.5; 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→107.84 Å / Num. obs: 25847 / % possible obs: 96.4 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.38120.9272.525700.8640.2780.968100
8.91-107.8410.70.01887.154310.0060.01999.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata processing
Aimless0.7.4data scaling
PHASER2.8.3phasing
Aimless0.7.4data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A8W

7a8w


Resolution: 2.3→65.922 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.014 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2559 1288 4.994 %
Rwork0.2101 24505 -
all0.212 --
obs-25793 96.343 %
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: 58.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.996 Å2-0 Å20 Å2
2---0.909 Å20 Å2
3---1.905 Å2
Refinement stepCycle: LAST / Resolution: 2.3→65.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 0 116 3575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173570
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133515
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.6294725
X-RAY DIFFRACTIONr_angle_other_deg1.181.68239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8075446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7622.922154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56215670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1411520
X-RAY DIFFRACTIONr_chiral_restr0.0590.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
X-RAY DIFFRACTIONr_nbd_refined0.1980.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.23045
X-RAY DIFFRACTIONr_nbtor_refined0.150.21641
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.212
X-RAY DIFFRACTIONr_nbd_other0.1930.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.25
X-RAY DIFFRACTIONr_mcbond_it1.8254.2611805
X-RAY DIFFRACTIONr_mcbond_other1.8254.261804
X-RAY DIFFRACTIONr_mcangle_it2.7026.3762241
X-RAY DIFFRACTIONr_mcangle_other2.7026.3772242
X-RAY DIFFRACTIONr_scbond_it2.0234.4841710
X-RAY DIFFRACTIONr_scbond_other2.0184.4841710
X-RAY DIFFRACTIONr_scangle_it3.1186.6222483
X-RAY DIFFRACTIONr_scangle_other3.1156.6222483
X-RAY DIFFRACTIONr_lrange_it4.62448.3093580
X-RAY DIFFRACTIONr_lrange_other4.60148.1823566
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection% reflection
Rfree0.311 89 -
Rwork0.266 1861 -
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)
15.141-1.79960.65596.67910.51514.86310.2072-0.2003-0.3773-0.03220.00030.60170.4389-0.1781-0.20750.11690.0139-0.10050.2443-0.00830.1414.4025-12.7317-23.6864
26.2734-1.00250.90123.9794-0.66024.07460.07150.17670.1575-0.1424-0.0162-0.15530.06150.0443-0.05530.0251-0.0040.0080.03010.01230.01520.3948-8.3142-14.2066
36.9531-0.28911.7642.41570.62221.7008-0.18740.4960.9339-0.3345-0.00490.1492-0.40560.01290.19230.2471-0.0048-0.0380.07420.10830.281425.94388.1959-16.8355
46.2088-0.4923-1.02736.0420.1285.13410.07060.30790.2059-0.15850.07790.5004-0.3092-0.4588-0.14850.07210.00040.06490.0772-0.02620.1791-27.307111.119310.7413
54.8929-0.49350.0384.50630.89565.69030.06810.0490.3392-0.03450.0215-0.2504-0.28820.3866-0.08960.0428-0.01170.05320.0290.01090.1079-11.92025.660.8292
63.5919-0.2656-0.35452.4763-0.1662.32280.1842-0.1161-0.01030.1155-0.15090.05540.08010.0886-0.03330.0328-0.0110.01270.0159-0.00380.0138-6.8221-10.82263.7802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA188 - 259
2X-RAY DIFFRACTION2ALLB186 - 262
3X-RAY DIFFRACTION3ALLC33 - 112
4X-RAY DIFFRACTION4ALLD187 - 259
5X-RAY DIFFRACTION5ALLE186 - 262
6X-RAY DIFFRACTION6ALLF32 - 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