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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qzd
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa)
Components
  • Avr-Pik
  • Resistance protein Pikp-1
KeywordsANTIFUNGAL PROTEIN / Plant immunity / pathogen effector / protein engineering / blast disease
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / 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
Avr-Pik / Resistance protein Pikp-1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaidment, J.H.R. / Franceschetti, M. / Longya, A. / Banfield, M.J.
Funding support Japan, 9items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 Japan
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 Japan
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9795 Japan
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M02198X Japan
European Research Council (ERC)743165 Japan
The Thailand Research Fund (TRF)PHD/0152/2556 Japan
John Innes Foundation Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 15H05779 Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 20H00421 Japan
Citation
Journal: Elife / Year: 2023
Title: Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor.
Authors: Maidment, J.H.R. / Shimizu, M. / Bentham, A.R. / Vera, S. / Franceschetti, M. / Longya, A. / Stevenson, C.E.M. / De la Concepcion, J.C. / Bialas, A. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2022
Title: Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor
Authors: Maidment, J. / Shimizu, M. / Vera, S. / Franceschetti, M. / Longya, A. / Stevenson, C. / De la Concepcion, J. / Bialas, A. / Kamoun, S. / Terauchi, R. / Banfield, M.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
C: Avr-Pik
E: Resistance protein Pikp-1
F: Resistance protein Pikp-1
G: Avr-Pik


Theoretical massNumber of molelcules
Total (without water)55,3906
Polymers55,3906
Non-polymers00
Water1,964109
1
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
C: Avr-Pik


Theoretical massNumber of molelcules
Total (without water)27,6953
Polymers27,6953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-5 kcal/mol
Surface area11610 Å2
2
E: Resistance protein Pikp-1
F: Resistance protein Pikp-1
G: Avr-Pik


Theoretical massNumber of molelcules
Total (without water)27,6953
Polymers27,6953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-6 kcal/mol
Surface area11380 Å2
Unit cell
Length a, b, c (Å)67.381, 80.782, 103.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Resistance protein Pikp-1


Mass: 8430.855 Da / Num. of mol.: 4 / Mutation: S258E, N261K, K262E
Source method: isolated from a genetically manipulated source
Details: expressed protein corresponds to residues 186-263 of wild type sequence. N-terminal GP is a scar from the cleaved expression tag
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Pikp-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9KPB5
#2: Protein Avr-Pik / Avr-Pik protein


Mass: 10833.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: expressed protein corresponds to residues 22-113 of wild type sequence. N-terminal M was added.
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A219T3Y8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→103.8 Å / Num. obs: 28553 / % possible obs: 97.4 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.038 / Rrim(I) all: 0.105 / Net I/σ(I): 11.5 / Num. measured all: 195704 / Scaling rejects: 28
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
2.2-2.276.70.7511687025120.8440.3020.8142.299
9.07-103.860.03527454570.9990.0150.03932.593.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 2.2→63.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2758 / WRfactor Rwork: 0.2169 / FOM work R set: 0.731 / SU B: 17.721 / SU ML: 0.214 / SU R Cruickshank DPI: 0.2819 / SU Rfree: 0.2367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 1437 5 %RANDOM
Rwork0.2313 ---
obs0.234 27072 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.56 Å2 / Biso mean: 42.021 Å2 / Biso min: 19.77 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å2-0 Å2
2--3.51 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 2.2→63.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 0 109 3635
Biso mean---36.71 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133575
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163608
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.634807
X-RAY DIFFRACTIONr_angle_other_deg1.1921.68321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1765449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69323.373166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38815680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8461520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 115 -
Rwork0.363 2013 -
all-2128 -
obs--98.61 %
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)
16.1495-1.2535-2.00195.2342-1.67315.77120.052-0.02450.6615-0.0962-0.006-0.4332-0.49410.4071-0.0460.1142-0.03860.0470.08070.010.2531-5.136311.7525-7.9365
23.40331.70030.06244.44130.76824.29340.0126-0.17990.3344-0.03880.19230.4207-0.4187-0.4626-0.20490.0640.03810.03620.10410.01770.1107-20.51346.26511.5914
35.29060.56860.51972.53540.06322.04150.1554-0.0899-0.1282-0.1132-0.1064-0.11410.1938-0.0328-0.0490.03150.01080.00020.03250.01160.0088-25.965-10.3748-2.3826
43.89512.57321.29475.0828-1.50116.81220.26110.1102-0.35660.1424-0.0158-0.52540.55050.2757-0.24530.10510.0186-0.08760.14730.00790.2171-38.2956-12.839124.2548
53.7566-1.50991.05134.04232.13292.91550.0617-0.1339-0.25320.24950.03920.26330.1257-0.2512-0.10090.03720.00850.03250.20760.01410.0651-54.1909-7.96814.6831
64.831-0.33830.39631.5725-0.3953.40080.0228-0.20870.420.1665-0.03760.0132-0.3893-0.02830.01480.11060.00790.02160.0519-0.03690.0522-59.67798.76318.3762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 259
2X-RAY DIFFRACTION2B187 - 263
3X-RAY DIFFRACTION3C32 - 113
4X-RAY DIFFRACTION4E188 - 259
5X-RAY DIFFRACTION5F187 - 262
6X-RAY DIFFRACTION6G32 - 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