[English] 日本語
Yorodumi
- PDB-5zng: The crystal complex of immune receptor RGA5A_S of Pia from rice (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zng
TitleThe crystal complex of immune receptor RGA5A_S of Pia from rice (Oryzae sativa) with rice blast (Magnaporthe oryzae) effector protein AVR1-CO39
Components
  • AVR1-CO39
  • NBS-LRR type protein
KeywordsIMMUNE SYSTEM / RGA5A_S / resistance protein / rice AVR1-CO39 / effector protein / Magnaporthe oryzae
Function / homology
Function and homology information


innate immune response-activating signaling pathway / plant-type hypersensitive response / ADP binding / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / : ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / : / Leucine-rich repeat region / Alpha-Beta Plaits - #100 / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein RGA5 / Uncharacterized protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 Å
AuthorsGuo, L.W. / Zhang, Y.K. / Liu, Q. / Ma, M.Q. / Liu, J.F. / Peng, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China315711057 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces
Authors: Guo, L. / Cesari, S. / de Guillen, K. / Chalvon, V. / Mammri, L. / Ma, M. / Meusnier, I. / Bonnot, F. / Padilla, A. / Peng, Y.L. / Liu, J. / Kroj, T.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 20, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NBS-LRR type protein
C: AVR1-CO39


Theoretical massNumber of molelcules
Total (without water)24,0042
Polymers24,0042
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.721, 66.721, 108.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein NBS-LRR type protein


Mass: 14895.397 Da / Num. of mol.: 1 / Fragment: S domain
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os11gRGA5 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J0N2
#2: Protein AVR1-CO39


Mass: 9108.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8J180
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.1 M ammonium tartrate dibasic 0.1 M sodium acetate-HCl, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.108→39.47 Å / Num. obs: 215689 / % possible obs: 1 % / Redundancy: 13.1 % / Net I/σ(I): 10.11
Reflection shellResolution: 2.189→2.268 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MYV

2myv


Resolution: 2.189→28.405 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.57 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.1966 1262 4.7 %
Rwork0.1619 --
obs0.1635 26844 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.189→28.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 0 37 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081101
X-RAY DIFFRACTIONf_angle_d0.8861490
X-RAY DIFFRACTIONf_dihedral_angle_d10.265676
X-RAY DIFFRACTIONf_chiral_restr0.066177
X-RAY DIFFRACTIONf_plane_restr0.005190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1895-2.27710.2787820.26612417X-RAY DIFFRACTION81
2.2771-2.38070.26321630.22292675X-RAY DIFFRACTION91
2.3807-2.50610.25391580.22092847X-RAY DIFFRACTION98
2.5061-2.6630.29141340.2162973X-RAY DIFFRACTION100
2.663-2.86850.25361770.2072902X-RAY DIFFRACTION100
2.8685-3.15680.23291360.19062951X-RAY DIFFRACTION100
3.1568-3.61280.20621270.16882958X-RAY DIFFRACTION100
3.6128-4.54880.17541690.13212922X-RAY DIFFRACTION100
4.5488-28.40740.13361160.13072937X-RAY DIFFRACTION99
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)
11.4768-1.9491-1.61915.04323.34232.6436-0.6683-3.5838-0.80991.04491.1526-1.95231.1274-0.176-1.54350.80010.23090.06861.36630.35071.0526-10.918720.5728-14.6554
24.2429-1.45344.19567.7581-1.26587.6491-0.0298-1.46580.3199-0.236-0.1405-0.0405-0.1111-0.98150.1340.2929-0.06940.02750.7634-0.04590.4583-22.477329.4918-26.5139
38.5286-4.58853.11443.8146-3.04262.4834-0.1245-0.3444-0.0944-0.290.38740.70010.2306-0.7049-0.17780.3223-0.0209-0.03210.62850.02650.5569-31.089824.846-26.9763
45.9415-0.2918-0.72527.729-3.01438.7148-0.2781-0.6714-0.04850.42970.10790.0509-0.17720.48860.34090.26710.0410.04440.764-0.06460.425-24.771726.4537-19.0506
56.5499-2.07531.75043.2726-0.51435.6698-0.1723-0.8060.5750.02930.0178-0.0735-0.31670.61940.38010.3670.02050.02810.6384-0.05540.4831-22.082230.3241-23.4997
65.1781-2.51124.55326.3651-2.38633.97080.3102-0.3337-0.5962-0.8702-0.0072-0.2541.17330.1836-0.09120.50360.00030.0550.60430.0110.4926-21.188419.5114-29.7016
79.42133.77285.75879.66552.59593.7526-0.0061-1.26360.1091-0.1805-0.1012-0.1972-0.29660.4505-0.03340.2489-0.07190.01980.8423-0.0690.5228-15.584129.4454-25.4719
85.85981.0224-1.05712.8684-2.07017.6944-0.12970.50530.1196-0.259-0.11860.2220.01110.01420.14330.33240.00310.03970.7706-0.04730.4877-33.261127.4726-17.0053
95.6154-0.7711.38012.1265-1.55776.856-0.0082-0.21120.15620.6268-0.4786-1.1423-0.27470.57370.48230.30140.03850.00220.64840.0180.5511-32.254426.626-5.9338
105.5752-0.8923-1.16348.6848-0.20354.4434-0.33260.236-0.051-0.00790.18850.3077-0.0169-0.24110.14350.26280.06220.01220.6768-0.06570.4478-39.889428.0274-10.363
112.24431.02060.64120.49380.20020.48380.55612.1131-1.1773-1.04911.2274-1.26092.37880.2907-2.10921.1220.04110.15681.0454-0.37470.9554-35.171112.2692-18.8675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 991 through 996 )
2X-RAY DIFFRACTION2chain 'A' and (resid 997 through 1008 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1009 through 1021 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1022 through 1031 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1032 through 1046 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1047 through 1058 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1059 through 1069 )
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 42 )
9X-RAY DIFFRACTION9chain 'C' and (resid 43 through 57 )
10X-RAY DIFFRACTION10chain 'C' and (resid 58 through 78 )
11X-RAY DIFFRACTION11chain 'C' and (resid 79 through 83 )

+
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