[English] 日本語
Yorodumi
- PDB-7mk3: Crystal structure of NPR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mk3
TitleCrystal structure of NPR1
ComponentsRegulatory protein NPR1
KeywordsPLANT PROTEIN / IMMUNE SYSTEM / NPR1 / SAR / plant immunity
Function / homology
Function and homology information


response to herbivore / regulation of salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / negative regulation of defense response / response to insect / regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / extracellular ATP signaling / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway ...response to herbivore / regulation of salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / negative regulation of defense response / response to insect / regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / extracellular ATP signaling / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / defense response to fungus / response to bacterium / response to wounding / RNA polymerase II transcription regulator complex / response to heat / response to hypoxia / protein ubiquitination / positive regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
NPR1/NIM1-like, C-terminal / Regulatory protein NPR, central domain / Regulatory protein NPR / Domain of unknown function (DUF3420) / NPR1/NIM1 like defence protein C terminal / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily ...NPR1/NIM1-like, C-terminal / Regulatory protein NPR, central domain / Regulatory protein NPR / Domain of unknown function (DUF3420) / NPR1/NIM1 like defence protein C terminal / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Regulatory protein NPR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsCheng, J. / Wu, Q. / Zhou, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)115355 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118036 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118036 United States
CitationJournal: Nature / Year: 2022
Title: Structural basis of NPR1 in activating plant immunity.
Authors: Shivesh Kumar / Raul Zavaliev / Qinglin Wu / Ye Zhou / Jie Cheng / Lucas Dillard / Jordan Powers / John Withers / Jinshi Zhao / Ziqiang Guan / Mario J Borgnia / Alberto Bartesaghi / Xinnian Dong / Pei Zhou /
Abstract: NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid. Despite the important role of NPR1 in plant immunity, understanding of its regulatory ...NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid. Despite the important role of NPR1 in plant immunity, understanding of its regulatory mechanisms has been hindered by a lack of structural information. Here we report cryo-electron microscopy and crystal structures of Arabidopsis NPR1 and its complex with the transcription factor TGA3. Cryo-electron microscopy analysis reveals that NPR1 is a bird-shaped homodimer comprising a central Broad-complex, Tramtrack and Bric-à-brac (BTB) domain, a BTB and carboxyterminal Kelch helix bundle, four ankyrin repeats and a disordered salicylic-acid-binding domain. Crystal structure analysis reveals a unique zinc-finger motif in BTB for interacting with ankyrin repeats and mediating NPR1 oligomerization. We found that, after stimulation, salicylic-acid-induced folding and docking of the salicylic-acid-binding domain onto ankyrin repeats is required for the transcriptional cofactor activity of NPR1, providing a structural explanation for a direct role of salicylic acid in regulating NPR1-dependent gene expression. Moreover, our structure of the TGA3-NPR1-TGA3 complex, DNA-binding assay and genetic data show that dimeric NPR1 activates transcription by bridging two fatty-acid-bound TGA3 dimers to form an enhanceosome. The stepwise assembly of the NPR1-TGA complex suggests possible hetero-oligomeric complex formation with other transcription factors, revealing how NPR1 reprograms the defence transcriptome.
History
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 22, 2022Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.5Oct 18, 2023Group: 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: Regulatory protein NPR1
B: Regulatory protein NPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,78319
Polymers86,5542
Non-polymers1,22917
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.980, 78.980, 395.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Regulatory protein NPR1 / BTB/POZ domain-containing protein NPR1 / Non-inducible immunity protein 1 / Nim1 / Nonexpresser of ...BTB/POZ domain-containing protein NPR1 / Non-inducible immunity protein 1 / Nim1 / Nonexpresser of PR genes 1 / Salicylic acid insensitive 1 / Sai1


Mass: 43277.023 Da / Num. of mol.: 2 / Fragment: UNP residues 39-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NPR1, NIM1, SAI1, At1g64280, F15H21.6 / Production host: Escherichia coli (E. coli) / References: UniProt: P93002
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 60 mM HEPES, pH 7.5, 9.5% PEG3350, 0.125 M tri-sodium citrate, 75 mM sodium chloride, 0.5 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.06→49.47 Å / Num. obs: 24848 / % possible obs: 99.84 % / Redundancy: 42.7 % / Biso Wilson estimate: 113.82 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 21.56
Reflection shellResolution: 3.06→3.17 Å / Num. unique obs: 2429 / CC1/2: 0.83

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSBuilt=20200417data reduction
XSCALEBuilt=20200417data scaling
PHASERdev_3922phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MK2

7mk2


Resolution: 3.06→49.42 Å / SU ML: 0.5425 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 1241 5 %
Rwork0.2441 23585 -
obs0.2454 24826 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.25 Å2
Refinement stepCycle: LAST / Resolution: 3.06→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 67 0 5534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165607
X-RAY DIFFRACTIONf_angle_d0.43847592
X-RAY DIFFRACTIONf_chiral_restr0.0364919
X-RAY DIFFRACTIONf_plane_restr0.004971
X-RAY DIFFRACTIONf_dihedral_angle_d3.657790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.180.45211350.41132564X-RAY DIFFRACTION99.96
3.18-3.330.35781350.34742548X-RAY DIFFRACTION99.89
3.33-3.50.29381350.29252557X-RAY DIFFRACTION100
3.5-3.720.32741350.28622570X-RAY DIFFRACTION99.96
3.72-4.010.31511370.27762593X-RAY DIFFRACTION99.96
4.01-4.410.29511370.22862606X-RAY DIFFRACTION99.96
4.41-5.050.24441380.22692609X-RAY DIFFRACTION99.57
5.05-6.360.29391390.27422663X-RAY DIFFRACTION99.82
6.36-49.420.21861500.20072875X-RAY DIFFRACTION99.87
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)
11.46746348616-0.208791830339-1.541575967990.7258956101981.292704879755.313169862970.0469143318679-0.0598055089287-0.046234411162-0.146168002140.0909563872951-0.192710160519-0.3360790376330.171425318131-0.1814138815490.854587941868-0.0902214018568-0.06519244052210.6547121272580.02989458532030.80569248734423.588389586178.8329606488118.727853128
23.7086323495-2.13808214052-0.8362276419145.734879554242.427399683874.80961913863-0.2646277949970.02719115918460.02416903521991.094624280660.1832125228510.07472806452270.22177335966-0.1504263696250.05906037421941.00052920576-0.0117552738816-0.09431877532030.6392126159660.06743107705820.97311778951424.477045097179.2781063263148.976752708
30.7259992873470.134471238794-1.127975798822.149616502321.248018353415.96579679420.110653607954-0.042067976541-0.039465273391-0.114911214020.185533585021-0.0485126969319-0.1941114626730.451911362851-0.281298212580.577581517705-0.0757045410384-0.03001202240010.8097667017710.08955202133990.76962286076935.389190356966.262913585478.8081578247
44.28898091503-1.61632069216-2.061942132294.162693483710.9511994815114.059109730860.2754066012380.457977699987-0.247974356862-0.0287841349294-0.3145259838550.1651345840470.104196687438-0.1445947988890.02044682741620.59278842535-0.0424283513525-0.08292366460650.985192957405-0.01659996973060.94396025613935.595691906265.636630541248.675071206
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 39 through 256 )AA39 - 2561 - 213
22chain 'A' and (resid 257 through 404 )AA257 - 404214 - 361
33chain 'B' and (resid 39 through 255 )BC39 - 2551 - 215
44chain 'B' and (resid 256 through 405 )BC256 - 405216 - 365

+
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