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- PDB-7tae: Crystal Structure of the NPR1-Interacting Domain of TGA3 -

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Basic information

Entry
Database: PDB / ID: 7tae
TitleCrystal Structure of the NPR1-Interacting Domain of TGA3
ComponentsTranscription factor TGA3
KeywordsDNA BINDING PROTEIN / TGA3 / NPR1-interacting domain / plant immunity / transcription factor
Function / homology
Function and homology information


systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / calmodulin binding / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / DNA-templated transcription / nucleus
Similarity search - Function
Transcription factor TGA like domain / Seed dormancy control / DOG1 domain profile. / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
PALMITIC ACID / Transcription factor TGA3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCheng, J. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor TGA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6794
Polymers28,2391
Non-polymers4413
Water3,081171
1
A: Transcription factor TGA3
hetero molecules

A: Transcription factor TGA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3598
Polymers56,4782
Non-polymers8816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5040 Å2
ΔGint-25 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.390, 101.740, 83.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

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Components

#1: Protein Transcription factor TGA3 / bZIP transcription factor 22 / AtbZIP22


Mass: 28238.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TGA3, BZIP22, At1g22070, F2E2.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39234
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM HEPES (pH 8.0), 75 mM NaCl, 0.5 mM TCEP. 0.05 M sodium acetate pH 5.0, 10% (v/v) MPD 5 mg/mL protein

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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 EIGER2 X 16M / Detector: PIXEL / Date: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→47.02 Å / Num. obs: 47111 / % possible obs: 99.83 % / Redundancy: 13.2 % / Biso Wilson estimate: 26.1 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04796 / Rpim(I) all: 0.01372 / Rrim(I) all: 0.04993 / Net I/σ(I): 25.51
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 4631 / CC1/2: 0.947 / CC star: 0.986

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TAD
Resolution: 1.5→47.02 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 2355 5 %
Rwork0.1886 44718 -
obs0.1897 47073 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.72 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 30 171 1830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581824
X-RAY DIFFRACTIONf_angle_d0.90322485
X-RAY DIFFRACTIONf_chiral_restr0.0619268
X-RAY DIFFRACTIONf_plane_restr0.0062332
X-RAY DIFFRACTIONf_dihedral_angle_d7.9722269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.36681350.30712581X-RAY DIFFRACTION99.12
1.53-1.560.34151360.2852579X-RAY DIFFRACTION99.63
1.56-1.60.27391360.24842592X-RAY DIFFRACTION99.71
1.6-1.640.2711370.23282606X-RAY DIFFRACTION99.82
1.64-1.680.24781370.23712596X-RAY DIFFRACTION99.78
1.68-1.730.24221370.24162607X-RAY DIFFRACTION99.85
1.73-1.790.31711390.2712637X-RAY DIFFRACTION100
1.79-1.850.32241380.27972608X-RAY DIFFRACTION99.89
1.85-1.930.27461370.23822616X-RAY DIFFRACTION99.96
1.93-2.020.23131380.19262604X-RAY DIFFRACTION100
2.02-2.120.23791390.19042654X-RAY DIFFRACTION100
2.12-2.260.20171380.18892620X-RAY DIFFRACTION99.86
2.26-2.430.19921390.17862625X-RAY DIFFRACTION99.89
2.43-2.670.18781400.18022658X-RAY DIFFRACTION100
2.67-3.060.21981400.1822664X-RAY DIFFRACTION100
3.06-3.860.17321410.15922687X-RAY DIFFRACTION100
3.86-47.020.19531480.18012784X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.97682498905-5.51798689694-2.818002484026.028254056184.393392473474.5760502775-0.0178328975119-0.09826182020290.1042940797240.161631588666-0.1182476180370.2462504171290.186945829674-0.3695830063770.08323026449120.179002788175-0.0807495370715-0.04250976663570.2867163762420.01946762632270.125461986979-32.6953789967-16.7613465364-12.8374483949
21.91134158623-0.52237421063-0.0261295215238.255884015715.204564447025.285677348570.06662686587620.110355632284-0.0735539883673-0.174952870601-0.2151873196560.2981989186790.0343461574266-0.06761259248690.2180863506180.143363590739-0.00449509130467-0.02109437630090.2135192385730.03430076472590.186547501077-27.4555159615-16.8802160382-20.9615649111
30.6831220766480.6394574043050.01698472043931.180827077780.118588427331.531393110840.0824871473409-0.163469742020.1073004517230.192917708710.0999786824793-0.212098185845-0.003852102841070.193248474108-0.1746250949520.2617574267750.00191988903665-0.03625983519040.264244163051-0.02084131143360.206056021459-17.9211202567-12.1712075379-8.70683174461
41.70178350663-1.88117424812-1.922897869084.407908812744.962544996085.482885332050.0771177695904-0.1625548446280.356164043926-0.1151832146330.917170927792-1.61622451006-0.3070161240.740569090112-1.027334620190.20108326378-0.05591741687320.01685780113150.376729321787-0.1231460010880.474614253435-8.06827805768-2.93840853933-12.7875527065
59.26484562595-2.11180652782.044084688111.8573914442-2.151380894312.583338970230.0150322916326-0.5145625319440.7195281955280.596528631017-0.110113306054-0.700961299737-0.6519045202390.1126187403860.9794322743330.582103474862-0.07094026290410.08187535996310.3804900169-0.06697943204190.435201490721-23.340926626727.5547581096-8.93119511139
60.738528128771-1.51816499976-0.2976806816432.851591675912.612694583491.135001238320.1041694448240.05299895522910.0328112958442-0.593796011030.023343270478-0.177437150457-0.3151253960180.0459995586841-0.1544483272330.256837757389-0.02124352447830.03738343714380.2083731890740.02562717296590.193658805038-18.2808696021-0.933171732609-18.2750455115
73.41296639065-2.75941254308-3.3506333645.224461162795.406273440814.12438476478-0.270706900971-0.308902695851-0.1188318768360.7168397108440.1506159616740.1592784928221.027468710.2270511521880.1150402097320.2561739125790.0173216793699-0.02167463398610.187272779310.02264240700410.17654041767-22.6535717544-21.9028341506-8.47807676486
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 166 through 193 )166 - 1931 - 28
22chain 'A' and (resid 194 through 225 )194 - 22529 - 60
33chain 'A' and (resid 226 through 266 )226 - 26661 - 101
44chain 'A' and (resid 267 through 304 )267 - 304102 - 139
55chain 'A' and (resid 305 through 315 )305 - 315140 - 144
66chain 'A' and (resid 316 through 349 )316 - 349145 - 178
77chain 'A' and (resid 350 through 377 )350 - 377179 - 206

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