[English] 日本語
Yorodumi
- PDB-5tec: Crystal structure of the TIR domain from the Arabidopsis thaliana... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tec
TitleCrystal structure of the TIR domain from the Arabidopsis thaliana NLR protein SNC1
ComponentsProtein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
KeywordsIMMUNE SYSTEM / TIR domain / plant NLR
Function / homology
Function and homology information


systemic acquired resistance, salicylic acid mediated signaling pathway / response to auxin / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / ADP binding / defense response to bacterium / intracellular membrane-bounded organelle / nucleotide binding / endoplasmic reticulum ...systemic acquired resistance, salicylic acid mediated signaling pathway / response to auxin / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / ADP binding / defense response to bacterium / intracellular membrane-bounded organelle / nucleotide binding / endoplasmic reticulum / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain ...Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, X. / Bentham, A. / Ve, T. / Williams, S.J. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Multiple functional self-association interfaces in plant TIR domains.
Authors: Zhang, X. / Bernoux, M. / Bentham, A.R. / Newman, T.E. / Ve, T. / Casey, L.W. / Raaymakers, T.M. / Hu, J. / Croll, T.I. / Schreiber, K.J. / Staskawicz, B.J. / Anderson, P.A. / Sohn, K.H. / ...Authors: Zhang, X. / Bernoux, M. / Bentham, A.R. / Newman, T.E. / Ve, T. / Casey, L.W. / Raaymakers, T.M. / Hu, J. / Croll, T.I. / Schreiber, K.J. / Staskawicz, B.J. / Anderson, P.A. / Sohn, K.H. / Williams, S.J. / Dodds, P.N. / Kobe, B.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and preliminary X-ray diffraction analyses of the TIR domains of three TIR-NB-LRR proteins that are involved in disease resistance in Arabidopsis thaliana.
Authors: Wan, L. / Zhang, X. / Williams, S.J. / Ve, T. / Bernoux, M. / Sohn, K.H. / Jones, J.D. / Dodds, P.N. / Kobe, B.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
B: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)39,6932
Polymers39,6932
Non-polymers00
Water3,711206
1
A: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)19,8471
Polymers19,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)19,8471
Polymers19,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.175, 82.175, 124.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1 / AtSNC1 / Disease resistance RPP5-like protein


Mass: 19846.580 Da / Num. of mol.: 2 / Fragment: UNP residues 17-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SNC1, BAL, At4g16890, dl4475c, FCAALL.51 / Production host: Escherichia coli (E. coli) / References: UniProt: O23530
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.63 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18%(w/v) PEG 3350, 9%(w/v) glycerol, 0.1 M MMT buffer pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.68 Å / Num. obs: 22223 / % possible obs: 99.8 % / Redundancy: 16.7 % / Net I/σ(I): 17.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OZI

3ozi


Resolution: 2.2→19.678 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.95
RfactorNum. reflection% reflection
Rfree0.2168 1081 5.12 %
Rwork0.1782 --
obs0.1801 21119 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 0 206 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132481
X-RAY DIFFRACTIONf_angle_d1.2863336
X-RAY DIFFRACTIONf_dihedral_angle_d13.146918
X-RAY DIFFRACTIONf_chiral_restr0.057372
X-RAY DIFFRACTIONf_plane_restr0.008418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.30.35861070.25432235X-RAY DIFFRACTION86
2.3-2.42110.23361390.21232340X-RAY DIFFRACTION91
2.4211-2.57250.25111330.20122393X-RAY DIFFRACTION93
2.5725-2.77060.22541350.18682471X-RAY DIFFRACTION95
2.7706-3.04850.23171420.18422519X-RAY DIFFRACTION97
3.0485-3.48750.19831520.16692585X-RAY DIFFRACTION99
3.4875-4.38590.20451340.14832674X-RAY DIFFRACTION100
4.3859-19.6790.1941390.17952821X-RAY DIFFRACTION100
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)
15.3811-1.9573-1.54572.80881.21622.45070.13590.1287-0.0457-0.1414-0.07990.04660.117-0.0797-0.02580.3087-0.00270.00450.2942-0.01660.199232.6031-9.99-24.9164
23.6469-1.1173.06065.989-4.20886.8565-0.21820.6350.4229-1.0273-0.1777-0.9773-0.0969-0.25480.41650.457-0.0317-0.01260.5168-0.01230.475823.9991-11.0854-28.4172
33.0274-0.4218-0.35994.9212-0.7483.57610.09390.09810.29-0.0956-0.05590.0834-0.3037-0.1126-0.0550.28770.03990.01850.3027-0.0170.274526.492.8243-19.3178
44.6665-2.17971.76918.3986-3.34284.44410.0662-0.17850.45720.22570.07870.0934-0.5808-0.6002-0.02010.45880.09830.05120.3634-0.04920.349821.626410.1455-17.8727
52.7695-3.0191-1.57653.43310.95653.12780.4571-0.03050.20310.0628-0.2772-0.0509-0.07470.3468-0.34670.304-0.0260.0120.355-0.01270.236834.8442-6.0564-9.2812
62.20210.7371-0.69972.64871.13343.1889-0.4138-0.51280.1260.1070.1680.37310.2679-0.01940.09210.3815-0.0080.04770.29330.03580.324831.153-15.7653-13.9913
75.9026-0.8543-0.9354.3078-0.78972.4403-0.1022-0.5959-0.19360.0837-0.0473-0.18160.14830.58870.08980.33240.07380.04030.49490.05260.291151.3454-16.2902-18.1114
87.09952.38561.94652.3351.84743.2768-0.995-1.09030.74550.404-0.11370.10390.01811.04020.40230.58490.126-0.04720.78140.23450.689357.1785-23.3838-14.8933
93.93830.7158-0.91233.08760.90821.9110.2155-0.78970.01870.468-0.1772-0.76750.42381.78840.20040.38970.2047-0.11120.64480.00090.367560.7952-14.582-21.5004
103.6387-0.8617-0.69765.2266-0.07061.8723-0.0343-0.56440.16510.1261-0.0991-0.93830.02250.77580.04420.30920.04170.01040.55140.07050.4664.1484-13.1951-26.1929
115.33352.44614.8582.93632.98185.02330.1687-1.44981.6782-0.2708-0.0815-0.6981-1.02020.87450.35260.6602-0.17510.12111.0262-0.21670.892169.05470.5771-23.3624
123.5363-0.2594-0.38843.03730.40063.43780.09160.061-0.1482-0.2011-0.1195-0.45350.21920.48840.01240.31410.06140.03020.34660.01880.338255.9459-15.5481-29.9524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 150 )
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 166 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 108 )
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 126 )
12X-RAY DIFFRACTION12chain 'B' and (resid 127 through 166 )

+
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://pdbjlvh1.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