[English] 日本語
Yorodumi
- PDB-4c6r: Crystal structure of the TIR domain from the Arabidopsis Thaliana... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c6r
TitleCrystal structure of the TIR domain from the Arabidopsis Thaliana disease resistance protein RPS4
ComponentsDISEASE RESISTANCE PROTEIN RPS4
KeywordsIMMUNE SYSTEM / PLANT TIR DOMAIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


plant-type hypersensitive response / innate immune response-activating signaling pathway / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / endomembrane system / ADP binding / defense response to bacterium / ATP binding / membrane ...plant-type hypersensitive response / innate immune response-activating signaling pathway / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / endomembrane system / ADP binding / defense response to bacterium / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein RPS4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWilliams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Ma, Y. / Segonzac, C. / Ve, T. / Sarris, P. / Ericsson, D.J. / Saucet, S.B. ...Williams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Ma, Y. / Segonzac, C. / Ve, T. / Sarris, P. / Ericsson, D.J. / Saucet, S.B. / Zhang, X. / Parker, J. / Dodds, P.N. / Jones, J.D.G. / Kobe, B.
CitationJournal: Science / Year: 2014
Title: Structural Basis for Assembly and Function of a Heterodimeric Plant Immune Receptor.
Authors: Williams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Sarris, P.F. / Segonzac, C. / Ve, T. / Ma, Y. / Saucet, S.B. / Ericsson, D.J. / Casey, L.W. / Lonhienne, T. / Winzor, D.J. / Zhang, X. / ...Authors: Williams, S.J. / Sohn, K.H. / Wan, L. / Bernoux, M. / Sarris, P.F. / Segonzac, C. / Ve, T. / Ma, Y. / Saucet, S.B. / Ericsson, D.J. / Casey, L.W. / Lonhienne, T. / Winzor, D.J. / Zhang, X. / Coerdt, A. / Parker, J.E. / Dodds, P.N. / Kobe, B. / Jones, J.D.G.
History
DepositionSep 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DISEASE RESISTANCE PROTEIN RPS4
B: DISEASE RESISTANCE PROTEIN RPS4
C: DISEASE RESISTANCE PROTEIN RPS4
D: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)78,4554
Polymers78,4554
Non-polymers00
Water6,179343
1
A: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DISEASE RESISTANCE PROTEIN RPS4


Theoretical massNumber of molelcules
Total (without water)19,6141
Polymers19,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.925, 78.637, 80.668
Angle α, β, γ (deg.)65.63, 78.64, 78.93
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9513, -0.2658, 0.1564), (-0.2736, -0.9614, 0.02998), (0.1424, -0.0713, -0.9872)6.722, 98.92, 34.12
2given(-0.9491, 0.2998, -0.09678), (0.2694, 0.613, -0.7427), (-0.1634, -0.7309, -0.6626)60.79, 36.53, 112.3
3given(-0.9995, -0.01386, -0.02914), (-0.01439, -0.6168, 0.787), (-0.02888, 0.787, 0.6162)66.02, 42.54, 56.9

-
Components

#1: Protein
DISEASE RESISTANCE PROTEIN RPS4 / / TIR-NBS-LRR CLASS DISEASE RESISTANCE PROTEIN


Mass: 19613.748 Da / Num. of mol.: 4
Fragment: TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN, RESIDUES 11-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9XGM3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.44 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6.5
Details: 23% (W/V) PEG 3350, 0.2 M AMMONIUM CITRATE (PH 6.5), 0.2 M SODIUM CHLORIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→19.6 Å / Num. obs: 43623 / % possible obs: 94 % / Observed criterion σ(I): 5.9 / Redundancy: 3.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9 / % possible all: 75.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OZI

3ozi


Resolution: 2.05→19.598 Å / SU ML: 0.25 / σ(F): 1.98 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1879 4.3 %
Rwork0.1864 --
obs0.1883 43618 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.36 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 0 343 5611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085358
X-RAY DIFFRACTIONf_angle_d1.097198
X-RAY DIFFRACTIONf_dihedral_angle_d12.4362068
X-RAY DIFFRACTIONf_chiral_restr0.049817
X-RAY DIFFRACTIONf_plane_restr0.006910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.10550.24441230.20412596X-RAY DIFFRACTION75
2.1055-2.16730.27831400.18753229X-RAY DIFFRACTION95
2.1673-2.23720.25141600.18893320X-RAY DIFFRACTION97
2.2372-2.3170.25821470.18483314X-RAY DIFFRACTION97
2.317-2.40960.22851430.18413314X-RAY DIFFRACTION97
2.4096-2.51910.26011520.19163291X-RAY DIFFRACTION98
2.5191-2.65160.27171460.20563302X-RAY DIFFRACTION97
2.6516-2.81730.23651480.1963314X-RAY DIFFRACTION96
2.8173-3.03410.24411430.19693274X-RAY DIFFRACTION96
3.0341-3.33810.26051430.18863262X-RAY DIFFRACTION96
3.3381-3.8180.21991520.18483191X-RAY DIFFRACTION94
3.818-4.79860.1981380.16653174X-RAY DIFFRACTION93
4.7986-19.59920.17491440.18263158X-RAY DIFFRACTION93
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)
13.7457-1.0067-0.5083.95841.28278.34220.07660.2565-0.1001-0.12270.1982-0.6860.2296-0.0552-0.17950.1199-0.00510.04550.1609-0.04480.234930.952123.795129.2856
22.40161.45280.63496.37773.62762.44150.320.126-0.1257-0.4197-0.1523-0.4977-0.34020.2886-0.12480.1050.0480.02120.16780.00030.15427.312515.662326.6334
31.53760.53140.54153.06150.56812.5343-0.12250.12130.1469-0.42550.2322-0.6996-0.2030.7027-0.10480.182-0.00890.09870.2868-0.04940.363435.267325.165527.1882
42.33471.70112.39981.56030.82075.2464-0.32880.550.3679-0.53120.2664-0.6335-0.07210.56330.1080.264-0.09320.19250.29460.00880.544436.029834.698120.9664
54.53160.8672-0.27182.99671.60553.5398-0.18460.24370.4204-0.46490.11570.0006-0.28060.0130.05540.2088-0.00760.0530.12730.03450.206625.877634.001127.2272
62.85540.929-1.23628.67561.59974.0512-0.17180.01720.03280.1308-0.00650.8425-0.2147-0.55050.13490.13620.01920.06660.1793-0.06030.332915.490933.856337.364
73.9019-0.49380.72725.5863-1.81566.2979-0.1639-0.42210.40850.659-0.1058-0.0633-0.4734-0.41560.23660.1820.00390.03860.203-0.11320.327826.667141.592741.0448
86.30235.19264.10835.30534.30955.9798-0.18920.24861.447-0.0486-0.11070.67-0.4885-0.33730.33290.26420.07050.02890.20550.02440.384220.790842.668731.2089
93.36781.3619-0.1012.7775-4.40388.5918-0.1471-0.1614-0.04390.59130.15290.5639-0.692-0.7521-0.0890.20490.02330.05660.1857-0.04490.222514.161523.159832.9145
104.27550.7187-0.9736.5659-4.06422.58750.0020.25450.0816-0.68290.26910.24820.4433-0.3475-0.21670.16060.0113-0.03380.138-0.01840.114418.288118.544422.4983
111.992-0.6671-0.09864.95040.59720.87610.0251-0.1299-0.09120.43340.0742-0.4510.24290.2255-0.0470.14380.0257-0.05550.20760.00480.148243.697765.08939.2505
123.5725-0.01551.15654.69221.0444.36590.11850.0333-0.34870.2775-0.11840.32280.2823-0.23530.00130.1379-0.0207-0.01230.177-0.0070.187132.460355.59863.1306
132.86620.8931-0.36935.1813-3.41647.0323-0.0178-0.08890.10980.03550.00780.26-0.2639-0.3538-0.01160.05750.01480.00270.1565-0.02780.191630.620174.63226.3903
143.47081.18480.79883.3635-1.32715.04770.0254-0.015-0.06870.10550.17240.0133-0.3295-0.2935-0.14040.08340.02770.00490.12770.0060.088639.265942.396571.0365
150.4366-0.58370.00251.7621-1.59364.50260.0349-0.15390.08140.22840.00210.5175-0.1652-0.4977-0.05190.133-0.00740.04160.24040.01350.20134.623347.852966.476
166.5171-0.72923.66865.1647-2.26893.03930.15760.09720.52890.3777-0.01320.2347-0.9775-0.3067-0.10330.19120.06240.05470.2066-0.0180.193837.629157.804563.2397
175.1166-2.3072-1.00613.422-0.3235.8126-0.02710.149-0.07910.1433-0.11190.00370.22470.12850.12990.0363-0.0260.02420.10930.04680.087744.216646.741362.4157
183.78221.50023.94064.03572.02384.2209-0.12070.1660.4446-0.31670.0531-0.1581-0.49820.2670.27150.16590.03580.03120.2190.06380.16845.70654.767858.4354
192.60710.63730.06857.24584.70785.05350.2195-0.36570.0830.1083-0.4985-0.1173-0.2869-0.21630.23080.11350.0099-0.04220.2236-0.020.188350.230947.548366.6799
207.36741.7202-1.2575.47261.09674.80820.2205-0.2163-0.53570.09030.0448-0.84950.21460.7193-0.1390.09610.0381-0.01060.25820.02580.226254.553439.530955.9746
216.4227-3.59492.84467.9561-5.32319.41410.18040.1918-0.2393-0.7181-0.18290.1240.4417-0.18320.08390.11240.03450.00370.1903-0.03150.12546.355541.715348.0093
228.21940.16174.36813.4345-0.65046.26840.0770.1559-0.2784-0.55180.0961-0.37610.19260.3796-0.14090.20720.00860.08250.1697-0.03540.196351.657151.165953.479
237.72640.5766-0.83454.9986-4.20235.4839-0.39480.2683-0.8205-0.8336-0.0287-0.07640.62790.00780.39420.1874-0.020.05220.1482-0.01660.269252.026131.670567.4963
244.1156-0.7297-0.646.9998-0.88063.3869-0.0062-0.18920.18840.92270.0806-0.6054-0.12150.0215-0.11250.15350.0126-0.05950.23330.00060.125350.162341.872976.9148
253.4789-1.2809-1.24844.1806-0.28643.74620.07740.15730.1758-0.09640.0269-0.07990.0868-0.4175-0.0340.0815-0.0502-0.02850.16350.01650.092834.259381.217636.507
262.11620.6989-1.76060.7898-1.0151.6827-0.01380.05360.196-0.14090.18020.23150.1307-0.127-0.12440.1358-0.0426-0.04010.22150.02950.195928.653477.305938.9761
279.0681-2.5588-2.67985.4454.35583.5473-0.32070.3256-0.67130.0613-0.00740.72660.7016-0.63370.25630.171-0.1009-0.02690.23250.03260.274227.522766.946843.3457
282.235-0.35390.03362.41480.7613.9384-0.0397-0.189-0.05650.18050.0703-0.07740.2041-0.0966-0.01770.0896-0.0208-0.0350.14240.03150.130539.624373.865851.3915
294.1106-0.01280.30875.7289-2.11592.5618-0.03390.243-0.0783-0.1047-0.0566-0.3395-0.01270.19940.06380.09090.00010.0360.1526-0.00690.110147.260880.049435.4765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 15 THROUGH 30 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 31 THROUGH 41 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 42 THROUGH 57 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 58 THROUGH 67 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 68 THROUGH 108 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 109 THROUGH 119 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 120 THROUGH 135 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 136 THROUGH 148 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 149 THROUGH 159 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 160 THROUGH 176 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 15 THROUGH 67 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 68 THROUGH 151 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 152 THROUGH 176 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 15 THROUGH 42 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 43 THROUGH 57 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 58 THROUGH 66 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 67 THROUGH 82 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 83 THROUGH 98 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 99 THROUGH 108 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 109 THROUGH 119 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 120 THROUGH 130 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 131 THROUGH 151 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 152 THROUGH 159 )
24X-RAY DIFFRACTION24CHAIN C AND (RESID 160 THROUGH 176 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 15 THROUGH 41 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 42 THROUGH 57 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 58 THROUGH 66 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 67 THROUGH 148 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 149 THROUGH 176 )

+
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