[English] 日本語
Yorodumi
- PDB-7xp3: DNA complex form of ORESARA1(ANAC092) NAC Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xp3
TitleDNA complex form of ORESARA1(ANAC092) NAC Domain
Components
  • DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')
  • DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')
  • NAC domain-containing protein 92
KeywordsTRANSCRIPTION / Transcription factor / plant protein / TRANSCRIPTION regulator / DNA binding protein
Function / homology
Function and homology information


floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / regulation of seed germination / response to ethylene / lateral root development / leaf senescence / response to auxin / response to abscisic acid / response to salt ...floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / regulation of seed germination / response to ethylene / lateral root development / leaf senescence / response to auxin / response to abscisic acid / response to salt / positive regulation of programmed cell death / stress-induced premature senescence / response to salt stress / response to hydrogen peroxide / positive regulation of DNA-binding transcription factor activity / regulation of gene expression / response to oxidative stress / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / protein homodimerization activity / nucleus
Similarity search - Function
NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / NAC domain-containing protein 92
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsChun, I.S. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Plant Commun. / Year: 2023
Title: Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.
Authors: Chun, I. / Kim, H.J. / Hong, S. / Kim, Y.G. / Kim, M.S.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: The crystal structure of ORE1(ANAC092) NAC domain in complex with DNA
Authors: Chun, I.S.
History
DepositionMay 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAC domain-containing protein 92
B: NAC domain-containing protein 92
C: NAC domain-containing protein 92
E: DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
F: DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')
G: DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')
H: DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)76,5977
Polymers76,5977
Non-polymers00
Water00
1
A: NAC domain-containing protein 92
B: NAC domain-containing protein 92
E: DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
F: DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)51,1054
Polymers51,1054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NAC domain-containing protein 92
G: DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')
H: DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)25,4923
Polymers25,4923
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.592, 92.592, 216.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11G-12-

DG

21G-12-

DG

-
Components

#1: Protein NAC domain-containing protein 92 / ANAC092 / AtNAC2 / AtNAC6 / Protein ORESARA 1


Mass: 18800.699 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NAC92, NAC2, NAC6, ORE1, At5g39610, MIJ24.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FKA0
#2: DNA chain DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Mass: 6745.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')


Mass: 6758.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#4: DNA chain DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')


Mass: 3693.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: half of occupancy nucleotide / Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#5: DNA chain DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Mass: 2997.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium sulfate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.24→46.3 Å / Num. obs: 16649 / % possible obs: 99.49 % / Redundancy: 17 % / CC1/2: 0.947 / Net I/σ(I): 18.4
Reflection shellResolution: 3.245→3.361 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 1663 / CC1/2: 0.928

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data collection
PHENIX1.17.1_3660phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XLJ

7xlj


Resolution: 3.25→46.3 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 832 5.04 %
Rwork0.2131 --
obs0.215 16504 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 1463 0 0 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0265236
X-RAY DIFFRACTIONf_angle_d1.5417391
X-RAY DIFFRACTIONf_dihedral_angle_d24.9962016
X-RAY DIFFRACTIONf_chiral_restr0.104785
X-RAY DIFFRACTIONf_plane_restr0.013682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.450.34581370.29022564X-RAY DIFFRACTION98
3.45-3.720.34661360.29512627X-RAY DIFFRACTION100
3.72-4.090.28651370.25292602X-RAY DIFFRACTION100
4.09-4.690.24471390.21222615X-RAY DIFFRACTION100
4.69-5.90.27111400.22012622X-RAY DIFFRACTION100
5.9-46.30.21511430.18032642X-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)
10.4403-0.2749-0.31460.1641-0.07280.3203-1.27-0.7102-1.55630.65140.21661.54131.35240.8354-01.0735-0.03880.06581.6317-0.02111.3779-34.2498-27.194242.9854
23.05790.3394-1.89190.59080.97183.4309-0.02980.043-0.0682-0.3121-0.47450.42-0.6663-0.696300.76980.0188-0.10921.3744-0.21640.9333-31.3024-24.506825.7999
32.0108-3.0886-0.34115.80131.19510.4477-2.3696-1.63090.61072.57960.97174.34790.0094-4.5598-0.37231.5619-0.0952-0.14222.498-0.28931.8684-38.1078-17.790134.5553
41.05930.3230.21612.2643-0.94530.22810.1593-0.05330.5097-0.16540.20021.3337-0.8545-1.1307-00.97170.066-0.00881.3625-0.09690.9257-26.2066-13.368119.2743
50.19681.05970.04412.95890.2460.71111.0196-0.542-1.3482-1.8723-1.0463-1.32760.11251.1128-0.03390.8524-0.068-0.08731.3405-0.0670.8936-13.2924-23.604331.0713
61.68360.29561.31912.7878-0.68421.43180.20120.7066-0.1988-0.5815-0.2778-0.3519-0.8905-0.355600.9597-0.03430.00581.2327-0.13740.6608-23.0026-17.476925.2
70.4753-0.70850.67011.98090.30280.9801-1.2383-0.1971-0.83020.43771.14770.74190.8826-0.411301.1979-0.042-0.15411.97020.07261.0762-33.9175-24.63351.6716
81.97735.09592.01552.7592.15843.31881.9952-3.2362-5.47710.3922.38021.36590.966-3.13132.98681.51080.27650.82152.21560.37531.9994-35.0558-30.642662.8193
91.2862-0.24390.33320.1336-0.66832.589-1.5791-1.0393-1.939-1.65432.3804-3.72412.5642-0.22630.12411.9416-0.111-0.24711.173-0.20592.1104-17.2771-33.316862.8898
101.2754-1.6487-0.28341.82780.34110.02120.42530.4684-1.3467-0.5531-0.70470.6271-0.1775-0.9822-01.2688-0.0297-0.15041.4987-0.55692.0119-24.3496-30.339655.824
110.33740.7269-0.46741.57830.09660.77420.3507-0.52440.1168-0.03210.0482-0.6166-0.5865-0.3781-01.3220.0384-0.06191.57320.10321.3517-15.457-22.003370.91
120.14690.4582-0.63611.4554-2.22663.92542.1645-1.41780.9876-2.57680.72970.2231-2.6595-1.47360.68811.9699-0.3373-0.17361.5077-0.3641.7037-27.8708-9.666256.7091
132.32041.61732.14223.46640.68181.3553-0.2917-0.0347-0.69620.47820.13570.42790.21110.0551-00.99430.0370.0671.1797-0.13911.3144-17.4131-19.877560.532
140.19990.32770.04551.6623-0.65680.5345-0.7202-0.88691.8637-1.64462.79920.3011-0.8080.83470.01252.26540.6050.89921.8457-0.04441.7959-35.3987-18.307373.767
150.9411.14220.14861.3282-0.01540.47062.0409-0.07960.99460.75450.4583-0.9165-0.1077-0.44910.00231.06230.0907-0.00191.7379-0.20421.2299-23.0848-24.77958.1262
163.0689-2.38482.89823.85860.0853.02840.50660.4945-0.617-1.80910.212-1.22121.16050.3915-02.0333-0.2870.3041.3345-0.2461.1362-35.05527.520768.5827
170.7989-0.94610.08891.16630.05280.0502-1.09490.81410.0698-0.08440.90832.7842-2.1122-1.354-0.06731.8-0.2152-0.64231.44430.06071.0704-44.803518.038972.9288
180.2913-0.24520.50540.1242-0.26940.5817-1.95622.43981.3089-1.92181.18471.3433-0.6532-0.189201.8528-0.4151-0.22111.4383-0.38841.8854-31.591115.29374.7051
191.97611.05610.47730.6434-0.42411.7542-0.0877-0.25680.62320.4230.28890.05560.1188-0.827701.1422-0.1839-0.15660.69950.01561.2539-28.883320.232285.0843
203.15171.02720.86510.50970.82881.58740.4321-3.006-1.1561-1.43251.8534-1.91093.32913.23940.2032.34880.4376-0.11521.4623-0.44411.659-28.1257-0.574882.638
213.481.43231.60430.48580.65183.4271.0181.45241.83740.2353-1.7697-1.86040.8962-1.1426-0.31291.2848-0.2588-0.17120.536-0.10351.4962-37.052417.477688.1689
221.4092-0.55451.59611.4341-1.49872.1540.2198-0.7190.5333-0.52970.8659-0.2161.0551-0.60530.00011.2131-0.36740.04320.7395-0.16391.4295-34.409910.390678.1916
230.49510.54470.7030.19460.61060.71290.25281.07720.59390.18860.12160.1405-1.58871.0101.8368-0.1672-0.00071.59740.05151.1512-14.2884-4.751922.3053
240.79590.29441.2402-0.02250.45310.8929-0.54090.11940.01240.64880.8244-0.0157-2.22550.3352-01.7192-0.1557-0.04911.6112-0.10961.1576-10.4349-9.747758.1721
250.64660.03630.023-0.0546-0.0276-0.0364-0.81321.0851-1.5381-0.74711.1886-0.2386-1.61891.75901.8018-0.1103-0.15841.6309-0.06051.2501-8.3493-17.952473.3816
260.3284-0.8698-0.48181.14350.78561.270.36290.46360.00070.6520.946-0.2537-0.05960.7675-01.7545-0.2062-0.34631.8002-0.14341.5203-11.0753-8.853149.5944
270.8662-0.53250.20870.1969-0.02390.08890.72111.56770.3664-0.71820.008-0.7733-0.8915-0.87502.1221-0.333-0.02731.5667-0.14571.4128-12.824-2.372622.1974
280.9664-0.76570.38160.4045-0.2478-0.2640.4037-1.11880.20010.5435-1.14430.2430.9581-0.556-0.00232.0406-0.5452-0.00221.2035-0.09011.7787-33.771212.887896.2455
290.41390.41560.6996-0.0770.09730.46021.6417-2.1013-1.45931.6348-1.6773-1.81711.1302-1.0254-0.02011.9293-0.6975-0.2761.33420.14882.1069-33.914710.241195.0733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 114 )
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 103 )
12X-RAY DIFFRACTION12chain 'B' and (resid 104 through 115 )
13X-RAY DIFFRACTION13chain 'B' and (resid 116 through 148 )
14X-RAY DIFFRACTION14chain 'B' and (resid 149 through 160 )
15X-RAY DIFFRACTION15chain 'B' and (resid 161 through 170 )
16X-RAY DIFFRACTION16chain 'C' and (resid 19 through 61 )
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 75 )
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 85 )
19X-RAY DIFFRACTION19chain 'C' and (resid 87 through 104 )
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 118 )
21X-RAY DIFFRACTION21chain 'C' and (resid 119 through 137 )
22X-RAY DIFFRACTION22chain 'C' and (resid 138 through 170 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 10 )
24X-RAY DIFFRACTION24chain 'E' and (resid 11 through 22 )
25X-RAY DIFFRACTION25chain 'F' and (resid 23 through 27 )
26X-RAY DIFFRACTION26chain 'F' and (resid 28 through 37 )
27X-RAY DIFFRACTION27chain 'F' and (resid 38 through 44 )
28X-RAY DIFFRACTION28chain 'G' and (resid 1 through 12 )
29X-RAY DIFFRACTION29chain 'H' and (resid 35 through 44 )

+
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