[English] 日本語
Yorodumi
- PDB-7xlj: The crystal structure of ORE1(ANAC092) NAC domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xlj
TitleThe crystal structure of ORE1(ANAC092) NAC domain
ComponentsNAC domain-containing protein 92
KeywordsTRANSCRIPTION / Transcription factor / plant protein / TRANSCRIPTION regulator
Function / homology
Function and homology information


floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / response to ethylene / lateral root development / leaf senescence / regulation of seed germination / response to auxin / response to abscisic acid / response to salt ...floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / response to ethylene / lateral root development / leaf senescence / regulation of seed germination / 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 / 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
NAC domain-containing protein 92
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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: Structure of ORESARA1_DNA Binding Domain at 2.45 angstroms resolution
Authors: Chun, I.S.
History
DepositionApr 21, 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 1.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAC domain-containing protein 92
B: NAC domain-containing protein 92


Theoretical massNumber of molelcules
Total (without water)37,6012
Polymers37,6012
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-11 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.333, 73.761, 78.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 18800.699 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria) / References: UniProt: Q9FKA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris pH 8.5, 7% PEG20K

-
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: Mar 30, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→36.88 Å / Num. obs: 15181 / % possible obs: 98.5 % / Redundancy: 6.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.048 / Χ2: 0.961 / Net I/σ(I): 26.58
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 1301 / CC1/2: 0.907 / CC star: 0.975 / Χ2: 0.722 / % possible all: 86.1

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data collection
HKL-2000data scaling
PHENIX1.17.1_3660phasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ULX

3ulx


Resolution: 2.45→36.88 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 750 4.95 %
Rwork0.217 --
obs0.2192 15143 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 0 8 2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092463
X-RAY DIFFRACTIONf_angle_d1.0923324
X-RAY DIFFRACTIONf_dihedral_angle_d24.081897
X-RAY DIFFRACTIONf_chiral_restr0.057342
X-RAY DIFFRACTIONf_plane_restr0.007413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.640.37131340.31732622X-RAY DIFFRACTION92
2.64-2.910.33071500.2882885X-RAY DIFFRACTION100
2.91-3.330.31251500.26692891X-RAY DIFFRACTION100
3.33-4.190.27571510.2282940X-RAY DIFFRACTION100
4.19-36.880.23281650.18793055X-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)
12.3257-0.9648-2.16511.7927-0.16132.96630.21241.22140.25210.48540.06060.51360.0303-1.5003-0.40230.774-0.08650.11591.0119-0.06640.866126.571513.017447.9201
26.4834-2.1795-1.68936.16741.05884.9942-0.18311.0654-1.0755-0.3723-0.25450.59340.6407-0.62730.44210.7176-0.0961-0.05770.868-0.10590.802836.561810.010535.4471
36.78323.33540.57863.8553-2.37753.3389-0.47432.39111.4145-1.25150.31270.494-0.2476-0.63740.13250.9484-0.05910.02070.96150.25320.8229.224929.477930.811
43.1016-0.4182-0.61194.2351-1.38531.7017-0.09270.74360.1229-0.4876-0.0993-0.3361-0.0585-0.52740.02550.8962-0.0568-0.07060.9090.07990.890434.879222.803233.1734
54.9113-1.0869-1.44723.4891-0.37622.30050.13280.61141.2411-0.0944-0.0679-0.4184-0.4414-0.3910.07310.7521-0.0868-0.00270.83130.19370.913645.22926.005735.1778
64.2774-0.8628-1.95336.88490.30873.3593-0.16920.9179-0.1525-0.62120.2187-0.51740.3706-0.0209-0.06020.7788-0.1004-0.08051.0329-0.01920.688444.982811.912932.8642
73.028-0.8377-1.79562.73332.74315.9023-0.2873-0.0275-0.35890.2603-0.42760.78250.0148-0.1740.75590.9882-0.03230.16250.8761-0.02790.944425.052218.703457.088
85.86480.74442.51953.46871.3275.1171-0.0031-1.1464-1.10651.359-0.7731-0.42131.641-0.13860.56241.7293-0.10660.09331.36790.37231.592829.11217.246871.1854
95.28722.38751.8442.4114-1.09254.1660.335-1.0456-0.58831.04080.3147-1.3340.23591.1442-0.58751.2866-0.0869-0.19931.6456-0.03081.273235.761520.565470.3854
104.7424-0.3232-1.06264.07181.98913.97150.0821-0.4044-0.22770.3438-0.112-0.857-0.47230.28040.15671.2072-0.1047-0.08170.9579-0.00541.361634.470431.842966.7603
118.1606-6.07492.99354.9303-3.76596.9809-0.4801-1.7534-1.27281.49580.56442.0465-0.31870.4482-0.11911.6051-0.07720.38811.68-0.16611.515215.962630.01271.8789
128.47340.1456-0.99084.9429-0.00654.9802-1.02430.72240.45240.06290.5398-1.71061.1450.03210.39731.12-0.11-0.09640.74790.07351.313236.924323.378964.2518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 145 )
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 99 )
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 149 )
11X-RAY DIFFRACTION11chain 'B' and (resid 150 through 162 )
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 170 )

+
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