[English] 日本語
Yorodumi
- PDB-5yzz: AtVAL1 B3 domain in complex with 13bp-DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yzz
TitleAtVAL1 B3 domain in complex with 13bp-DNA
Components
  • B3 domain-containing transcription repressor VAL1
  • DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3')
KeywordsTRANSCRIPTION/DNA / transcriptional factor / Val1 / B3 domain / DNA complex / FLC / plant / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to sucrose / response to abscisic acid / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function
DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. ...DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / B3 domain-containing transcription repressor VAL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsWu, B.X. / Zhang, M.M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
Authors: Wu, B.X. / Zhang, M.M. / Su, S.C. / Liu, H.H. / Gan, J.H. / Ma, J.B.
History
DepositionDec 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3')
B: DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3')
C: B3 domain-containing transcription repressor VAL1


Theoretical massNumber of molelcules
Total (without water)22,1353
Polymers22,1353
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.896, 86.896, 148.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: DNA chain DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3')


Mass: 3981.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3')


Mass: 3959.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein B3 domain-containing transcription repressor VAL1 / Protein HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE 2 / Protein VP1/ABI3-LIKE 1


Mass: 14194.220 Da / Num. of mol.: 1 / Fragment: B3 domain, DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL1, HSI2, At2g30470, T6B20.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8W4L5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG 5000 MME, 0.1M Tris base/Hydrochloric acid pH 8.0, 0.2M Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.58→74.97 Å / Num. obs: 9191 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.4
Reflection shellResolution: 2.58→2.67 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZY

5yzy


Resolution: 2.58→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.293 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.547 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25522 415 5.3 %RANDOM
Rwork0.22598 ---
obs0.22757 7414 84.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.58→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 527 0 0 1393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0161475
X-RAY DIFFRACTIONr_bond_other_d0.0020.021135
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.6262104
X-RAY DIFFRACTIONr_angle_other_deg1.32632647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4975110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02423.15838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03715152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211280
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02305
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8114.473443
X-RAY DIFFRACTIONr_mcbond_other3.7834.464442
X-RAY DIFFRACTIONr_mcangle_it6.4916.667552
X-RAY DIFFRACTIONr_mcangle_other6.4966.681553
X-RAY DIFFRACTIONr_scbond_it3.9724.4691032
X-RAY DIFFRACTIONr_scbond_other3.9534.461030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4596.6291552
X-RAY DIFFRACTIONr_long_range_B_refined8.86543.3041744
X-RAY DIFFRACTIONr_long_range_B_other8.86543.2791744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.585→2.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 11 -
Rwork0.494 182 -
obs--28.55 %

+
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