[English] 日本語
Yorodumi
- PDB-7yul: Crystal structure of human BEND6 BEN domain in complex with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yul
TitleCrystal structure of human BEND6 BEN domain in complex with DNA
Components
  • BEN domain-containing protein 6
  • DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')
KeywordsDNA BINDING PROTEIN / complex structure
Function / homology
Function and homology information


negative regulation of Notch signaling pathway / positive regulation of neuron differentiation / transcription corepressor activity / nervous system development / chromatin binding / DNA binding / nucleus
Similarity search - Function
BEN domain-containing protein 6 / BEN domain / BEN domain / BEN domain profile. / BEN
Similarity search - Domain/homology
GLYCOLIC ACID / DNA / DNA (> 10) / BEN domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLiu, K. / Xiao, Y.Q. / Zhang, J. / Min, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770834 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into DNA recognition by the BEN domain of the transcription factor BANP.
Authors: Liu, K. / Zhang, J. / Xiao, Y. / Yang, A. / Song, X. / Li, Y. / Chen, Y. / Hughes, T.R. / Min, J.
History
DepositionAug 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2May 24, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 31, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BEN domain-containing protein 6
C: DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5463
Polymers15,4702
Non-polymers761
Water2,522140
1
A: BEN domain-containing protein 6
C: DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')
hetero molecules

A: BEN domain-containing protein 6
C: DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0926
Polymers30,9404
Non-polymers1522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6270 Å2
ΔGint-14 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.092, 39.514, 43.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21C-206-

HOH

-
Components

#1: Protein BEN domain-containing protein 6 / BEND6


Mass: 11806.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BEND6, C6orf65 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SZJ8
#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene glycol, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 12.5% MPD (v/v), 12.5% PEG 1000 (v/v), 12.5% PEG3350 (v/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.82→27.11 Å / Num. obs: 11195 / % possible obs: 99.4 % / Redundancy: 7.69 % / Rmerge(I) obs: 0.0451 / Net I/σ(I): 34.15
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.26 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 9.77 / Num. unique obs: 483 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINT5.8.0267data reduction
SAINT3.27data scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YUG

7yug


Resolution: 1.82→27.11 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.207 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 567 5.1 %RANDOM
Rwork0.1575 ---
obs0.1594 10599 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.64 Å2 / Biso mean: 16.862 Å2 / Biso min: 5.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.82→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 243 5 140 1125
Biso mean--21.6 26.48 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121044
X-RAY DIFFRACTIONr_bond_other_d0.0010.018896
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.5151455
X-RAY DIFFRACTIONr_angle_other_deg1.4881.8112073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.303595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54423.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78515157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.154155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02244
LS refinement shellResolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 40 -
Rwork0.174 713 -
all-753 -
obs--93.42 %

+
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