[English] 日本語
Yorodumi
- PDB-7yug: Structure of human BANP BEN domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yug
TitleStructure of human BANP BEN domain
ComponentsProtein BANP
KeywordsDNA BINDING PROTEIN / BANP
Function / homology
Function and homology information


Regulation of TP53 Activity through Association with Co-factors / chromatin organization / nuclear speck / nuclear body / DNA binding / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Protein BANP / BEN domain / BEN domain / BEN domain / BEN domain profile. / BEN / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Chem-PG6 / TRIETHYLENE GLYCOL / Protein BANP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsZhang, J. / Xiao, Y.Q. / Chen, Y.X. / Liu, K. / 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 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 1.2May 31, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein BANP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3396
Polymers13,7721
Non-polymers5675
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint4 kcal/mol
Surface area7550 Å2
Unit cell
Length a, b, c (Å)39.650, 50.041, 54.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Protein BANP / BEN domain-containing protein 1 / Btg3-associated nuclear protein / Scaffold/matrix-associated ...BEN domain-containing protein 1 / Btg3-associated nuclear protein / Scaffold/matrix-associated region-1-binding protein


Mass: 13771.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANP, BEND1, SMAR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N9N5

-
Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% v/v PEG500*MME;10% w/v PEG 20000,0.09 M Halogens, and 0.1 M Tris(base); BICINE pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 44514 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 45.45
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 9.92 / Num. unique obs: 2190 / CC1/2: 0.974 / CC star: 0.993 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold structure prediction

Resolution: 1.1→32 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.66 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1446 2348 5.3 %RANDOM
Rwork0.1245 ---
obs0.1256 42104 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.43 Å2 / Biso mean: 11.54 Å2 / Biso min: 4.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.39 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.1→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 31 189 1173
Biso mean--18.08 25.64 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131038
X-RAY DIFFRACTIONr_bond_other_d0.0020.017973
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6551393
X-RAY DIFFRACTIONr_angle_other_deg1.6091.5842265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.765127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.23520.15664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9121512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02238
X-RAY DIFFRACTIONr_rigid_bond_restr16.16232011
LS refinement shellResolution: 1.1→1.127 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.187 161 -
Rwork0.16 3004 -
obs--96.85 %

+
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