[English] 日本語
Yorodumi
- PDB-8r7z: transcription factor BARHL2 homodimer with spacing four bp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r7z
Titletranscription factor BARHL2 homodimer with spacing four bp
Components
  • BarH-like 2 homeobox protein
  • DNA (5'-D(P*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*T)-3')
  • DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*CP*AP*AP*TP*TP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*AP*AP*TP*TP*GP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')
KeywordsTRANSCRIPTION / transcription factor / homeobox protein / homodimer / complex with specific DNA
Function / homology
Function and homology information


amacrine cell differentiation / cell fate determination / regulation of axon extension / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II ...amacrine cell differentiation / cell fate determination / regulation of axon extension / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
: / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / BarH-like 2 homeobox protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsMorgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research CouncilC24905003 Sweden
CitationJournal: Nature / Year: 2025
Title: DNA-guided transcription factor interactions extend human gene regulatory code.
Authors: Xie, Z. / Sokolov, I. / Osmala, M. / Yue, X. / Bower, G. / Pett, J.P. / Chen, Y. / Wang, K. / Cavga, A.D. / Popov, A. / Teichmann, S.A. / Morgunova, E. / Kvon, E.Z. / Yin, Y. / Taipale, J.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: 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 1.2Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: BarH-like 2 homeobox protein
D: DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')
A: BarH-like 2 homeobox protein
G: BarH-like 2 homeobox protein
H: DNA (5'-D(P*CP*TP*AP*AP*TP*TP*GP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')
I: DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*CP*AP*AP*TP*TP*AP*G)-3')
K: BarH-like 2 homeobox protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8819
Polymers45,8588
Non-polymers231
Water1086
1
E: BarH-like 2 homeobox protein
D: DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8334
Polymers12,8103
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-9 kcal/mol
Surface area6250 Å2
MethodPISA
2
A: BarH-like 2 homeobox protein
G: BarH-like 2 homeobox protein
H: DNA (5'-D(P*CP*TP*AP*AP*TP*TP*GP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')
I: DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*CP*AP*AP*TP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)25,7094
Polymers25,7094
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-22 kcal/mol
Surface area12400 Å2
MethodPISA
3
K: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)7,3391
Polymers7,3391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.955, 159.955, 159.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11E-500-

NA

21B-101-

HOH

-
Components

-
Protein , 1 types, 4 molecules EAGK

#1: Protein
BarH-like 2 homeobox protein


Mass: 7339.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: the residue 63 - NA is a sodium ion / Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pETG20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43

-
DNA chain , 4 types, 4 molecules DBHI

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


Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*CP*TP*AP*AP*TP*TP*GP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*G)-3')


Mass: 5481.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*CP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*CP*AP*AP*TP*TP*AP*G)-3')


Mass: 5548.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 2 types, 7 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M Sodium Cacodilate buffer (pH 6.5), PEG (4000), PEG(200)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.26→46.17 Å / Num. obs: 10697 / % possible obs: 99.3 % / Redundancy: 21.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.041 / Rrim(I) all: 0.184 / Χ2: 1.02 / Net I/σ(I): 8.7 / Num. measured all: 230484
Reflection shellResolution: 3.26→3.52 Å / % possible obs: 96.9 % / Redundancy: 19.6 % / Rmerge(I) obs: 5.142 / Num. measured all: 41538 / Num. unique obs: 2115 / CC1/2: 0.204 / Rpim(I) all: 1.171 / Rrim(I) all: 5.28 / Χ2: 1.01 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→43 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.949 / SU B: 56.323 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25246 521 4.9 %RANDOM
Rwork0.19764 ---
obs0.20067 10173 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 175.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.26→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 1107 1 6 3073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0113230
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162519
X-RAY DIFFRACTIONr_angle_refined_deg2.2971.8344575
X-RAY DIFFRACTIONr_angle_other_deg0.5621.7715789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.338529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52410386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023125
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02754
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_it12.37310.706907
X-RAY DIFFRACTIONr_mcbond_other12.36810.709907
X-RAY DIFFRACTIONr_mcangle_it17.92919.1781127
X-RAY DIFFRACTIONr_mcangle_other17.93519.1741128
X-RAY DIFFRACTIONr_scbond_it13.0310.8262323
X-RAY DIFFRACTIONr_scbond_other13.02710.8262324
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.36219.5023449
X-RAY DIFFRACTIONr_long_range_B_refined23.385116.874062
X-RAY DIFFRACTIONr_long_range_B_other23.382116.864063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.262→3.347 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 29 -
Rwork0.382 681 -
obs--91.03 %
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)
110.6985-0.9335-0.72055.95071.0838.01070.2242-0.14370.2450.1202-0.23960.3327-0.2304-0.24010.01540.09820.05810.09710.09240.0490.1107-25.3437-14.5958-3.1847
28.7401-3.88875.67331.982-2.18514.7785-0.699-1.33280.01160.31560.7851-0.4404-0.82690.1006-0.08610.896-0.0891-0.24471.22490.24111.112813.9287-18.488921.2001
312.4529-3.8587-4.53212.6021-0.56584.4841-0.5363-1.4582-0.88620.43280.44020.3439-0.06790.40030.09610.3445-0.1692-0.03370.40110.25440.4009-27.4665-24.60766.7299
410.5133-2.85290.890811.1666-1.49598.91130.2026-0.4907-0.04530.1908-0.0452-0.90710.01580.7609-0.15740.20850.0282-0.10160.4155-0.00890.20233.9997-15.15064.0106
53.3798-0.24191.3686.15930.00637.29310.11840.4131-0.0046-0.26810.5028-1.1939-0.01060.8093-0.62120.98510.0152-0.01411.50190.16181.616430.7339-28.910921.8642
610.57372.682-0.50214.34332.05081.3937-0.0774-0.58580.00830.5129-0.18750.10140.32070.18890.26490.49380.03980.01830.72430.33770.656611.7272-39.572230.8772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E232 - 291
2X-RAY DIFFRACTION2I1 - 18
3X-RAY DIFFRACTION2H1 - 18
4X-RAY DIFFRACTION3B10 - 18
5X-RAY DIFFRACTION3D1 - 9
6X-RAY DIFFRACTION4A223 - 291
7X-RAY DIFFRACTION5G232 - 291
8X-RAY DIFFRACTION6K240 - 287

+
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