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- PDB-8r7f: Transcription factor BARHL2 homodimer with spacing two bp -

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Basic information

Entry
Database: PDB / ID: 8r7f
TitleTranscription factor BARHL2 homodimer with spacing two bp
Components
  • (BarH-like 2 homeobox protein) x 2
  • DNA (5'-D(*CP*TP*AP*AP*AP*CP*GP*GP*GP*CP*AP*AP*TP*TP*AP*G)-3')
  • DNA (5'-D(*CP*TP*AP*AP*TP*TP*GP*CP*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: 1.98 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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*TP*AP*AP*AP*CP*GP*GP*GP*CP*AP*AP*TP*TP*AP*G)-3')
D: DNA (5'-D(*CP*TP*AP*AP*TP*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*G)-3')
A: BarH-like 2 homeobox protein
E: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)25,1024
Polymers25,1024
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-27 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.335, 63.169, 51.323
Angle α, β, γ (deg.)90.00, 111.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*CP*TP*AP*AP*AP*CP*GP*GP*GP*CP*AP*AP*TP*TP*AP*G)-3')


Mass: 4931.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*TP*AP*AP*TP*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*G)-3')


Mass: 4864.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein BarH-like 2 homeobox protein


Mass: 7637.618 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pETG20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43
#4: Protein BarH-like 2 homeobox protein


Mass: 7668.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pETG20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Cacodilate buffer (pH 6.5), PEG (4000) 5% butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.61992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 1.98→47.68 Å / Num. obs: 18391 / % possible obs: 98.2 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.092 / Χ2: 0.66 / Net I/σ(I): 4.6 / Num. measured all: 100419
Reflection shellResolution: 1.98→2.03 Å / % possible obs: 88.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 3.426 / Num. measured all: 5704 / Num. unique obs: 1164 / CC1/2: 0.414 / Rpim(I) all: 1.656 / Rrim(I) all: 3.821 / Χ2: 0.58 / Net I/σ(I) obs: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→47.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 23.172 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27262 905 5 %RANDOM
Rwork0.23269 ---
obs0.23476 17365 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.212 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å2-0 Å21.66 Å2
2--2.56 Å20 Å2
3----4.35 Å2
Refinement stepCycle: 1 / Resolution: 1.98→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 650 0 9 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0111822
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161426
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.8362588
X-RAY DIFFRACTIONr_angle_other_deg0.5711.773281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.576516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7710213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
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_it5.4395.387506
X-RAY DIFFRACTIONr_mcbond_other5.4365.389506
X-RAY DIFFRACTIONr_mcangle_it7.6679.607629
X-RAY DIFFRACTIONr_mcangle_other7.6659.607630
X-RAY DIFFRACTIONr_scbond_it5.1575.4941316
X-RAY DIFFRACTIONr_scbond_other5.1555.4951317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3379.9121960
X-RAY DIFFRACTIONr_long_range_B_refined9.6957.842328
X-RAY DIFFRACTIONr_long_range_B_other9.68457.842328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.984→2.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 60 -
Rwork0.498 1116 -
obs--84.54 %
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)
11.32390.8568-2.60151.2448-1.66215.74770.0804-0.04440.08050.0290.03880.053-0.17820.0593-0.11920.20450.02140.0880.1647-0.0280.05099.2335.30552.6551
21.32180.7112-2.16381.4242-2.29376.18130.0292-0.13160.09530.11280.06620.04450.0991-0.0352-0.09530.1478-0.03670.08820.1349-0.05730.07729.06847.43673.5167
34.01611.7913-1.69316.87420.52953.64910.0601-0.3716-0.1950.3659-0.001-0.440.11170.2494-0.05910.11640.0510.03950.08940.03130.0765.9527-6.104415.419
44.73480.21811.08396.9476-0.71033.62110.0879-0.06490.22480.2557-0.2809-0.4648-0.06350.2950.1930.1216-0.06050.06940.0657-0.00940.109916.933917.7246-7.1105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 16
2X-RAY DIFFRACTION2D1 - 16
3X-RAY DIFFRACTION3A232 - 293
4X-RAY DIFFRACTION4E230 - 292

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