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- PDB-8pna: transcription factor BARHL2 bound to TAATG DNA sequence -

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Basic information

Entry
Database: PDB / ID: 8pna
Titletranscription factor BARHL2 bound to TAATG DNA sequence
Components
  • (DNA) x 2
  • BarH-like 2 homeobox protein
KeywordsTRANSCRIPTION / homeobox transcription factor / BARHL2 / DNA-binding domain / protein-DNA complex
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
ACETATE ION / DNA / DNA (> 10) / BarH-like 2 homeobox protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMorgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Interfacial water confers transcription factors with dinucleotide specificity.
Authors: Morgunova, E. / Nagy, G. / Yin, Y. / Zhu, F. / Nayak, S.P. / Xiao, T. / Sokolov, I. / Popov, A. / Laughton, C. / Grubmuller, H. / Taipale, J.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 23, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA
A: BarH-like 2 homeobox protein
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4794
Polymers15,4203
Non-polymers591
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.853, 46.881, 71.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA


Mass: 3693.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein BarH-like 2 homeobox protein


Mass: 8095.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pET20A-SBP / Details (production host): vector / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43
#3: DNA chain DNA


Mass: 3631.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: PEG 4000, sodium malonate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.45→39.25 Å / Num. obs: 23842 / % possible obs: 99.1 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.029 / Rrim(I) all: 0.086 / Net I/σ(I): 13.1 / Num. measured all: 189240 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.473.31.62733399990.2880.9661.9070.686.2
7.93-39.257.30.037135318510.0140.0442.799.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.211 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1114 4.7 %RANDOM
Rwork0.1936 ---
obs0.1953 22673 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.1 Å2 / Biso mean: 22.18 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0 Å2
2--0.2 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.45→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 486 4 230 1290
Biso mean--17.44 31.6 -
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121232
X-RAY DIFFRACTIONr_bond_other_d0.0010.015900
X-RAY DIFFRACTIONr_angle_refined_deg2.5131.711743
X-RAY DIFFRACTIONr_angle_other_deg1.2751.5882074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.995.554177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.46319.31844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12715123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4081510
X-RAY DIFFRACTIONr_chiral_restr0.2150.23199
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021029
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02267
LS refinement shellResolution: 1.45→1.486 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.413 75 -
Rwork0.438 1479 -
obs--89.46 %
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)
14.03460.19290.01461.54360.08930.5868-0.1710.4260.0534-0.15040.07370.0125-0.007-0.04980.09730.0218-0.01910.00440.06370.01830.0557-10.45970.3426-7.7581
22.48670.8494-0.22694.59670.35171.19130.0317-0.03660.18050.2436-0.04530.0853-0.0156-0.030.01360.0142-0.00160.00170.01140.00080.0242-11.22031.52483.3872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 12
2X-RAY DIFFRACTION1D1 - 12
3X-RAY DIFFRACTION2A227 - 293

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