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- PDB-8pmn: transcription factor BARHL2 bound to DNA sequences -

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Basic information

Entry
Database: PDB / ID: 8pmn
Titletranscription factor BARHL2 bound to DNA sequences
Components
  • (DNA) x 2
  • BarH-like 2 homeobox protein
KeywordsTRANSCRIPTION / homeobox transcription factor BARHL2 / DNA-binding domain / complex with 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: 1.3 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 29, 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

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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


Theoretical massNumber of molelcules
Total (without water)14,8343
Polymers14,8343
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-13 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.658, 47.118, 72.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein BarH-like 2 homeobox protein


Mass: 7509.488 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: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.16 Å3/Da / Density % sol: 44.58 %
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: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.3→47.12 Å / Num. obs: 32926 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.86 / Net I/σ(I): 10.2 / Num. measured all: 233390
Reflection shellResolution: 1.3→1.33 Å / % possible obs: 94.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 2.156 / Num. measured all: 9957 / Num. unique obs: 1518 / CC1/2: 0.264 / Rpim(I) all: 0.883 / Rrim(I) all: 2.336 / Χ2: 0.65 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.11 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.144 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21327 1583 4.8 %RANDOM
Rwork0.18169 ---
obs0.18317 31279 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.917 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.3→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 486 0 268 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0151124
X-RAY DIFFRACTIONr_bond_other_d0.0010.015804
X-RAY DIFFRACTIONr_angle_refined_deg2.5361.7091576
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5821852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4665.637185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.30219.51241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.947159
X-RAY DIFFRACTIONr_chiral_restr0.2130.239187
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
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_it0.7881.246252
X-RAY DIFFRACTIONr_mcbond_other0.7771.246251
X-RAY DIFFRACTIONr_mcangle_it1.1321.867315
X-RAY DIFFRACTIONr_mcangle_other1.1311.867316
X-RAY DIFFRACTIONr_scbond_it1.3781.34872
X-RAY DIFFRACTIONr_scbond_other1.3781.34872
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0582.0041262
X-RAY DIFFRACTIONr_long_range_B_refined3.54834.1633907
X-RAY DIFFRACTIONr_long_range_B_other3.54734.1583908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 111 -
Rwork0.44 2193 -
obs--96.16 %
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)
13.78780.49250.15751.659-0.06760.6959-0.11660.45940.0197-0.16760.07670.00870.0179-0.02960.03990.0188-0.01680.00260.0593-0.00110.0307-10.44210.1635-7.8618
22.54540.8919-0.22623.05770.70461.62990.0527-0.16630.11370.2853-0.05040.07090.0355-0.0417-0.00230.0281-0.00140.00460.0138-0.0060.0094-11.53490.43845.4071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 12
2X-RAY DIFFRACTION1D1 - 12
3X-RAY DIFFRACTION2A232 - 293

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