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- PDB-8pmv: transcription factor BARHL2 bound to TAAGC DNA sequence -

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Basic information

Entry
Database: PDB / ID: 8pmv
Titletranscription factor BARHL2 bound to TAAGC 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
DNA / DNA (> 10) / BarH-like 2 homeobox protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
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
A: BarH-like 2 homeobox protein
B: DNA
C: DNA
D: BarH-like 2 homeobox protein
E: DNA
F: DNA
G: BarH-like 2 homeobox protein
H: DNA
I: DNA
J: BarH-like 2 homeobox protein
K: DNA
L: DNA


Theoretical massNumber of molelcules
Total (without water)59,46112
Polymers59,46112
Non-polymers00
Water2,180121
1
A: BarH-like 2 homeobox protein
B: DNA
C: DNA


Theoretical massNumber of molelcules
Total (without water)14,8653
Polymers14,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-13 kcal/mol
Surface area7710 Å2
2
D: BarH-like 2 homeobox protein
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)14,8653
Polymers14,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-10 kcal/mol
Surface area7580 Å2
3
G: BarH-like 2 homeobox protein
H: DNA
I: DNA


Theoretical massNumber of molelcules
Total (without water)14,8653
Polymers14,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-13 kcal/mol
Surface area7720 Å2
4
J: BarH-like 2 homeobox protein
K: DNA
L: DNA


Theoretical massNumber of molelcules
Total (without water)14,8653
Polymers14,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-14 kcal/mol
Surface area7230 Å2
Unit cell
Length a, b, c (Å)39.080, 133.773, 64.990
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
BarH-like 2 homeobox protein


Mass: 7539.536 Da / Num. of mol.: 4
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
#2: DNA chain
DNA


Mass: 3678.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA


Mass: 3647.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.74 Å3/Da / Density % sol: 57.13 %
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: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.1→46.63 Å / Num. obs: 38886 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Rrim(I) all: 0.132 / Χ2: 0.97 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 97.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 5.172 / Num. measured all: 18000 / Num. unique obs: 3154 / CC1/2: 0.087 / Rpim(I) all: 2.322 / Rrim(I) all: 5.681 / Χ2: 0.96 / Net I/σ(I) obs: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 25.69 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27763 2041 5.3 %RANDOM
Rwork0.2512 ---
obs0.25264 36812 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.801 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å21.64 Å2
2--0.05 Å2-0 Å2
3----2.25 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 1942 0 121 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124417
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153128
X-RAY DIFFRACTIONr_angle_refined_deg2.171.7086180
X-RAY DIFFRACTIONr_angle_other_deg1.1231.5847213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0595.653722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.62520156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87615415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.491532
X-RAY DIFFRACTIONr_chiral_restr0.1720.239736
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
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_it1.0762.265968
X-RAY DIFFRACTIONr_mcbond_other1.0722.265967
X-RAY DIFFRACTIONr_mcangle_it1.7743.3891203
X-RAY DIFFRACTIONr_mcangle_other1.7743.391204
X-RAY DIFFRACTIONr_scbond_it1.1782.2423449
X-RAY DIFFRACTIONr_scbond_other1.1782.2423449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.863.3634978
X-RAY DIFFRACTIONr_long_range_B_refined4.69457.77615015
X-RAY DIFFRACTIONr_long_range_B_other4.69157.74814999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A18440.13
12D18440.13
21A19190.12
22G19190.12
31A18170.12
32J18170.12
41B22330.06
42E22330.06
51B22980.03
52H22980.03
61B22350.08
62K22350.08
71D18570.14
72G18570.14
81D18510.13
82J18510.13
91E22430.07
92H22430.07
101E22570.04
102K22570.04
111G18790.1
112J18790.1
121H22390.08
122K22390.08
LS refinement shellResolution: 2.1→2.152 Å
RfactorNum. reflection% reflection
Rfree0.408 154 -
Rwork0.424 2675 -
obs--97.45 %
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)
14.0784-2.0392-0.75217.5506-0.53346.4355-0.0599-0.02170.0858-0.36060.0038-0.01810.39810.18410.05610.0537-0.0195-0.06750.4580.04740.462113.203-3.2267.233
25.3301-0.76821.06052.8462-0.53534.3584-0.4087-0.69110.44210.41030.2290.064-0.070.04250.17970.08380.0512-0.07390.5713-0.0180.624212.3024.71917.239
34.570.67160.90795.7884-0.20874.93690.12420.1989-0.2514-0.3464-0.13790.24210.58720.16840.01370.22090.1329-0.04880.46180.00680.396717.665-27.73211.801
44.6052-0.1625-0.94594.81310.5216.4160.0940.0063-0.0205-0.0195-0.1442-0.47040.21470.89820.05020.18540.1206-0.00320.65360.06690.435829.531-25.75317.864
52.47321.5711-0.95596.82010.41835.29760.1591-0.1117-0.01720.0540.0381-0.2015-0.30370.0141-0.19720.03150.0239-0.05010.44740.0680.57133.22818.697-0.749
66.97660.4985-1.06242.4945-0.72883.1301-0.30620.5882-0.4785-0.26770.1767-0.04580.19810.0210.12940.0597-0.0185-0.07340.4257-0.00290.569732.23710.171-10.423
74.9734-1.84961.36737.4015-1.65774.4071-0.29120.02210.6296-0.40130.2052-0.0724-0.6575-0.4070.0860.50010.0618-0.08740.6581-0.01790.61546.878-17.603-19.891
82.9478-0.6379-2.66863.90820.16458.1295-0.0597-0.0293-0.116-0.27080.03840.03420.1779-0.19060.02140.34320.0231-0.00880.5169-0.00170.391410.518-30.162-16.576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A231 - 292
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION2C13 - 24
4X-RAY DIFFRACTION3D232 - 291
5X-RAY DIFFRACTION4E1 - 12
6X-RAY DIFFRACTION4F13 - 24
7X-RAY DIFFRACTION5G231 - 292
8X-RAY DIFFRACTION6H1 - 12
9X-RAY DIFFRACTION6I13 - 24
10X-RAY DIFFRACTION7J232 - 290
11X-RAY DIFFRACTION8K1 - 12
12X-RAY DIFFRACTION8L13 - 24

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