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- PDB-8pm5: transcription factor BARHL2 bound to TAAAT DNA sequence -

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Basic information

Entry
Database: PDB / ID: 8pm5
Titletranscription factor BARHL2 bound to TAAAT DNA sequence
Components
  • BarH-like 2 homeobox protein
  • DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
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: 2.4 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 28, 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 (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
C: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')
D: BarH-like 2 homeobox protein
E: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
F: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')
G: BarH-like 2 homeobox protein
H: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
I: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')
J: BarH-like 2 homeobox protein
K: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
L: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')
M: BarH-like 2 homeobox protein
N: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)74,53214
Polymers74,53214
Non-polymers00
Water4,702261
1
A: BarH-like 2 homeobox protein
B: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
C: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,8633
Polymers14,8633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area7570 Å2
MethodPISA
2
D: BarH-like 2 homeobox protein
E: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
F: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,8633
Polymers14,8633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-15 kcal/mol
Surface area7470 Å2
MethodPISA
3
G: BarH-like 2 homeobox protein
H: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
I: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,8633
Polymers14,8633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-16 kcal/mol
Surface area7650 Å2
MethodPISA
4
J: BarH-like 2 homeobox protein
K: DNA (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')
L: DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,8633
Polymers14,8633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-13 kcal/mol
Surface area7290 Å2
MethodPISA
5
M: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)7,5401
Polymers7,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3910 Å2
MethodPISA
6
N: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)7,5401
Polymers7,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.015, 134.298, 65.625
Angle α, β, γ (deg.)90.00, 92.60, 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
1313
1414
1515
1616

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

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Components

#1: Protein
BarH-like 2 homeobox protein


Mass: 7539.536 Da / Num. of mol.: 6
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 (5'-D(*CP*GP*CP*TP*AP*AP*AP*TP*GP*GP*TP*T)-3')


Mass: 3677.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(*AP*AP*CP*CP*AP*TP*TP*TP*AP*GP*CP*G)-3')


Mass: 3646.405 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.: 261 / 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: 2.5 Å3/Da / Density % sol: 52.4 %
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: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.33→46.95 Å / Num. obs: 27918 / % possible obs: 96.6 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.063 / Rrim(I) all: 0.167 / Χ2: 0.96 / Net I/σ(I): 8.8
Reflection shellResolution: 2.33→2.41 Å / % possible obs: 72.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 2.965 / Num. measured all: 13576 / Num. unique obs: 2056 / CC1/2: 0.179 / Rpim(I) all: 1.233 / Rrim(I) all: 3.22 / Χ2: 0.94 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 23.574 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.512 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28042 1251 4.8 %RANDOM
Rwork0.22863 ---
obs0.23118 24935 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.849 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å21.68 Å2
2--4 Å20 Å2
3----1.35 Å2
Refinement stepCycle: 1 / Resolution: 2.4→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 1942 0 261 4802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0154931
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153636
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.7036878
X-RAY DIFFRACTIONr_angle_other_deg1.1131.5878368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6815.67778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92520.051197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17715519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7491540
X-RAY DIFFRACTIONr_chiral_restr0.1740.236800
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021090
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_it0.9912.1131198
X-RAY DIFFRACTIONr_mcbond_other0.9872.1111197
X-RAY DIFFRACTIONr_mcangle_it1.6323.1591487
X-RAY DIFFRACTIONr_mcangle_other1.6313.1611488
X-RAY DIFFRACTIONr_scbond_it1.1072.2263733
X-RAY DIFFRACTIONr_scbond_other1.1072.2263734
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7823.3195392
X-RAY DIFFRACTIONr_long_range_B_refined3.9857.98416204
X-RAY DIFFRACTIONr_long_range_B_other3.9857.98516205
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)
11A18200.15
12D18200.15
21A18560.14
22G18560.14
31A18070.13
32J18070.13
41A16480.12
42M16480.12
51B22410.05
52E22410.05
61B22490.04
62H22490.04
71B22320.07
72K22320.07
81D18450.15
82G18450.15
91D18410.12
92J18410.12
101D16660.12
102M16660.12
111E22240.05
112H22240.05
121E22290.04
122K22290.04
131G18740.11
132J18740.11
141G16790.12
142M16790.12
151H22070.07
152K22070.07
161J16910.1
162M16910.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 74 -
Rwork0.504 1861 -
obs--99.95 %
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)
17.1407-1.00152.74994.8804-0.94964.7331-0.2398-0.72940.08330.1750.1612-0.0757-0.1050.05090.07860.050.041-0.0820.24180.00990.18812.27044.499518.2767
23.076-1.88610.01897.2904-0.41655.8807-0.02560.02230.0524-0.2939-0.12120.06170.2650.26890.14670.1063-0.0211-0.12590.09670.05460.209413.0319-3.65927.659
34.5531-0.15650.4416.3137-0.42846.11870.19230.1369-0.095-0.5004-0.2560.04060.70020.37050.06370.26930.1251-0.13980.1143-0.02380.154517.5517-27.858711.2567
45.9787-0.2158-2.75144.30.40037.52150.12690.14650.106-0.0695-0.0346-0.52530.30421.203-0.09230.12780.0984-0.09720.38670.02240.269729.1891-26.130417.5515
53.0177-0.3691-0.41385.7616-0.01415.7080.0975-0.09350.14870.09360.0089-0.1345-0.2412-0.0717-0.10640.1018-0.0025-0.15470.04590.01110.308433.316718.83280.2739
66.90031.598-1.5474.3763-0.92884.2697-0.22850.4797-0.357-0.16650.1671-0.32150.22140.04860.06140.069-0.0336-0.09960.14790.03820.295432.2110.1724-9.342
74.12510.4782-0.625.57030.02515.5518-0.03270.04370.2384-0.06170.12450.4766-0.5168-0.6726-0.09180.34910.0627-0.16130.24610.06240.28745.8643-17.2258-20.9016
81.32370.2497-1.43453.3921-1.09678.4936-0.1248-0.10730.0335-0.0210.1965-0.15970.3443-0.0308-0.07160.2077-0.008-0.09440.2104-0.02510.24629.8391-29.958-17.311
93.8137-0.1509-0.01675.30730.461110.77250.06570.1460.04570.0223-0.0977-0.39510.25190.11150.0320.3766-0.0516-0.13860.1289-0.04940.418823.2171-1.3439-23.0917
100.5452-1.3155-1.42656.27531.25385.6509-0.1026-0.0227-0.01610.10150.33730.0830.05480.0534-0.23460.4809-0.06940.00880.4293-0.03710.518230.66317.771522.2198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 24
2X-RAY DIFFRACTION2A232 - 292
3X-RAY DIFFRACTION3D232 - 291
4X-RAY DIFFRACTION4E1 - 24
5X-RAY DIFFRACTION5G231 - 292
6X-RAY DIFFRACTION6H1 - 24
7X-RAY DIFFRACTION7J233 - 291
8X-RAY DIFFRACTION8K1 - 24
9X-RAY DIFFRACTION9M239 - 289
10X-RAY DIFFRACTION10P11 - 18

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