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- PDB-8pmc: transcription factor BARHL2 bound to TAATT DNA sequence -

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Basic information

Entry
Database: PDB / ID: 8pmc
Titletranscription factor BARHL2 bound to TAATT DNA sequence
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: 1.85 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
B: DNA
I: DNA
D: DNA
J: DNA
F: DNA
K: DNA
H: DNA
L: DNA
A: BarH-like 2 homeobox protein
C: BarH-like 2 homeobox protein
E: BarH-like 2 homeobox protein
G: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)59,45712
Polymers59,45712
Non-polymers00
Water5,675315
1
B: DNA
I: DNA
A: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)14,8643
Polymers14,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-16 kcal/mol
Surface area7580 Å2
MethodPISA
2
D: DNA
J: DNA
C: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)14,8643
Polymers14,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area7520 Å2
MethodPISA
3
F: DNA
K: DNA
E: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)14,8643
Polymers14,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-13 kcal/mol
Surface area7680 Å2
MethodPISA
4
H: DNA
L: DNA
G: BarH-like 2 homeobox protein


Theoretical massNumber of molelcules
Total (without water)14,8643
Polymers14,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-14 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.595, 123.148, 62.198
Angle α, β, γ (deg.)90.000, 94.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12B
22F
13B
23H
14D
24F
15D
25H
16F
26H
17A
27C
18A
28E
19A
29G
110C
210E
111C
211G
112E
212G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DCDCDGDGB - IA - B1 - 241 - 12
21DCDCDGDGD - JC - D1 - 241 - 12
12DCDCDGDGB - IA - B1 - 241 - 12
22DCDCDGDGF - KE - F1 - 241 - 12
13DCDCDGDGB - IA - B1 - 241 - 12
23DCDCDGDGH - LG - H1 - 241 - 12
14DCDCDGDGD - JC - D1 - 241 - 12
24DCDCDGDGF - KE - F1 - 241 - 12
15DCDCDGDGD - JC - D1 - 241 - 12
25DCDCDGDGH - LG - H1 - 241 - 12
16DCDCDGDGF - KE - F1 - 241 - 12
26DCDCDGDGH - LG - H1 - 241 - 12
17LYSLYSLYSLYSAI231 - 2881 - 58
27LYSLYSLYSLYSCJ231 - 2881 - 58
18PROPROGLNGLNAI232 - 2902 - 60
28PROPROGLNGLNEK232 - 2902 - 60
19PROPROGLNGLNAI232 - 2902 - 60
29PROPROGLNGLNGL232 - 2902 - 60
110PROPROLYSLYSCJ232 - 2882 - 58
210PROPROLYSLYSEK232 - 2882 - 58
111PROPROLYSLYSCJ232 - 2882 - 58
211PROPROLYSLYSGL232 - 2882 - 58
112PROPROTHRTHREK232 - 2912 - 61
212PROPROTHRTHRGL232 - 2912 - 61

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

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Components

#1: DNA chain
DNA


Mass: 3613.366 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain
DNA


Mass: 3711.442 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 51.85 %
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 PILATUS3 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: 1.85→43.7 Å / Num. obs: 50287 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.047 / Rrim(I) all: 0.093 / Net I/σ(I): 8.5 / Num. measured all: 190158
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
1.85-1.893.73.0191130030390.1541.7743.5130.496.2
9.07-43.73.50.02415604430.9980.0150.02937.997.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 11.977 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 2442 4.9 %RANDOM
Rwork0.2179 ---
obs0.2196 47812 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.3 Å2 / Biso mean: 45.478 Å2 / Biso min: 24.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20.65 Å2
2--0.51 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.85→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 1944 0 315 4330
Biso mean---45.87 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0144432
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153155
X-RAY DIFFRACTIONr_angle_refined_deg2.551.7396213
X-RAY DIFFRACTIONr_angle_other_deg1.251.5847289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8295.746733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.49319.937159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92615423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7531533
X-RAY DIFFRACTIONr_chiral_restr0.1860.239740
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02946
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B22620.05
12D22620.05
21B22310.07
22F22310.07
31B21550.1
32H21550.1
41D22320.08
42F22320.08
51D21440.12
52H21440.12
61F21640.1
62H21640.1
71A18490.11
72C18490.11
81A18830.12
82E18830.12
91A19160.12
92G19160.12
101C18500.1
102E18500.1
111C18850.11
112G18850.11
121E19320.14
122G19320.14
LS refinement shellResolution: 1.851→1.899 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 199 -
Rwork0.397 3453 -
all-3652 -
obs--96.87 %
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)
16.14540.22491.75043.5904-0.58413.1266-0.2418-0.51610.21530.16640.1595-0.2888-0.15230.12320.08220.04790.036-0.04710.1624-0.05390.256413.9085.327517.0134
26.0493-0.569-1.71733.0455-0.25173.7191-0.28130.5-0.1762-0.14880.1497-0.19490.16620.13240.13160.0617-0.0213-0.06740.13160.00180.274433.87256.5259-11.2095
33.7448-1.7569-1.46564.79651.71076.67470.0364-0.2170.2446-0.03770.1898-0.4519-0.040.3453-0.22620.0760.0434-0.14090.2065-0.03820.361331.8311-24.838920.1304
42.7850.10481.16575.5726-2.08854.24510.0010.1959-0.1234-0.3942-0.1302-0.10250.4154-0.09450.12920.18730.0144-0.16320.108-0.01550.279613.5311-27.9635-11.6042
54.9149-1.93310.50125.60470.3584.05330.0867-0.058-0.0517-0.23110.056-0.18890.0275-0.0396-0.14270.0341-0.0047-0.06340.03580.00430.214914.3383-4.06438.1797
63.85990.2784-0.20174.55120.70714.6848-0.04350.0210.0623-0.03340.0849-0.2503-0.11660.2797-0.04130.0354-0.0114-0.08990.04110.02560.289134.578516.0078-2.0682
73.8953-1.5295-0.26216.70360.96283.4455-0.0688-0.1385-0.2383-0.00630.0890.14230.1378-0.0214-0.02020.08890.0045-0.14730.09920.01430.290420.2782-28.153614.8235
83.8691-0.61990.7074.9343-1.11327.29190.10960.30850.1194-0.3562-0.1154-0.1198-0.190.04380.00570.16680.0818-0.12870.11440.0070.249910.5129-15.8845-15.9144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 24
2X-RAY DIFFRACTION2D1 - 24
3X-RAY DIFFRACTION3F1 - 24
4X-RAY DIFFRACTION4H1 - 24
5X-RAY DIFFRACTION5A231 - 292
6X-RAY DIFFRACTION6C231 - 289
7X-RAY DIFFRACTION7E232 - 291
8X-RAY DIFFRACTION8G232 - 291

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