PDB-8pnc: Transcription factor BARHL2 bound to TAAGT DNA sequence

ID or keywords:

Entry

Database: PDB / ID: 8pnc

Title

Transcription factor BARHL2 bound to TAAGT DNA sequence

Components

(DNA) x 2
BarH-like 2 homeobox protein

Keywords

TRANSCRIPTION / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.05 Å

Authors

Morgunova, E. / Popov, A. / Yin, Y. / Taipale, J.

Funding support

1items

Citation

Journal: 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

Deposition	Jun 30, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pnc.cif.gz	230.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8pnc.ent.gz	179.6 KB	Display	PDB format
PDBx/mmJSON format	8pnc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pnc_validation.pdf.gz	486.9 KB	Display	wwPDB validaton report
Full document	8pnc_full_validation.pdf.gz	497.7 KB	Display
Data in XML	8pnc_validation.xml.gz	19.9 KB	Display
Data in CIF	8pnc_validation.cif.gz	28.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnc ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnc	HTTPS FTP

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Related structure data

Related structure data	7z5iC 7z5kC 8pm5C 8pm7C 8pmcC 8pmfC 8pmnC 8pmvC 8pn4C 8pnaC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (7) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

B: DNA

A: BarH-like 2 homeobox protein

D: DNA

C: DNA

E: BarH-like 2 homeobox protein

F: DNA

G: DNA

H: BarH-like 2 homeobox protein

I: DNA

J: DNA

K: BarH-like 2 homeobox protein

L: DNA

59.5 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: DNA

A: BarH-like 2 homeobox protein

D: DNA

defined by author&software
14.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: DNA

E: BarH-like 2 homeobox protein

F: DNA

defined by author&software
14.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: DNA

H: BarH-like 2 homeobox protein

I: DNA

defined by author&software
14.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: DNA

K: BarH-like 2 homeobox protein

L: DNA

defined by author&software
14.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.519, 123.711, 62.365
Angle α, β, γ (deg.)	90.000, 93.940, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	DC	DC	DT	DT	B	A	1 - 12	1 - 12
2	1	DC	DC	DT	DT	C	D	1 - 12	1 - 12
1	2	DC	DC	DT	DT	B	A	1 - 12	1 - 12
2	2	DC	DC	DT	DT	G	G	1 - 12	1 - 12
1	3	DC	DC	DT	DT	B	A	1 - 12	1 - 12
2	3	DC	DC	DT	DT	J	J	1 - 12	1 - 12
1	4	PRO	PRO	ALA	ALA	A	B	232 - 292	2 - 62
2	4	PRO	PRO	ALA	ALA	E	E	232 - 292	2 - 62
1	5	PRO	PRO	ARG	ARG	A	B	232 - 289	2 - 59
2	5	PRO	PRO	ARG	ARG	H	H	232 - 289	2 - 59
1	6	PRO	PRO	GLN	GLN	A	B	232 - 290	2 - 60
2	6	PRO	PRO	GLN	GLN	K	K	232 - 290	2 - 60
1	7	DA	DA	DG	DG	D	C	1 - 12	1 - 12
2	7	DA	DA	DG	DG	F	F	1 - 12	1 - 12
1	8	DA	DA	DG	DG	D	C	1 - 12	1 - 12
2	8	DA	DA	DG	DG	I	I	1 - 12	1 - 12
1	9	DA	DA	DG	DG	D	C	1 - 12	1 - 12
2	9	DA	DA	DG	DG	L	L	1 - 12	1 - 12
1	10	DC	DC	DT	DT	C	D	1 - 12	1 - 12
2	10	DC	DC	DT	DT	G	G	1 - 12	1 - 12
1	11	DC	DC	DT	DT	C	D	1 - 12	1 - 12
2	11	DC	DC	DT	DT	J	J	1 - 12	1 - 12
1	12	PRO	PRO	ARG	ARG	E	E	232 - 289	2 - 59
2	12	PRO	PRO	ARG	ARG	H	H	232 - 289	2 - 59
1	13	PRO	PRO	GLN	GLN	E	E	232 - 290	2 - 60
2	13	PRO	PRO	GLN	GLN	K	K	232 - 290	2 - 60
1	14	DA	DA	DG	DG	F	F	1 - 12	1 - 12
2	14	DA	DA	DG	DG	I	I	1 - 12	1 - 12
1	15	DA	DA	DG	DG	F	F	1 - 12	1 - 12
2	15	DA	DA	DG	DG	L	L	1 - 12	1 - 12
1	16	DC	DC	DT	DT	G	G	1 - 12	1 - 12
2	16	DC	DC	DT	DT	J	J	1 - 12	1 - 12
1	17	LYS	LYS	ARG	ARG	H	H	231 - 289	1 - 59
2	17	LYS	LYS	ARG	ARG	K	K	231 - 289	1 - 59
1	18	DA	DA	DG	DG	I	I	1 - 12	1 - 12
2	18	DA	DA	DG	DG	L	L	1 - 12	1 - 12

NCS ensembles :

#1: DNA chain	DNA Mass: 3693.414 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: 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
#3: DNA chain	DNA Mass: 3631.394 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.: 351 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 52.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: PEG 4000, sodium malonate, sodium acetate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.8856 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.8856 Å / Relative weight: 1

Reflection

Resolution: 2.05→43.87 Å / Num. obs: 37375 / % possible obs: 99.6 % / Redundancy: 5.2 % / CC_1/2: 0.993 / R_merge(I) obs: 0.17 / R_pim(I) all: 0.083 / R_rim(I) all: 0.19 / Net I/σ(I): 7.7 / Num. measured all: 194035 / Scaling rejects: 215

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.05-2.11	4.8	2.305	13664	2846	0.188	1.176	2.599	0.8	97.1
8.93-43.87	5.1	0.049	2389	469	0.994	0.023	0.055	28.1	98.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.7	data scaling
PHASER		phasing
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→39.46 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.931 / SU B: 15.007 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2672	1912	5.1 %	RANDOM
R_work	0.232	-	-	-
obs	0.2337	35433	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 109.37 Å² / B_iso mean: 41.355 Å² / B_iso min: 20.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.07 Å²	0 Å²	-0.35 Å²
2-	-	1.18 Å²	0 Å²
3-	-	-	-0.06 Å²

Refinement step

Cycle: final / Resolution: 2.05→39.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2085	1944	0	351	4380
B_iso mean	-	-	-	43.43	-
Num. residues	-	-	-	-	339

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	4471
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	3184
X-RAY DIFFRACTION	r_angle_refined_deg	2.397	1.707	6272
X-RAY DIFFRACTION	r_angle_other_deg	1.183	1.584	7351
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.041	5.636	741
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.717	20.244	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.121	15	427
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.324	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.204	0.239	745
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	3645
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	961

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	B	1085	0.06
1	2	C	1085	0.06
2	1	B	1081	0.06
2	2	G	1081	0.06
3	1	B	1085	0.05
3	2	J	1085	0.05
4	1	A	2033	0.1
4	2	E	2033	0.1
5	1	A	1961	0.09
5	2	H	1961	0.09
6	1	A	2002	0.1
6	2	K	2002	0.1
7	1	D	1021	0.08
7	2	F	1021	0.08
8	1	D	1014	0.08
8	2	I	1014	0.08
9	1	D	1022	0.08
9	2	L	1022	0.08
10	1	C	1100	0.03
10	2	G	1100	0.03
11	1	C	1090	0.06
11	2	J	1090	0.06
12	1	E	1925	0.11
12	2	H	1925	0.11
13	1	E	1946	0.12
13	2	K	1946	0.12
14	1	F	1028	0.04
14	2	I	1028	0.04
15	1	F	1036	0.05
15	2	L	1036	0.05
16	1	G	1089	0.06
16	2	J	1089	0.06
17	1	H	1966	0.09
17	2	K	1966	0.09
18	1	I	1027	0.06
18	2	L	1027	0.06

LS refinement shell

Resolution: 2.05→2.102 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_free	0.41	145	-
R_work	0.366	2555	-
obs	-	-	96.81 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.8123	-0.1783	0.3803	2.5981	0.9837	4.371	-0.0038	-0.068	0.0435	0.0786	-0.0361	-0.0703	0.3088	0.1531	0.0399	0.2343	0.0059	-0.0279	0.0221	0.0102	0.4065	6.197	-7.084	12.117
2	3.0758	-0.1848	0.2669	3.4613	0.0726	3.8352	0.1449	-0.3058	0.0338	0.3552	-0.0195	-0.0139	-0.052	0.1232	-0.1254	0.2196	-0.0696	0.0009	0.0581	0.0032	0.4591	9.334	4.806	16.799
3	4.8133	0.1784	0.8787	2.8533	0.7776	2.7809	-0.3723	0.8606	0.5228	-0.3237	0.2936	0.1448	-0.2718	-0.0317	0.0787	0.1032	-0.0795	0.0281	0.2076	0.0962	0.426	6.156	25.301	-17.319
4	4.2139	1.2114	0.457	4.1008	-0.1117	4.5745	0.015	0.0995	-0.026	0.1544	-0.0163	0.0404	0.1864	-0.0554	0.0013	0.0178	-0.0058	0.0383	0.0045	-0.0156	0.3859	5.295	15.999	-8.027
5	6.0717	1.1742	-2.4227	2.6506	0.5121	3.6473	-0.2999	-0.4924	-0.0133	0.2215	0.2136	0.0571	0.0451	-0.1486	0.0863	0.0796	0.0831	0.0149	0.1903	-0.0042	0.3704	25.504	27.711	10.698
6	4.4056	-0.6473	-0.3982	4.7484	-0.4126	4.4739	-0.0386	-0.019	0.1747	-0.1287	0.0707	0.1436	-0.208	-0.1585	-0.0321	0.0476	-0.0152	0.0434	0.0212	-0.0443	0.3826	24.697	37.005	1.816
7	3.9085	0.6235	-1.0372	3.5957	-1.0307	5.6091	0.0765	-0.0466	0.1201	0.0091	0.1585	0.2529	0.2349	-0.4206	-0.235	0.1356	-0.0586	-0.0497	0.1109	0.001	0.4819	-11.906	-4.048	-19.622
8	5.2056	0.56	0.3917	4.815	-0.7121	2.7363	0.0788	-0.0477	-0.4482	0.0314	-0.1062	-0.2871	0.2232	-0.0812	0.0274	0.1359	-0.0308	-0.0108	0.0118	0.0342	0.3911	-0.796	-7.806	-14.807

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 12
2	X-RAY DIFFRACTION	1	D	1 - 12
3	X-RAY DIFFRACTION	2	A	232 - 292
4	X-RAY DIFFRACTION	3	C	1 - 12
5	X-RAY DIFFRACTION	3	F	1 - 12
6	X-RAY DIFFRACTION	4	E	232 - 292
7	X-RAY DIFFRACTION	5	G	1 - 12
8	X-RAY DIFFRACTION	5	I	1 - 12
9	X-RAY DIFFRACTION	6	H	231 - 290
10	X-RAY DIFFRACTION	7	J	1 - 12
11	X-RAY DIFFRACTION	7	L	1 - 12
12	X-RAY DIFFRACTION	8	K	231 - 291

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi