PDB-4usg: Crystal structure of PC4 W89Y mutant complex with DNA

ID or keywords:

Entry

Database: PDB / ID: 4usg

Title

Crystal structure of PC4 W89Y mutant complex with DNA

Components

5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*TP*G)-3'
ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15

Keywords

TRANSCRIPTION

Function / homology

Function and homology information

negative regulation of DNA metabolic process / negative regulation of DNA duplex unwinding / RNA polymerase II promoter clearance / positive regulation of transcription initiation by RNA polymerase II / single-stranded DNA binding / transcription regulator complex / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleolus / regulation of transcription by RNA polymerase II ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 1.973 Å

Authors

Zhao, Y. / Liu, J.

Citation

Journal: Sci.Rep. / Year: 2015
Title: Substitution of Tryptophan 89 with Tyrosine Switches the DNA Binding Mode of Pc4.
Authors: Huang, J. / Zhao, Y. / Liu, H. / Huang, D. / Cheng, X. / Zhao, W. / Taylor, I.A. / Liu, J. / Peng, Y.L.

History

Deposition	Jul 8, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4usg.cif.gz	83.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4usg.ent.gz	64.6 KB	Display	PDB format
PDBx/mmJSON format	4usg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4usg_validation.pdf.gz	432.5 KB	Display	wwPDB validaton report
Full document	4usg_full_validation.pdf.gz	434.4 KB	Display
Data in XML	4usg_validation.xml.gz	8.9 KB	Display
Data in CIF	4usg_validation.cif.gz	12.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/us/4usg ftp://data.pdbj.org/pub/pdb/validation_reports/us/4usg	HTTPS FTP

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Related structure data

Related structure data	4bhmC C: citing same article (ref.)
Similar structure data	1wbc-d 3tc2-1 3ped-1 4zhg-5 4qae-3 5kic-2 4h9w-d 1fyv-d 4wbc-d 3tc2-2 Search similar-shape structures by Omokage search (details) 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) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
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Thymine Dimers
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DNA Helicase
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#253 - Jan 2021
Expressome
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#172 - Apr 2014
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#180 - Dec 2014
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#135 - Mar 2011
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#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
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similarity (1)
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lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#31 - Jul 2002
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similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
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similarity (1)
#119 - Nov 2009
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similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
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#23 - Nov 2001
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Deposited unit

A: ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15

B: ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15

C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*TP*G)-3'

21.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	67.660, 67.660, 120.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15 / POSITIVE COFACTOR 4 / PC4 / SUB1 HOMOLOG / P14 Mass: 7760.988 Da / Num. of mol.: 2 / Fragment: RESIDUES 63-217 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53999
#2: DNA chain	5'-D(TPTPTPTPTPTPTPTPTPTPTPTPTPTP TPTPTPTPTPG)-3' / DT19G1 Mass: 6063.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	MUTATION AT 89,FROM W TO Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.85 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 287 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.97→47.8 Å / Num. obs: 20387 / % possible obs: 100 % / Observed criterion σ(I): 6.8 / Redundancy: 2 % / B_iso Wilson estimate: 24.1 Å² / R_merge(I) obs: 0.01

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.973→47.843 Å / SU ML: 0.18 / σ(F): 0.62 / Phase error: 19.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.212	3691	9.8 %
R_work	0.1853	-	-
obs	0.1879	20386	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.973→47.843 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1086	280	0	128	1494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1410
X-RAY DIFFRACTION	f_angle_d	1.192	1942
X-RAY DIFFRACTION	f_dihedral_angle_d	21.483	582
X-RAY DIFFRACTION	f_chiral_restr	0.05	206
X-RAY DIFFRACTION	f_plane_restr	0.007	206

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.973-1.999	0.2993	139	0.2361	1306	X-RAY DIFFRACTION	100
1.999-2.0264	0.2213	140	0.2247	1275	X-RAY DIFFRACTION	100
2.0264-2.0553	0.2363	140	0.1876	1335	X-RAY DIFFRACTION	100
2.0553-2.086	0.258	135	0.1881	1278	X-RAY DIFFRACTION	100
2.086-2.1186	0.2303	149	0.1957	1326	X-RAY DIFFRACTION	100
2.1186-2.1533	0.1897	143	0.179	1278	X-RAY DIFFRACTION	100
2.1533-2.1905	0.211	150	0.1675	1322	X-RAY DIFFRACTION	100
2.1905-2.2303	0.1725	145	0.1604	1307	X-RAY DIFFRACTION	100
2.2303-2.2732	0.205	146	0.1708	1296	X-RAY DIFFRACTION	100
2.2732-2.3196	0.177	143	0.1839	1280	X-RAY DIFFRACTION	100
2.3196-2.37	0.2205	140	0.1796	1306	X-RAY DIFFRACTION	100
2.37-2.4252	0.2051	138	0.1802	1299	X-RAY DIFFRACTION	100
2.4252-2.4858	0.2102	144	0.1819	1316	X-RAY DIFFRACTION	100
2.4858-2.553	0.2418	140	0.1881	1288	X-RAY DIFFRACTION	100
2.553-2.6281	0.2462	143	0.197	1318	X-RAY DIFFRACTION	100
2.6281-2.7129	0.2496	142	0.1831	1315	X-RAY DIFFRACTION	100
2.7129-2.8099	0.2224	137	0.1942	1317	X-RAY DIFFRACTION	100
2.8099-2.9224	0.242	138	0.1894	1294	X-RAY DIFFRACTION	100
2.9224-3.0554	0.2238	139	0.1966	1298	X-RAY DIFFRACTION	100
3.0554-3.2164	0.1864	137	0.1878	1310	X-RAY DIFFRACTION	100
3.2164-3.4179	0.1994	146	0.1663	1304	X-RAY DIFFRACTION	100
3.4179-3.6817	0.2059	139	0.165	1302	X-RAY DIFFRACTION	100
3.6817-4.052	0.1686	141	0.1655	1309	X-RAY DIFFRACTION	100
4.052-4.6379	0.1664	147	0.1645	1298	X-RAY DIFFRACTION	100
4.6379-5.8417	0.203	143	0.2029	1302	X-RAY DIFFRACTION	100
5.8417-47.8569	0.2905	147	0.2381	1302	X-RAY DIFFRACTION	100

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	3.4655	1.1783	1.802	3.2589	0.1007	0.9773	-0.0132	0.1685	0.1001	-0.2202	-0.0397	-0.2538	-0.1785	-0.0106	-0.0556	0.2154	-0.0129	0.0326	0.1344	-0.0133	0.1545	-19.1568	18.7444	6.1739
2	6.3488	4.6046	2.7529	4.4221	2.9698	2.7619	0.0415	0.0156	-0.009	-0.1042	0.1503	-0.7536	-0.1523	-0.0045	-0.1624	0.2112	0.0301	0.0923	0.1059	-0.0588	0.2573	-12.7009	20.5381	9.879
3	8.0171	-1.3006	-5.2167	2.8013	0.2732	5.5783	-0.2018	0.0039	-0.3843	-0.0409	0.1162	0.2685	0.3229	-0.327	0.0894	0.1785	-0.0244	0.0015	0.1469	0.0103	0.1427	-33.719	8.2871	13.8375
4	4.19	0.5422	0.69	4.0028	0.3482	4.5004	0.134	-0.537	-0.0654	0.2985	-0.0264	-0.1307	-0.1593	0.1165	-0.0632	0.2215	-0.0139	0.0359	0.1542	-0.0141	0.1577	-25.923	6.5191	20.2261
5	6.2502	-4.7249	1.0653	8.6359	0.291	1.3445	-0.0973	-0.2133	0.1379	0.6097	0.0641	-0.4698	0.0125	-0.1291	0.0263	0.2123	-0.024	-0.0057	0.1402	-0.022	0.1358	-19.1319	6.7889	21.0216
6	6.0772	1.2182	2.8287	1.8456	1.2596	2.6911	0.015	-0.2319	0.5921	-0.3099	0.0565	0.0858	-0.3915	-0.5085	0.1904	0.2404	0.0475	0.0366	0.1755	-0.0233	0.2452	-31.823	20.173	12.9486
7	7.5172	-2.0801	-3.8874	3.1867	2.9011	3.2889	0.0855	0.4993	0.2505	-0.2968	-0.1079	0.0064	-0.5068	-0.5385	-0.0021	0.3002	0.0292	-0.0482	0.2373	-0.0023	0.2056	-29.844	15.3119	-2.1216
8	2.4345	1.0615	0.8311	4.2714	-1.9325	4.518	-0.2942	-0.2519	-0.3582	0.0513	-0.0016	-0.6359	-0.3072	0.3364	0.2232	0.4489	0.0045	-0.0178	0.3257	-0.0702	0.5782	-13.6033	12.9056	15.9931

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 62 THROUGH 90 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 91 THROUGH 106 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 107 THROUGH 127 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 62 THROUGH 79 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 80 THROUGH 106 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 107 THROUGH 116 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 117 THROUGH 127 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 5 THROUGH 22 )

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