PDB-4bhm: The crystal structure of MoSub1-DNA complex reveals a novel DNA b...

ID or keywords:

Entry

Database: PDB / ID: 4bhm

Title

The crystal structure of MoSub1-DNA complex reveals a novel DNA binding mode

Components

5'-D(*TP*TP*TP*TP*TP*TP*TP*TP)-3'
MOSUB1 TRANSCRIPTION COFACTOR

Keywords

TRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / SSDNA BINDING PROTEIN

Function / homology

Function and homology information

positive regulation of transcription initiation by RNA polymerase II / transcription coactivator activity / DNA binding / nucleus
Similarity search - Function

Biological species

MAGNAPORTHE ORYZAE (rice blast fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.7 Å

Authors

Huang, J. / Liu, H. / Zhao, Y. / Huang, D. / liu, J. / Peng, Y.

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	Apr 4, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4bhm.cif.gz	216 KB	Display	PDBx/mmCIF format
PDB format	pdb4bhm.ent.gz	176.4 KB	Display	PDB format
PDBx/mmJSON format	4bhm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4bhm_validation.pdf.gz	497.5 KB	Display	wwPDB validaton report
Full document	4bhm_full_validation.pdf.gz	506.3 KB	Display
Data in XML	4bhm_validation.xml.gz	20.2 KB	Display
Data in CIF	4bhm_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bh/4bhm ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bhm	HTTPS FTP

-
Related structure data

Related structure data	4usgC C: citing same article (ref.)
Similar structure data	4mcv-d 5k9i-d 4dgg-d 4xtk-1 3u51-d 4zti-1 4zcm-2 3d7u-1 3d7t-d 3e95-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MOSUB1 TRANSCRIPTION COFACTOR

B: MOSUB1 TRANSCRIPTION COFACTOR

C: MOSUB1 TRANSCRIPTION COFACTOR

D: MOSUB1 TRANSCRIPTION COFACTOR

E: MOSUB1 TRANSCRIPTION COFACTOR

F: MOSUB1 TRANSCRIPTION COFACTOR

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

H: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP)-3'

I: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP)-3'

hetero molecules

60.9 kDa, 9 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)	84.190, 57.970, 83.760
Angle α, β, γ (deg.)	90.00, 107.02, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	MOSUB1 TRANSCRIPTION COFACTOR Mass: 8875.049 Da / Num. of mol.: 6 / Fragment: RESIDUES 42-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MAGNAPORTHE ORYZAE (rice blast fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G4NEJ8
#2: DNA chain	5'-D(TPTPTPTPTPTPTPTP)-3' / SSDNA Mass: 2388.585 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) MAGNAPORTHE ORYZAE (rice blast fungus)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 31.61 % / Description: NONE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9715
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9715 Å / Relative weight: 1
Reflection	Resolution: 2.7→30 Å / Num. obs: 20278 / % possible obs: 94.3 % / Observed criterion σ(I): 2.15 / Redundancy: 2.9 % / B_iso Wilson estimate: 43.28 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 6.33

-
Processing

Software

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

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.7→29.171 Å / SU ML: 0.44 / σ(F): 1.24 / Phase error: 27.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2435	1872	5.2 %
R_work	0.1839	-	-
obs	0.187	20265	87.49 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→29.171 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3531	460	25	125	4141

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4285
X-RAY DIFFRACTION	f_angle_d	1.256	5838
X-RAY DIFFRACTION	f_dihedral_angle_d	20.136	1655
X-RAY DIFFRACTION	f_chiral_restr	0.084	612
X-RAY DIFFRACTION	f_plane_restr	0.004	680

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 (%)
2.7-2.773	0.382	139	0.2959	2773	X-RAY DIFFRACTION	91
2.773-2.8545	0.3073	130	0.2674	2652	X-RAY DIFFRACTION	88
2.8545-2.9465	0.2956	141	0.2518	2813	X-RAY DIFFRACTION	92
2.9465-3.0517	0.3531	200	0.2337	2827	X-RAY DIFFRACTION	93
3.0517-3.1738	0.2673	160	0.2195	2769	X-RAY DIFFRACTION	93
3.1738-3.318	0.2934	128	0.2011	2806	X-RAY DIFFRACTION	92
3.318-3.4927	0.2523	119	0.1883	2238	X-RAY DIFFRACTION	73
3.4927-3.7111	0.3025	115	0.2212	2061	X-RAY DIFFRACTION	69
3.7111-3.997	0.257	93	0.1817	2341	X-RAY DIFFRACTION	76
3.997-4.398	0.1955	172	0.1364	2816	X-RAY DIFFRACTION	93
4.398-5.0316	0.1683	168	0.1248	2756	X-RAY DIFFRACTION	92
5.0316-6.3286	0.2107	140	0.1593	2886	X-RAY DIFFRACTION	94
6.3286-29.1724	0.2184	167	0.17	2747	X-RAY DIFFRACTION	91

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	1.7655	1.1793	-0.7786	8.747	-6.7705	5.2233	0.1174	-0.4484	1.875	0.4064	-0.361	1.6256	-0.7513	-1.66	-0.5003	0.5496	0.2239	0.0053	0.7243	-0.1247	1.1134	20.767	18.5673	0.1938
2	1.7776	-0.0018	0.5767	6.9269	0.5456	3.8594	0.0977	-0.3888	0.143	0.1038	-0.2003	0.7133	-0.3217	-0.5922	0.0192	0.2902	0.0209	0.0303	0.4063	-0.0459	0.2827	26.4937	15.3182	6.6348
3	1.7862	-1.9711	-2.146	3.8019	1.2191	4.6792	0.0791	0.0518	-0.1722	-0.1086	-0.2187	0.5926	0.3711	-0.2877	0.1731	0.2658	-0.0449	-0.064	0.2839	-0.001	0.2895	34.3597	5.5805	4.1654
4	8.7485	2.6237	1.3279	8.7213	3.4288	6.5665	0.2832	-0.6352	-0.5285	0.893	-0.1494	-0.4718	-0.0311	0.4796	-0.2365	0.385	0.0233	-0.0121	0.3463	0.0378	0.2917	42.2499	2.9385	12.6678
5	3.2448	-0.2238	-0.6367	2.9442	-2.4608	5.4291	0.0731	-0.0538	0.0012	0.0975	-0.0421	-0.1901	-0.2522	0.1773	0.0163	0.3005	-0.0077	-0.0124	0.2382	-0.044	0.3506	34.7927	9.3582	3.0486
6	8.9268	3.0328	-1.5591	4.1818	2.7923	3.7251	1.356	1.2195	2.1287	-1.0323	-1.5085	-2.945	0.1166	-0.287	0.0497	1.0914	0.0782	0.2722	0.5932	0.2258	0.8393	40.1329	39.2445	21.5632
7	3.6648	-1.6294	0.5297	5.7995	-1.2248	3.5791	0.0489	0.1232	0.3112	-0.0113	0.0205	0.1731	-0.416	0.139	-0.0563	0.418	-0.0383	0.0195	0.2518	-0.0248	0.2522	30.3329	32.015	27.3544
8	4.2722	4.2881	3.9947	4.6403	3.5966	4.3454	0.451	0.9129	0.2636	-0.5867	-0.2047	-1.1695	0.2511	0.5531	-0.1235	1.0907	0.0068	0.1306	0.4924	0.0862	0.4863	34.5086	12.7895	31.3953
9	6.8233	-2.0472	-4.1122	3.8247	-1.8514	5.4376	0.2446	-0.1145	-0.0521	-0.2845	0.2339	2.0562	-0.4377	-0.3439	-0.2062	0.5961	0.0829	0.0604	0.5172	0.0936	0.7193	15.8758	19.1726	39.1587
10	5.532	0.96	-2.0336	7.9241	-2.1046	6.4148	0.1075	-0.0988	0.1905	0.597	0.1366	0.8769	0.0414	-0.4525	-0.0685	0.4931	-0.003	0.0503	0.361	0.0945	0.3487	19.9076	25.8416	36.1226
11	5.9882	2.2526	0.1501	5.406	1.5112	2.9151	-0.0279	-0.281	0.0573	0.1311	-0.061	0.1246	-0.0378	-0.36	0.0508	0.4895	0.026	0.0564	0.3135	0.0486	0.1644	27.833	28.1701	31.211
12	9.178	1.788	0.9784	8.3669	2.5389	2.2421	-0.0627	0.7488	-0.1887	-1.198	0.3784	0.0768	0.3134	0.4234	-0.2028	0.628	-0.0057	-0.1122	0.3978	-0.0102	0.4364	10.6781	-16.9657	-4.7179
13	8.3688	-1.6795	-0.9728	5.0604	-2.0936	5.962	0.0509	0.33	-0.1505	-0.3607	-0.1163	0.1353	0.2129	0.1957	0.0863	0.3397	-0.0159	-0.0967	0.2353	-0.0364	0.4603	7.395	-12.4132	5.0454
14	3.9527	-3.4528	-1.439	3.0837	0.6478	6.1588	-0.3585	-1.0141	1.1807	1.0884	-0.1972	-0.2616	-1.0912	0.669	0.0097	0.9994	-0.1231	-0.1578	0.5479	-0.1711	0.7561	4.5572	-1.0226	20.7168
15	2.6082	-1.5246	-2.9999	6.265	4.1716	4.4813	-0.1906	-1.6736	-0.0056	1.6202	0.4633	-0.4629	0.1296	0.428	0.0953	0.6239	-0.0522	-0.1552	0.4473	0.0645	0.5642	8.4469	-11.4423	18.7884
16	7.1056	0.3115	0.9159	2.716	-4.8434	8.9842	-0.0966	-0.375	0.7179	0.9866	0.0514	-0.4925	-1.07	-0.2873	0.1291	0.3748	0.0043	-0.0762	0.2918	-0.0709	0.5195	7.4289	-2.8463	12.8384
17	6.0156	-1.3793	1.5752	7.3186	-4.5792	8.9815	-0.0692	0.3723	1.22	0.6685	-0.2117	-1.0959	-0.4188	-0.0508	0.3405	0.4082	0.0066	-0.0434	0.2235	-0.0338	0.5975	7.6614	-0.5668	8.1855
18	9.1104	3.6377	2.7648	2.404	-0.7548	5.6815	0.3838	-1.6291	-0.0164	1.0946	0.1087	-0.0318	-0.286	0.0076	-0.0497	0.6192	-0.0758	-0.0352	0.6161	0.0769	0.4009	17.4701	-4.1434	19.2916
19	5.9808	2.7053	1.4651	8.5058	1.6853	2.8403	0.0337	-0.0961	-0.1318	-0.1839	0.1852	0.6543	0.3268	-0.2034	-0.0502	0.4368	0.0552	-0.1082	0.3296	-0.015	0.4525	2.3974	-17.4363	3.4263
20	2.5275	-1.2477	-0.8789	5.7265	0.0432	2.6852	-0.422	-0.7923	0.5293	0.4672	0.499	0.7286	-0.5389	-0.117	-0.2233	0.8478	0.1243	-0.0967	0.518	-0.1255	0.5652	25.5226	22.8141	17.1731
21	9.2287	-1.408	0.2852	5.9973	-2.2137	5.905	0.4912	-1.2544	-0.1652	0.2112	0.136	-0.1475	-0.1926	-0.0155	-0.5414	0.554	0.0255	0.1562	0.4072	-0.0224	0.4125	25.2747	2.1748	14.5658
22	7.8152	1.3866	4.8763	4.7257	2.1699	9.082	0.3268	1.0884	-0.0984	0.3262	0.9412	-0.0495	-0.5082	1.4897	-1.3458	0.4087	0.0375	-0.041	0.5381	-0.1078	0.4932	22.0172	40.67	15.4291

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 38 THROUGH 47 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 48 THROUGH 76 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 77 THROUGH 116 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 39 THROUGH 75 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 76 THROUGH 116 )
6	X-RAY DIFFRACTION	6	CHAIN C AND (RESID 38 THROUGH 47 )
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESID 48 THROUGH 111 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 112 THROUGH 116 )
9	X-RAY DIFFRACTION	9	CHAIN D AND (RESID 39 THROUGH 47 )
10	X-RAY DIFFRACTION	10	CHAIN D AND (RESID 48 THROUGH 62 )
11	X-RAY DIFFRACTION	11	CHAIN D AND (RESID 63 THROUGH 116 )
12	X-RAY DIFFRACTION	12	CHAIN E AND (RESID 40 THROUGH 62 )
13	X-RAY DIFFRACTION	13	CHAIN E AND (RESID 63 THROUGH 116 )
14	X-RAY DIFFRACTION	14	CHAIN F AND (RESID 39 THROUGH 47 )
15	X-RAY DIFFRACTION	15	CHAIN F AND (RESID 48 THROUGH 54 )
16	X-RAY DIFFRACTION	16	CHAIN F AND (RESID 55 THROUGH 62 )
17	X-RAY DIFFRACTION	17	CHAIN F AND (RESID 63 THROUGH 72 )
18	X-RAY DIFFRACTION	18	CHAIN F AND (RESID 73 THROUGH 85 )
19	X-RAY DIFFRACTION	19	CHAIN F AND (RESID 86 THROUGH 116 )
20	X-RAY DIFFRACTION	20	CHAIN G AND (RESID 14 THROUGH 21 )
21	X-RAY DIFFRACTION	21	CHAIN H AND (RESID 17 THROUGH 24 )
22	X-RAY DIFFRACTION	22	CHAIN I AND (RESID 14 THROUGH 20 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-
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

-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

-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

-
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

-
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