PDB-5umu: Crystal structure of the middle double PH domain of human FACT co...

ID or keywords:

Entry

Database: PDB / ID: 5umu

Title

Crystal structure of the middle double PH domain of human FACT complex subunit SPT16

Components

FACT complex subunit SPT16

Keywords

TRANSCRIPTION / Histone Chaperone / human FACT / PH domain

Function / homology

Function and homology information

FACT complex / positive regulation of DNA-templated transcription, elongation / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / nucleosome binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.903 Å

Authors

Hu, Q. / Thompson, J.R. / Heroux, A. / Su, D. / Botuyan, M.V. / Mer, G.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA132878	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM116829	United States

Citation

Journal: To Be Published
Title: Crystal structure of the middle double PH domain of human FACT complex subunit SPT16
Authors: Hu, Q. / Su, D. / Thompson, J.R. / Botuyan, M.V. / Mer, G.

History

Deposition	Jan 29, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5umu.cif.gz	339.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5umu.ent.gz	284.5 KB	Display	PDB format
PDBx/mmJSON format	5umu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5umu_validation.pdf.gz	463.7 KB	Display	wwPDB validaton report
Full document	5umu_full_validation.pdf.gz	465.1 KB	Display
Data in XML	5umu_validation.xml.gz	25.5 KB	Display
Data in CIF	5umu_validation.cif.gz	37.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/5umu ftp://data.pdbj.org/pub/pdb/validation_reports/um/5umu	HTTPS FTP

-
Related structure data

Related structure data	5umr 5ums 5umt
Similar structure data	4llo-4 4llo-2 4llo-1 5jcp-1 3h6s-3 6iyb-1 3dkg-d 3r5s-d 3rd6-2 3q7q-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: FACT complex subunit SPT16

B: FACT complex subunit SPT16

hetero molecules

68.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: FACT complex subunit SPT16

hetero molecules

defined by author&software
33.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: FACT complex subunit SPT16

hetero molecules

defined by author&software
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.221, 99.819, 120.314
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	FACT complex subunit SPT16 / Chromatin-specific transcription elongation factor 140 kDa subunit / FACT 140 kDa subunit / ...Chromatin-specific transcription elongation factor 140 kDa subunit / FACT 140 kDa subunit / FACTp140 / Facilitates chromatin transcription complex subunit SPT16 / hSPT16 Mass: 33305.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT16H, FACT140, FACTP140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5B9
#2: Chemical	... ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.82 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2% Tacsimate pH 5.0, 100 mM Sodium citrate tribasic dihydrate pH 5.6, 10-20% Polyethylene glycol 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 91465 / % possible obs: 99.8 % / Redundancy: 10.4 % / R_merge(I) obs: 0.096 / Net I/σ(I): 23.8
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 9.1 % / R_merge(I) obs: 0.613 / Num. unique obs: 4677 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.903→46.1 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.85 / Phase error: 16.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1911	3785	4.14 %
R_work	0.1567	-	-
obs	0.1581	91458	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.903→46.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4231	0	95	469	4795

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4510
X-RAY DIFFRACTION	f_angle_d	0.688	6055
X-RAY DIFFRACTION	f_dihedral_angle_d	11.06	2703
X-RAY DIFFRACTION	f_chiral_restr	0.047	659
X-RAY DIFFRACTION	f_plane_restr	0.004	776

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 (%)
1.9033-1.9274	0.2211	137	0.2311	3159	X-RAY DIFFRACTION	96
1.9274-1.9528	0.2408	136	0.2003	3252	X-RAY DIFFRACTION	100
1.9528-1.9795	0.2022	143	0.2001	3220	X-RAY DIFFRACTION	100
1.9795-2.0078	0.2479	141	0.1845	3295	X-RAY DIFFRACTION	100
2.0078-2.0378	0.2171	142	0.1858	3222	X-RAY DIFFRACTION	100
2.0378-2.0696	0.1854	132	0.1788	3247	X-RAY DIFFRACTION	100
2.0696-2.1036	0.1984	140	0.1749	3289	X-RAY DIFFRACTION	100
2.1036-2.1398	0.2283	137	0.1641	3212	X-RAY DIFFRACTION	100
2.1398-2.1788	0.1992	143	0.1597	3277	X-RAY DIFFRACTION	100
2.1788-2.2207	0.1769	136	0.1571	3217	X-RAY DIFFRACTION	100
2.2207-2.266	0.1584	145	0.1525	3279	X-RAY DIFFRACTION	100
2.266-2.3153	0.2154	142	0.1509	3242	X-RAY DIFFRACTION	100
2.3153-2.3691	0.1811	140	0.1492	3258	X-RAY DIFFRACTION	100
2.3691-2.4284	0.2175	143	0.1595	3219	X-RAY DIFFRACTION	100
2.4284-2.494	0.2131	140	0.1518	3279	X-RAY DIFFRACTION	100
2.494-2.5674	0.2207	141	0.154	3238	X-RAY DIFFRACTION	100
2.5674-2.6503	0.1878	143	0.1488	3282	X-RAY DIFFRACTION	100
2.6503-2.745	0.1561	141	0.1532	3225	X-RAY DIFFRACTION	100
2.745-2.8549	0.2225	139	0.1525	3244	X-RAY DIFFRACTION	100
2.8549-2.9848	0.1518	144	0.1524	3252	X-RAY DIFFRACTION	100
2.9848-3.1421	0.2077	138	0.154	3277	X-RAY DIFFRACTION	100
3.1421-3.3389	0.2039	138	0.1492	3270	X-RAY DIFFRACTION	100
3.3389-3.5966	0.2025	139	0.1467	3211	X-RAY DIFFRACTION	100
3.5966-3.9584	0.1827	142	0.1367	3265	X-RAY DIFFRACTION	100
3.9584-4.5307	0.151	142	0.1219	3240	X-RAY DIFFRACTION	100
4.5307-5.7065	0.1441	139	0.1387	3257	X-RAY DIFFRACTION	100
5.7065-46.1139	0.2248	142	0.205	3245	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	1.8287	0.0846	-0.1395	3.1761	0.516	1.9863	-0.0178	0.1579	-0.2492	0.0486	0.0341	0.0369	0.3575	-0.0624	-0.0265	0.1965	-0.0346	0.0638	0.1177	-0.0108	0.1499	23.4266	34.7917	70.1121
2	1.917	-1.4746	-0.6914	5.0809	1.8439	3.6902	-0.0731	-0.0133	-0.0535	-0.013	0.1236	-0.3963	0.2879	0.1215	-0.0725	0.1399	-0.0289	0.0718	0.1023	0.0154	0.1963	25.9909	46.3697	76.1123
3	4.8126	-0.1077	-1.3614	2.4789	0.2802	3.6111	-0.061	0.1072	0.2181	-0.0821	-0.04	0.2292	-0.0929	-0.6272	0.0985	0.089	0.0206	-0.0154	0.1742	-0.0057	0.1274	7.5758	64.1885	84.0399
4	1.7497	-0.6722	-0.154	2.2877	0.4293	2.3348	-0.1376	-0.2132	-0.1957	0.4865	0.0838	0.341	0.5376	-0.0613	0.0469	0.3378	-0.0109	0.1032	0.1334	-0.0089	0.1764	28.3217	33.9625	117.3801
5	1.9915	-0.0013	-0.2052	5.7274	-1.0312	4.2304	0.029	-0.0069	-0.1067	0.0962	0.0505	0.7943	0.2563	-0.2829	-0.0128	0.0857	-0.0204	0.0623	0.118	-0.0485	0.2615	25.3803	44.775	109.2666
6	3.6012	-0.6327	-0.7275	1.8382	-0.0172	4.0816	0.0616	0.1295	0.2784	-0.0169	-0.0642	-0.2516	-0.1611	0.6196	0.0453	0.0957	-0.0382	-0.006	0.1555	0.0038	0.1413	42.739	63.7976	102.504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 649 through 710 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 711 through 832 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 833 through 926 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 649 through 710 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 711 through 832 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 833 through 926 )

-
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://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