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- PDB-5xm2: Human N-terminal domain of FACT complex subunit SPT16 -

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Basic information

Entry
Database: PDB / ID: 5xm2
TitleHuman N-terminal domain of FACT complex subunit SPT16
ComponentsFACT complex subunit SPT16
KeywordsTRANSCRIPTION / FACT subunit / Spt16N / Histone chaperone / DNA damage repair
Function / homology
Function and homology information


FACT complex / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / 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 / Formation of HIV elongation complex in the absence of HIV Tat ...FACT complex / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / 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 / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / nucleosome binding / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / DNA repair / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain ...: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / PH-like domain superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.187 Å
AuthorsXu, S. / Li, H. / Dou, Y. / Chen, Y. / Jiang, H. / Lu, D. / Wang, M. / Su, D.
Funding support China, 5items
OrganizationGrant numberCountry
National Science Foundation of China31370735 China
National Science Foundation of China3167040397 China
Key Technology Research and Development Program of Sichuan Province2014KJT021-2014SZ China
Key Technology Research and Development Program of Sichuan Province2015JQO029 China
National Key Research and Development Program of China2017YFA0505900 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The structural basis of human Spt16 N-terminal domain interaction with histone (H3-H4)2tetramer.
Authors: Jiang, H. / Xu, S. / Chen, Y. / Li, H. / Tian, L. / Zhou, H. / Zhao, Z. / Yang, C. / Zhong, Z. / Cai, G. / Su, D.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACT complex subunit SPT16
B: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2405
Polymers98,9362
Non-polymers3043
Water4,738263
1
A: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5602
Polymers49,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6803
Polymers49,4681
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.983, 247.983, 247.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-731-

HOH

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Components

#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: 49467.895 Da / Num. of mol.: 2 / Fragment: UNP residues 1-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT16H, FACT140, FACTP140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5B9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Buffer composition of protein solution:20mM Hepes pH7.0, 200mM NaCl,1mM DTT,1Mm EDTA,5%Glycerol; Composition of reservoir protein: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 23% v/v ...Details: Buffer composition of protein solution:20mM Hepes pH7.0, 200mM NaCl,1mM DTT,1Mm EDTA,5%Glycerol; Composition of reservoir protein: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 23% v/v Jeffamine ED-2001 pH 7.0; Protein concentration 19.7 (mg /ml);

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.187→50 Å / Num. obs: 64924 / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.035 / Χ2: 0.686 / Net I/σ(I): 22.6
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 20.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4271 / Rpim(I) all: 0.194 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.187→41.33 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 3184 4.91 %0.05
Rwork0.1664 ---
obs0.1687 64859 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.187→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6794 0 20 263 7077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087104
X-RAY DIFFRACTIONf_angle_d1.0289568
X-RAY DIFFRACTIONf_dihedral_angle_d14.4262699
X-RAY DIFFRACTIONf_chiral_restr0.0451066
X-RAY DIFFRACTIONf_plane_restr0.0041229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1874-2.22010.3231250.21572742X-RAY DIFFRACTION100
2.2201-2.25480.2811570.20732652X-RAY DIFFRACTION100
2.2548-2.29170.26541340.19452605X-RAY DIFFRACTION100
2.2917-2.33130.28111720.19632643X-RAY DIFFRACTION100
2.3313-2.37360.24581280.19052719X-RAY DIFFRACTION100
2.3736-2.41930.25051440.19362622X-RAY DIFFRACTION100
2.4193-2.46870.28971350.18212730X-RAY DIFFRACTION100
2.4687-2.52230.25861550.18282601X-RAY DIFFRACTION100
2.5223-2.5810.23551280.18762703X-RAY DIFFRACTION100
2.581-2.64550.24271390.18522654X-RAY DIFFRACTION100
2.6455-2.71710.21981410.18782661X-RAY DIFFRACTION100
2.7171-2.7970.22921440.19222646X-RAY DIFFRACTION100
2.797-2.88730.25131160.18272726X-RAY DIFFRACTION100
2.8873-2.99040.17571210.18052672X-RAY DIFFRACTION100
2.9904-3.11010.28931350.1982684X-RAY DIFFRACTION100
3.1101-3.25160.25141500.19062670X-RAY DIFFRACTION100
3.2516-3.4230.21541410.18532688X-RAY DIFFRACTION100
3.423-3.63730.22221310.1682688X-RAY DIFFRACTION100
3.6373-3.91790.2081350.1542691X-RAY DIFFRACTION100
3.9179-4.31180.20141280.13342705X-RAY DIFFRACTION100
4.3118-4.93490.14321130.11952737X-RAY DIFFRACTION100
4.9349-6.2140.20131500.14632710X-RAY DIFFRACTION100
6.214-41.33790.16581620.15292726X-RAY DIFFRACTION98
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)
11.84050.4058-0.03350.68820.07551.8539-0.02110.0270.04460.0202-0.03010.04470.0047-0.03210.04260.23530.0013-0.00980.16730.00510.22653.6204-46.489-18.0464
21.52070.45190.23061.25370.06141.44570.0683-0.1057-0.10710.1134-0.0582-0.1940.0010.1475-0.0050.2161-0.0375-0.02650.18850.02030.260433.8792-45.6059-0.3856
31.67870.0137-0.16390.8160.29941.75710.0426-0.02910.00690.0646-0.03450.03730.05120.046-0.00860.23110.0014-0.00950.18650.00220.252217.8784-77.4512-3.446
41.54020.01490.22991.30440.38291.584-0.03030.14960.0003-0.1818-0.0540.096-0.1114-0.12680.07580.26750.0246-0.02360.182-0.03850.22320.1211-78.2452-33.8218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resseq 1:171)
2X-RAY DIFFRACTION2(chain B and resseq 172:432)
3X-RAY DIFFRACTION3(chain A and resseq 1:171)
4X-RAY DIFFRACTION4(chain A and resseq 172:432)

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