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- PDB-5umt: Crystal structure of N-terminal domain of human FACT complex subu... -

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Basic information

Entry
Database: PDB / ID: 5umt
TitleCrystal structure of N-terminal domain of human FACT complex subunit SPT16
ComponentsFACT complex subunit SPT16FACT (biology)
KeywordsTRANSCRIPTION / Histone chaperone / FACT complex / SPT16
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 / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 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 / nucleosome binding / 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 / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / Regulation of TP53 Activity through Phosphorylation / DNA replication / 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
FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsSu, D. / Hu, Q. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: To Be Published
Title: Crystal structure of N-terminal domain of human FACT complex subunit SPT16
Authors: Hu, Q. / Su, D. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
History
DepositionJan 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_detector ...chem_comp / diffrn_detector / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _diffrn_detector.detector ..._chem_comp.name / _diffrn_detector.detector / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,74511
Polymers49,0951
Non-polymers65110
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.249, 78.068, 111.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FACT complex subunit SPT16 / FACT (biology) / 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: 49094.582 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10mM HEPES, 150mM NaCl, 5% glycerol, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→33.48 Å / Num. obs: 32096 / % possible obs: 99.4 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.2
Reflection shellResolution: 2.09→2.17 Å / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 2190 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIXdev_972refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CB6

3cb6


Resolution: 2.092→33.479 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 1982 6.18 %
Rwork0.1717 --
obs0.1735 32096 98.2 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.488 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2811 Å2-0 Å20 Å2
2---1.5592 Å20 Å2
3---3.8403 Å2
Refinement stepCycle: LAST / Resolution: 2.092→33.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 42 414 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033673
X-RAY DIFFRACTIONf_angle_d0.5574933
X-RAY DIFFRACTIONf_dihedral_angle_d12.0061423
X-RAY DIFFRACTIONf_chiral_restr0.052550
X-RAY DIFFRACTIONf_plane_restr0.003628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0923-2.14470.22691340.18952056X-RAY DIFFRACTION95
2.1447-2.20260.18491390.17812088X-RAY DIFFRACTION97
2.2026-2.26740.2131370.18142065X-RAY DIFFRACTION95
2.2674-2.34060.25351400.17742098X-RAY DIFFRACTION98
2.3406-2.42420.25451420.18172149X-RAY DIFFRACTION99
2.4242-2.52130.19881390.16242125X-RAY DIFFRACTION99
2.5213-2.6360.22291410.17032145X-RAY DIFFRACTION99
2.636-2.77490.26741430.17642177X-RAY DIFFRACTION99
2.7749-2.94860.20411420.16532169X-RAY DIFFRACTION100
2.9486-3.17610.20041440.16452178X-RAY DIFFRACTION100
3.1761-3.49550.2071440.1752179X-RAY DIFFRACTION99
3.4955-4.00050.19651420.16582181X-RAY DIFFRACTION98
4.0005-5.03750.14051430.14022189X-RAY DIFFRACTION98
5.0375-33.48290.2111520.20652315X-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)
13.03580.5863-0.67013.9415-0.21134.7299-0.0240.18570.2281-0.22570.0328-0.1402-0.1765-0.02640.0070.15320.00490.05520.2020.02630.235323.631623.209510.11
21.7320.8515-0.37531.9647-0.33640.899-0.07350.1118-0.1163-0.15590.0333-0.03160.1083-0.03810.04180.19130.0378-0.0080.17450.02090.14921.6921-1.810417.6676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 157 )
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 434 )

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