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

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Basic information

Entry
Database: PDB / ID: 5umu
TitleCrystal structure of the middle double PH domain of human FACT complex subunit SPT16
ComponentsFACT complex subunit SPT16FACT (biology)
KeywordsTRANSCRIPTION / Histone Chaperone / human FACT / PH domain
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
PH-domain like - #150 / : / 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 ...PH-domain like - #150 / : / 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 / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.903 Å
AuthorsHu, Q. / Thompson, J.R. / Heroux, A. / Su, D. / 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 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
DepositionJan 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)68,05732
Polymers66,6112
Non-polymers1,44630
Water8,449469
1
A: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,85813
Polymers33,3061
Non-polymers55212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,19919
Polymers33,3061
Non-polymers89418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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 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: 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 / Formic acid


Mass: 46.025 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 91465 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.613 / Num. unique obs: 4677 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1911 3785 4.14 %
Rwork0.1567 --
obs0.1581 91458 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.903→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 95 469 4795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044510
X-RAY DIFFRACTIONf_angle_d0.6886055
X-RAY DIFFRACTIONf_dihedral_angle_d11.062703
X-RAY DIFFRACTIONf_chiral_restr0.047659
X-RAY DIFFRACTIONf_plane_restr0.004776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9033-1.92740.22111370.23113159X-RAY DIFFRACTION96
1.9274-1.95280.24081360.20033252X-RAY DIFFRACTION100
1.9528-1.97950.20221430.20013220X-RAY DIFFRACTION100
1.9795-2.00780.24791410.18453295X-RAY DIFFRACTION100
2.0078-2.03780.21711420.18583222X-RAY DIFFRACTION100
2.0378-2.06960.18541320.17883247X-RAY DIFFRACTION100
2.0696-2.10360.19841400.17493289X-RAY DIFFRACTION100
2.1036-2.13980.22831370.16413212X-RAY DIFFRACTION100
2.1398-2.17880.19921430.15973277X-RAY DIFFRACTION100
2.1788-2.22070.17691360.15713217X-RAY DIFFRACTION100
2.2207-2.2660.15841450.15253279X-RAY DIFFRACTION100
2.266-2.31530.21541420.15093242X-RAY DIFFRACTION100
2.3153-2.36910.18111400.14923258X-RAY DIFFRACTION100
2.3691-2.42840.21751430.15953219X-RAY DIFFRACTION100
2.4284-2.4940.21311400.15183279X-RAY DIFFRACTION100
2.494-2.56740.22071410.1543238X-RAY DIFFRACTION100
2.5674-2.65030.18781430.14883282X-RAY DIFFRACTION100
2.6503-2.7450.15611410.15323225X-RAY DIFFRACTION100
2.745-2.85490.22251390.15253244X-RAY DIFFRACTION100
2.8549-2.98480.15181440.15243252X-RAY DIFFRACTION100
2.9848-3.14210.20771380.1543277X-RAY DIFFRACTION100
3.1421-3.33890.20391380.14923270X-RAY DIFFRACTION100
3.3389-3.59660.20251390.14673211X-RAY DIFFRACTION100
3.5966-3.95840.18271420.13673265X-RAY DIFFRACTION100
3.9584-4.53070.1511420.12193240X-RAY DIFFRACTION100
4.5307-5.70650.14411390.13873257X-RAY DIFFRACTION100
5.7065-46.11390.22481420.2053245X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.82870.0846-0.13953.17610.5161.9863-0.01780.1579-0.24920.04860.03410.03690.3575-0.0624-0.02650.1965-0.03460.06380.1177-0.01080.149923.426634.791770.1121
21.917-1.4746-0.69145.08091.84393.6902-0.0731-0.0133-0.0535-0.0130.1236-0.39630.28790.1215-0.07250.1399-0.02890.07180.10230.01540.196325.990946.369776.1123
34.8126-0.1077-1.36142.47890.28023.6111-0.0610.10720.2181-0.0821-0.040.2292-0.0929-0.62720.09850.0890.0206-0.01540.1742-0.00570.12747.575864.188584.0399
41.7497-0.6722-0.1542.28770.42932.3348-0.1376-0.2132-0.19570.48650.08380.3410.5376-0.06130.04690.3378-0.01090.10320.1334-0.00890.176428.321733.9625117.3801
51.9915-0.0013-0.20525.7274-1.03124.23040.029-0.0069-0.10670.09620.05050.79430.2563-0.2829-0.01280.0857-0.02040.06230.118-0.04850.261525.380344.775109.2666
63.6012-0.6327-0.72751.8382-0.01724.08160.06160.12950.2784-0.0169-0.0642-0.2516-0.16110.61960.04530.0957-0.0382-0.0060.15550.00380.141342.73963.7976102.504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 649 through 710 )
2X-RAY DIFFRACTION2chain 'A' and (resid 711 through 832 )
3X-RAY DIFFRACTION3chain 'A' and (resid 833 through 926 )
4X-RAY DIFFRACTION4chain 'B' and (resid 649 through 710 )
5X-RAY DIFFRACTION5chain 'B' and (resid 711 through 832 )
6X-RAY DIFFRACTION6chain 'B' and (resid 833 through 926 )

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