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- PDB-8i17: Structural basis for H2A-H2B recognitions by human Spt16 -

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Basic information

Entry
Database: PDB / ID: 8i17
TitleStructural basis for H2A-H2B recognitions by human Spt16
Components
  • FACT complex subunit SPT16
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
KeywordsCHAPERONE / histone chaperone / histone
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 / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / protein localization to CENP-A containing chromatin / nucleosome binding / RNA Polymerase II Transcription Elongation / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Formation of RNA Pol II elongation complex / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / RNA Polymerase II Pre-transcription Events / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / TP53 Regulates Transcription of DNA Repair Genes / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Regulation of TP53 Activity through Phosphorylation / killing of cells of another organism / Estrogen-dependent gene expression / transcription by RNA polymerase II / DNA replication / defense response to Gram-positive bacterium / Ub-specific processing proteases / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA repair / extracellular space / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-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, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-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 / Histone, subunit A / Histone, subunit A / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHuang, H. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171206 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural basis for H2A-H2B recognitions by human Spt16.
Authors: Li, Y. / Huang, H.
History
DepositionJan 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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 / _citation_author.name
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H2A type 1-B/E
B: Histone H2B type 1-J
D: Histone H2A type 1-B/E
E: Histone H2B type 1-J
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
F: FACT complex subunit SPT16
I: FACT complex subunit SPT16
C: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,88211
Polymers80,8119
Non-polymers712
Water1,72996
1
A: Histone H2A type 1-B/E
B: Histone H2B type 1-J
C: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9734
Polymers26,9373
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-62 kcal/mol
Surface area9930 Å2
MethodPISA
2
D: Histone H2A type 1-B/E
E: Histone H2B type 1-J
F: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9734
Polymers26,9373
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-61 kcal/mol
Surface area9670 Å2
MethodPISA
3
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: FACT complex subunit SPT16


Theoretical massNumber of molelcules
Total (without water)26,9373
Polymers26,9373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-46 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.852, 49.084, 85.195
Angle α, β, γ (deg.)85.95, 74.31, 61.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 11014.780 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli B (bacteria) / References: UniProt: P04908
#2: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 11253.011 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli B (bacteria) / References: UniProt: P06899
#3: Protein/peptide 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: 4669.268 Da / Num. of mol.: 3 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT16H, FACT140, FACTP140 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q9Y5B9
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 42483 / % possible obs: 94.8 % / Redundancy: 2.9 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Χ2: 1.015 / Net I/σ(I): 24.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.98-2.012.50.5118960.411186.6
2.01-2.052.70.41121200.452191.9
2.05-2.092.80.33720870.474194.9
2.09-2.132.90.29122160.474196.1
2.13-2.182.90.2320870.514195.9
2.18-2.232.90.19522160.545196
2.23-2.292.90.15820520.588194.6
2.29-2.352.90.13421670.667194.7
2.35-2.4230.11821500.695197.2
2.42-2.493.10.10821770.723196.5
2.49-2.5830.09221880.792196.5
2.58-2.6930.08120900.817196.4
2.69-2.812.90.07320830.993192.9
2.81-2.9630.06421791.125196.1
2.96-3.1430.06221601.439196.9
3.14-3.3930.05621711.697196.6
3.39-3.732.90.0520732.008192.2
3.73-4.263.10.04321761.813197.1
4.26-5.3730.0420951.765193.7
5.37-503.10.03921001.852193.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXPhenix1.19.2-4158refinement
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 1.98→40.191 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 2181 5.14 %
Rwork0.1704 --
obs0.1724 42470 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→40.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 2 96 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064394
X-RAY DIFFRACTIONf_angle_d0.7215923
X-RAY DIFFRACTIONf_dihedral_angle_d17.6192695
X-RAY DIFFRACTIONf_chiral_restr0.048683
X-RAY DIFFRACTIONf_plane_restr0.004762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02070.32631220.2862244X-RAY DIFFRACTION85
2.0207-2.06770.28171460.23782461X-RAY DIFFRACTION93
2.0677-2.11940.26651520.22342552X-RAY DIFFRACTION96
2.1194-2.17670.26261510.19972503X-RAY DIFFRACTION96
2.1767-2.24080.22161510.18682582X-RAY DIFFRACTION96
2.2408-2.31310.21811650.17152424X-RAY DIFFRACTION93
2.3131-2.39580.22671350.17462576X-RAY DIFFRACTION97
2.3958-2.49170.231190.17062621X-RAY DIFFRACTION97
2.4917-2.60510.22851260.17272609X-RAY DIFFRACTION97
2.6051-2.74240.23451120.18442576X-RAY DIFFRACTION96
2.7424-2.91420.21351470.18862462X-RAY DIFFRACTION94
2.9142-3.13910.23961430.18692557X-RAY DIFFRACTION97
3.1391-3.45480.20321540.17162562X-RAY DIFFRACTION96
3.4548-3.95440.18281190.15732502X-RAY DIFFRACTION94
3.9544-4.98060.16311170.14632574X-RAY DIFFRACTION96
4.9806-40.1910.22251220.16472484X-RAY DIFFRACTION93
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)
12.68770.3820.47566.83951.20794.56-0.0626-0.0843-0.0483-0.35860.05280.10530.2275-0.17310.0070.2807-0.1037-0.00580.3220.01070.19320.5078-2.3524-0.079
22.43250.73931.33823.49071.15544.5855-0.29490.05070.1771-0.28180.20430.0643-0.2719-0.03720.07830.2767-0.01640.02520.27420.01260.2531.4463.69530.5298
36.2311-3.23951.43464.3338-0.27372.67210.10030.0690.079-0.1604-0.045-0.01-0.1147-0.0225-0.03870.2868-0.0546-0.01410.24280.00550.240917.40482.499323.9936
45.1786-2.06671.38983.9126-1.05362.59420.0672-0.0138-0.1396-0.1504-0.0987-0.11330.06060.28920.03050.2225-0.02030.02550.273-0.02270.206122.487-0.694723.5929
55.07152.8519-0.57985.7754-1.81546.210.18250.2997-0.0130.6326-0.0202-0.1157-0.1560.315-0.14610.42620.0347-0.06480.4640.00720.229925.3602-9.872850.8652
62.60472.2965-1.64324.1773-2.68746.24570.3980.0179-0.04870.6317-0.17770.14380.08780.0067-0.20370.41710.0301-0.02550.30150.00940.311220.5954-13.327252.9631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 16 through 100)
2X-RAY DIFFRACTION2(chain 'B' and resid 35 through 124)
3X-RAY DIFFRACTION3(chain 'D' and resid 16 through 99)
4X-RAY DIFFRACTION4(chain 'E' and resid 34 through 124)
5X-RAY DIFFRACTION5(chain 'G' and resid 18 through 99)
6X-RAY DIFFRACTION6(chain 'H' and resid 34 through 123)

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