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- PDB-6kbb: Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition -

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Basic information

Entry
Database: PDB / ID: 6kbb
TitleRole of the DEF/Y motif of Swc5 in histone H2A.Z deposition
Components
  • Histone H2A type 1-D
  • Histone H2B type 2-E
  • SWR1-complex protein 5
KeywordsTRANSCRIPTION / Histone chaperone
Function / homology
Function and homology information


: / Swr1 complex / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 ...: / Swr1 complex / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / 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 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / defense response to Gram-positive bacterium / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
BCNT-C domain / Bucentaur or craniofacial development / Bucentaur C-terminal (BCNT-C) domain profile. / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...BCNT-C domain / Bucentaur or craniofacial development / Bucentaur C-terminal (BCNT-C) domain profile. / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A type 1-D / SWR1-complex protein 5 / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.365 Å
AuthorsHuang, Y. / Zhou, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing.
Authors: Huang, Y. / Sun, L. / Pierrakeas, L. / Dai, L. / Pan, L. / Luk, E. / Zhou, Z.
History
DepositionJun 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Histone H2A type 1-D
D: Histone H2B type 2-E
F: SWR1-complex protein 5
A: Histone H2A type 1-D
B: Histone H2B type 2-E
E: SWR1-complex protein 5


Theoretical massNumber of molelcules
Total (without water)62,1086
Polymers62,1086
Non-polymers00
Water1,06359
1
C: Histone H2A type 1-D
D: Histone H2B type 2-E
F: SWR1-complex protein 5


Theoretical massNumber of molelcules
Total (without water)31,0543
Polymers31,0543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-47 kcal/mol
Surface area10740 Å2
MethodPISA
2
A: Histone H2A type 1-D
B: Histone H2B type 2-E
E: SWR1-complex protein 5


Theoretical massNumber of molelcules
Total (without water)31,0543
Polymers31,0543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-44 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.072, 65.521, 84.821
Angle α, β, γ (deg.)90.000, 122.830, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 16 through 98)
21chain C
12(chain B and resid 31 through 123)
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLYGLY(chain A and resid 16 through 98)AD16 - 986 - 88
21THRTHRGLYGLYchain CCA16 - 986 - 88
12ARGARGSERSER(chain B and resid 31 through 123)BE31 - 12310 - 102
22ARGARGSERSERchain DDB31 - 12310 - 102

NCS ensembles :
ID
1
2

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Components

#1: Protein Histone H2A type 1-D / Histone H2A.3 / Histone H2A/g


Mass: 10466.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AD, H2AFG / Production host: Escherichia coli (E. coli) / References: UniProt: P20671
#2: Protein Histone H2B type 2-E / Histone H2B-GL105 / Histone H2B.q / H2B/q


Mass: 11645.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H2BE, H2BFQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q16778
#3: Protein SWR1-complex protein 5


Mass: 8942.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SWC5, AOR1, YBR231C, YBR1529 / Production host: Escherichia coli (E. coli) / References: UniProt: P38326
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate tribasic dihydrate, pH 5.3, 19.5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.365→50 Å / Num. obs: 20109 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.76 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.235
Reflection shellResolution: 2.365→2.49 Å / Rmerge(I) obs: 0.953 / Num. unique obs: 1999

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CV5

2cv5


Resolution: 2.365→44.986 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2256 969 4.93 %
Rwork0.1876 --
obs0.1894 19642 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.14 Å2 / Biso mean: 50.6289 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 2.365→44.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 59 3067
Biso mean---45.97 -
Num. residues----381
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A512X-RAY DIFFRACTION8.488TORSIONAL
12C512X-RAY DIFFRACTION8.488TORSIONAL
21B566X-RAY DIFFRACTION8.488TORSIONAL
22D566X-RAY DIFFRACTION8.488TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3648-2.48950.2661190.2492164228378
2.4895-2.64540.28541420.23192688283098
2.6454-2.84960.2771330.218327432876100
2.8496-3.13630.25781510.207227582909100
3.1363-3.590.21751280.193327452873100
3.59-4.52240.19371590.154827542913100
4.5224-44.9940.20551370.171228212958100
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)
14.88910.4289-0.1835.45684.93844.54410.45250.13170.3811-0.035-1.14240.6062-1.79170.55630.74311.2839-0.0695-0.17171.123-0.28541.0442-22.661-37.837106.112
23.4427-1.1523-1.62921.27850.95953.8538-0.13280.24260.0093-0.08040.1878-0.0898-0.20390.7695-0.07220.54390.0405-0.070.4004-0.1160.4234-33.284-33.224111.296
32.0145-8.413-7.57016.02365.41854.8553-0.1946-0.3016-0.30020.00510.7954-0.22090.13381.5542-0.5170.63620.091-0.1030.6699-0.16380.454-31.909-30.058121.922
42.88980.11262.8411.95151.97226.4973-0.1315-0.0718-0.04970.59620.5331-0.36710.33020.2762-0.3560.49310.1444-0.00540.3316-0.04280.3511-37.413-48.42101.945
53.59310.9754-0.09483.09360.45756.8071-0.0391-0.314-0.08120.5796-0.02870.22320.1613-0.92810.05620.34760.0760.06720.33970.08160.2694-48.253-51.1998.117
60.8154-1.5464-1.57074.34084.90395.69480.3609-0.0025-0.1410.1554-0.1508-0.23570.22470.011-0.16960.6740.0243-0.03820.488-0.05210.5495-42.455-31.2104.608
73.25070.89150.75684.93241.89554.26640.0140.51080.3253-0.20850.2046-0.6131-0.190.7875-0.21190.28650.0570.06540.3411-0.03090.3526-36.089-43.18993.163
80.40940.3880.60791.37861.27191.1329-0.558-1.01480.58350.98880.1623-0.105-0.6317-1.25470.42060.85560.2652-0.05560.723-0.21290.4839-42.831-39.36112.95
91.43420.8109-0.64460.57840.18193.28490.0594-1.14320.43040.6560.29570.34671.14310.94450.29231.20760.2575-0.25070.93-0.19070.5786-31.436-37.731126.615
102.9063-0.8666-0.25774.13590.87813.9220.1015-0.5770.02690.8560.2537-0.89880.70840.384-0.32370.83160.3168-0.13480.6154-0.08340.3717-31.927-48.566115.082
118.17266.02743.95876.749-0.02216.21670.7608-0.0068-0.8793-0.193-0.77770.70361.03220.96840.11390.62510.18590.02970.91420.08150.7511-64.951-41.14886.604
122.11091.58132.74633.30420.27185.42220.16721.12270.2236-0.25980.29620.2335-0.368-0.056-0.4270.53250.14780.05910.36910.08990.467-49.002-38.71986.473
133.5285-3.6095-3.45373.87024.00864.9883-0.4598-1.1510.29321.22220.2692-0.3472-0.33030.60890.07810.40630.078-0.04330.49580.03050.3787-64.741-31.78589.305
143.12790.2371-0.49482.99661.39894.5777-0.2061-0.0831-0.28820.16870.0422-0.01230.23920.02550.19420.22680.00240.00850.24150.00770.2713-65.2-36.22477.66
154.0756-3.5027-3.26455.77615.50725.3181-0.3312-0.39730.32620.32890.68860.3296-0.05211.0051-0.4470.346-0.0235-0.00250.4658-0.09310.4008-54.596-39.14974.655
164.7465-1.7355-1.00061.50380.04530.4671-0.0007-0.05880.67580.18650.1097-0.2972-0.1575-0.0458-0.11220.2486-0.0049-0.00460.2-0.03880.2709-75.469-21.23677.447
175.5225-3.5286-4.99514.643.48077.9329-0.25260.226-0.67470.04020.17581.1636-0.1625-0.24230.12530.246-0.02790.07020.34280.04980.2913-92.479-21.60776.101
189.55083.6591-1.5132.84730.02422.6703-0.20580.94570.4395-0.99350.34370.3862-0.0258-0.0956-0.18530.2602-0.0097-0.01790.32050.05220.2628-85.252-17.37667.673
196.645-2.7378-1.62332.5549-2.50477.52130.20870.64430.4499-0.4543-0.6146-0.2907-0.2135-0.43440.32420.36490.0436-0.01860.35820.06430.327-75.849-18.02764.732
203.5281-2.18180.12767.6260.980.8797-0.1738-0.1785-0.32920.43360.04510.02020.1884-0.07130.07770.1721-0.02150.02190.19430.03390.2263-80.519-30.02979.572
213.5902-2.7959-0.07251.5741-0.60190.70140.07010.8001-0.4054-0.1804-0.1995-0.3170.03090.12560.19810.278-0.00760.01160.3351-0.06750.3901-64.458-30.53369.043
224.6504-1.07381.34193.769-1.08465.6834-0.1375-0.33970.84650.22460.0059-0.561-0.21410.01440.10650.2196-0.03650.00050.2445-0.09740.464-61.178-21.16177.252
232.3053-0.9366-2.07762.50861.08911.91330.0533-1.1722-0.96340.3083-0.03050.8433-0.6426-2.0967-0.17980.8087-0.19160.3921.3589-0.12221.4131-90.53-33.19179.044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 17:22 )C17 - 22
2X-RAY DIFFRACTION2( CHAIN C AND RESID 23:38 )C23 - 38
3X-RAY DIFFRACTION3( CHAIN C AND RESID 39:45 )C39 - 45
4X-RAY DIFFRACTION4( CHAIN C AND RESID 46:73 )C46 - 73
5X-RAY DIFFRACTION5( CHAIN C AND RESID 74:98 )C74 - 98
6X-RAY DIFFRACTION6( CHAIN D AND RESID 32:38 )D32 - 38
7X-RAY DIFFRACTION7( CHAIN D AND RESID 39:56 )D39 - 56
8X-RAY DIFFRACTION8( CHAIN D AND RESID 57:84 )D57 - 84
9X-RAY DIFFRACTION9( CHAIN D AND RESID 85:91 )D85 - 91
10X-RAY DIFFRACTION10( CHAIN D AND RESID 92:123 )D92 - 123
11X-RAY DIFFRACTION11( CHAIN F AND RESID 15:19 )F15 - 19
12X-RAY DIFFRACTION12( CHAIN F AND RESID 20:31 )F20 - 31
13X-RAY DIFFRACTION13( CHAIN A AND RESID 16:22 )A16 - 22
14X-RAY DIFFRACTION14( CHAIN A AND RESID 23:38 )A23 - 38
15X-RAY DIFFRACTION15( CHAIN A AND RESID 39:45 )A39 - 45
16X-RAY DIFFRACTION16( CHAIN A AND RESID 46:73 )A46 - 73
17X-RAY DIFFRACTION17( CHAIN A AND RESID 74:80 )A74 - 80
18X-RAY DIFFRACTION18( CHAIN A AND RESID 81:89 )A81 - 89
19X-RAY DIFFRACTION19( CHAIN A AND RESID 90:100 )A90 - 100
20X-RAY DIFFRACTION20( CHAIN B AND RESID 32:56 )B32 - 56
21X-RAY DIFFRACTION21( CHAIN B AND RESID 57:91 )B57 - 91
22X-RAY DIFFRACTION22( CHAIN B AND RESID 92:124 )B92 - 124
23X-RAY DIFFRACTION23( CHAIN E AND RESID 26:31 )E26 - 31

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