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- PDB-5kdm: Crystal structure of EBV tegument protein BNRF1 in complex with h... -

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Basic information

Entry
Database: PDB / ID: 5kdm
TitleCrystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4
Components
  • Death domain-associated protein 6
  • Histone H3.3H3F3A
  • Histone H4
  • Major tegument protein
KeywordsCHAPERONE / DNA BINDING PROTEIN / histone chaperone / Gene repression / CHAPERONE - DNA BINDING PROTEIN complex
Function / homology
Function and homology information


cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / intracellular transport of virus / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / viral tegument / transcription regulator inhibitor activity / nucleosomal DNA binding ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / intracellular transport of virus / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / viral tegument / transcription regulator inhibitor activity / nucleosomal DNA binding / nuclear androgen receptor binding / protein kinase activator activity / androgen receptor signaling pathway / chromosome, centromeric region / regulation of protein ubiquitination / extrinsic apoptotic signaling pathway via death domain receptors / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of protein kinase activity / cellular response to unfolded protein / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / 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 / JNK cascade / cellular response to copper ion / cellular response to cadmium ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / heat shock protein binding / Meiotic synapsis / telomere organization / molecular condensate scaffold activity / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SUMOylation of transcription cofactors / 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 / 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 / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PML body / PKMTs methylate histone lysines / 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 / transcription corepressor activity / nucleosome / Regulation of TP53 Degradation / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / regulation of gene expression / regulation of apoptotic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / transcription coactivator activity / nuclear body / chromatin remodeling / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription
Similarity search - Function
Herpes virus tegument protein / Tegument protein, herpes virus, N-terminal domain / dsDNA viral tegument protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2170 / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain ...Herpes virus tegument protein / Tegument protein, herpes virus, N-terminal domain / dsDNA viral tegument protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2170 / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Histone, subunit A / Histone, subunit A / Class I glutamine amidotransferase-like / Histone H4, conserved site / Histone H4 signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Histone H3.3 / Major tegument protein / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHuang, H. / Patel, D.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis underlying viral hijacking of a histone chaperone complex.
Authors: Huang, H. / Deng, Z. / Vladimirova, O. / Wiedmer, A. / Lu, F. / Lieberman, P.M. / Patel, D.J.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_struct_oper_list
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: Death domain-associated protein 6
D: Major tegument protein


Theoretical massNumber of molelcules
Total (without water)74,6334
Polymers74,6334
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.216, 161.216, 117.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone H3.3 / H3F3A


Mass: 15229.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-codon plus / References: UniProt: P84243
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-codon plus / References: UniProt: P62805
#3: Protein Death domain-associated protein 6 / Daxx / hDaxx / ETS1-associated protein 1 / EAP1 / Fas death domain-associated protein


Mass: 24725.328 Da / Num. of mol.: 1 / Fragment: residues 178-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Production host: Escherichia coli BL21(DE3) coli (bacteria) / Strain (production host): BL21(DE3)-codon plus / References: UniProt: Q9UER7
#4: Protein Major tegument protein / MTP / Protein p140


Mass: 23414.498 Da / Num. of mol.: 1 / Fragment: residues 381-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain AG876) / Strain: AG876 / Gene: BNRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-codon plus / References: UniProt: Q1HVJ0

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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: 5.92 Å3/Da / Density % sol: 79.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH 6.0, 0.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 22487 / % possible obs: 99.2 % / Redundancy: 11 % / Net I/σ(I): 14.6
Reflection shellResolution: 3.4→3.73 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H9N

4h9n


Resolution: 3.5→48.157 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.22
RfactorNum. reflection% reflection
Rfree0.2796 1134 5.04 %
Rwork0.2345 --
obs0.2368 22487 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 0 0 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134418
X-RAY DIFFRACTIONf_angle_d1.6835975
X-RAY DIFFRACTIONf_dihedral_angle_d18.7031656
X-RAY DIFFRACTIONf_chiral_restr0.062674
X-RAY DIFFRACTIONf_plane_restr0.01783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4974-3.65650.3841440.37572615X-RAY DIFFRACTION98
3.6565-3.84920.38171390.3452625X-RAY DIFFRACTION99
3.8492-4.09030.30861250.30662645X-RAY DIFFRACTION99
4.0903-4.40590.29571400.26522643X-RAY DIFFRACTION99
4.4059-4.84890.30691450.22762653X-RAY DIFFRACTION99
4.8489-5.54970.2521540.22152676X-RAY DIFFRACTION99
5.5497-6.98860.27951350.26562706X-RAY DIFFRACTION99
6.9886-48.16160.24581520.1762790X-RAY DIFFRACTION99
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)
10.68770.8384-0.76990.7997-0.42150.24780.27340.24310.71031.5177-0.583-0.381.21550.9257-0.00471.1479-0.21680.13551.46570.03631.5116-0.8411-73.8828-8.4967
20.47840.1864-0.773-0.0001-0.54830.63830.8531.74650.2880.2748-0.3586-1.8257-0.38971.18530.00221.31650.04940.15351.7676-0.01441.24428.097-70.7517-21.7987
31.01650.08940.39631.64892.13752.0526-0.3132.025-0.3575-0.4994-0.37750.4908-0.38491.968-0.00551.41150.20190.18932.135-0.17451.241520.1207-74.1355-39.6488
41.9599-0.63841.70560.1972-0.34730.9280.54370.15410.237-0.8553-1.07890.4091-0.05120.0866-0.00251.13110.00710.06511.40950.11091.362617.8889-61.4049-26.924
50.8115-0.3626-0.37320.15810.27080.353.8426-0.03160.34861.4115-3.86761.1561-2.76860.1402-0.00351.8338-0.13050.34781.61190.10041.611715.0526-40.1377-28.0438
60.5486-0.016-0.13390.0879-0.28720.03880.07020.57310.47380.2467-0.20590.5996-1.60770.78370.00150.9627-0.0148-0.04061.3333-0.11991.476626.1064-48.497-27.8847
70.78870.74790.1022.1634-1.24861.0751-0.50480.56231.69510.602-0.97042.081.2695-3.227-0.00251.17360.1358-0.22771.3008-0.03631.6159.0496-56.6256-34.8126
81.9498-0.1138-1.61940.1571-0.21082.09691.09753.6180.75830.12960.1036-1.03620.0798-4.609-0.0161.59210.397-0.0671.85590.09641.829510.7726-47.4165-31.0117
9-0.02390.42970.99230.95890.81584.78770.4290.4486-0.1136-1.5502-0.1533-0.30.24890.04430.00030.9885-0.18670.05151.56940.24081.696125.1551-65.2312-34.9155
100.1107-0.20030.180.1407-0.2590.34771.49163.62030.7077-0.7812-1.136-1.21.79060.0621-0.01411.21960.27560.10711.3747-0.18481.857128.4111-84.0033-31.3692
111.98880.5965-0.89880.266-0.66651.45660.012-0.2203-1.0360.82890.1848-0.9308-0.18241.194201.15270.22150.12851.6757-0.09671.204626.7876-69.9949-21.094
120.9436-0.71310.70733.045-1.30231.15360.7612-0.5781-1.65210.8751-0.8339-1.3306-0.6170.9714-0.01261.31970.0198-0.22481.38380.1021.2854-0.6262-84.6413-19.1378
130.88472.13861.56741.15461.01374.2326-0.2053-0.06950.3027-0.24730.10890.7348-0.14360.0026-0.00061.39970.13510.10841.4309-0.05631.27515.0282-68.5307-21.0955
143.49-1.6550.29291.245-1.0571.61610.3996-0.63171.0094-1.0729-1.01390.3363-2.2343-2.51630.00421.93620.27720.37261.4587-0.11942.08495.5559-43.5241-14.4514
151.2457-0.19410.20672.9678-2.08190.6746-0.11790.01230.7445-0.0265-0.1614-0.4017-0.1480.3020.00071.35440.0367-0.07771.4066-0.0031.413124.0149-57.6821-21.9661
163.87650.00870.20473.1547-3.50063.0810.12950.1074-0.73940.26220.45140.1815-0.1729-0.33020.00331.2192-0.1083-0.01511.0126-0.0581.316718.0622-82.33460.8554
172.47763.0822-1.13174.9025-2.27251.90240.1399-0.6748-0.23241.2599-0.6243-1.21770.38350.297-0.00011.34050.0024-0.24941.34880.01431.282119.9511-80.01017.6435
181.75290.4985-1.21540.28280.03540.7588-0.2139-1.29230.36341.76740.308-0.7783-0.13530.54090.00521.517-0.0637-0.30281.5907-0.07441.29624.0415-69.71928.28
194.44820.1099-3.42972.5131-1.34143.1523-0.3356-0.2841-0.05740.2635-0.04450.480.1619-0.5967-0.00091.1969-0.07920.01491.33080.03341.41968.7416-83.77565.6928
201.5508-0.1461.38742.423-1.76371.53041.3127-0.93550.0150.8828-1.2678-0.2313-1.1960.00330.01171.45130.11430.011.3546-0.2581.293913.7714-66.95350.5588
210.49450.1322-0.54841.2594-1.37950.54750.18771.57751.52540.9144-0.91180.058-0.96060.3730.00381.2875-0.2481-0.11041.8731-0.0921.602319.0787-67.7711-2.801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 109 )
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 40 )
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 47 )
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 102 )
12X-RAY DIFFRACTION12chain 'C' and (resid 182 through 207 )
13X-RAY DIFFRACTION13chain 'C' and (resid 208 through 266 )
14X-RAY DIFFRACTION14chain 'C' and (resid 267 through 299 )
15X-RAY DIFFRACTION15chain 'C' and (resid 300 through 386 )
16X-RAY DIFFRACTION16chain 'D' and (resid 383 through 413 )
17X-RAY DIFFRACTION17chain 'D' and (resid 414 through 488 )
18X-RAY DIFFRACTION18chain 'D' and (resid 489 through 512 )
19X-RAY DIFFRACTION19chain 'D' and (resid 513 through 546 )
20X-RAY DIFFRACTION20chain 'D' and (resid 547 through 564 )
21X-RAY DIFFRACTION21chain 'D' and (resid 565 through 581 )

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