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- PDB-5e5a: Crystal structure of the chromatin-tethering domain of Human cyto... -

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Basic information

Entry
Database: PDB / ID: 5e5a
TitleCrystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle
Components
  • C-terminal domain of Regulatory protein IE1
  • DNA (146-MER)
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsPROTEIN BINDING/VIRAL PROTEIN/DNA / NCP / IE1 / hCMV / CTD / PROTEIN BINDING-VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-templated viral transcription / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein heterodimerization activity / host cell nucleus ...DNA-templated viral transcription / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein heterodimerization activity / host cell nucleus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Immediate early protein IE1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A / Regulatory protein IE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Human herpesvirus 5 strain Towne
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.809 Å
AuthorsFang, Q. / Chen, P. / Wang, M. / Fang, J. / Yang, N. / Li, G. / Xu, R.M.
Funding support China, 7items
OrganizationGrant numberCountry
Ministry Ministry of Science and Technologyof Science and Technology2015CB856200 China
National Natural Science Foundation of China31430018 China
National Natural Science Foundation of China31521002 China
National Natural Science Foundation of China91219202 China
National Natural Science Foundation of China31471218 China
National Natural Science Foundation of China31210103914 China
Strategic Priority Research Program of Chinese Academy of SciencesXDB08010100 China
CitationJournal: Elife / Year: 2016
Title: Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome
Authors: Fang, Q. / Chen, P. / Wang, M. / Fang, J. / Yang, N. / Li, G. / Xu, R.M.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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
I: DNA (146-MER)
J: DNA (146-MER)
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
K: C-terminal domain of Regulatory protein IE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,10115
Polymers201,00311
Non-polymers974
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59180 Å2
ΔGint-400 kcal/mol
Surface area72740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.700, 109.474, 181.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain E
12chain B
22chain F
13chain C
23chain G
14chain D
24chain H
15chain I
25chain J

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
11LYSLYSALAALAchain AAC37 - 13538 - 136
21PROPROALAALAchain EEG38 - 13539 - 136
12ASPASPGLYGLYchain BBD24 - 10225 - 103
22ARGARGGLYGLYchain FFH17 - 10218 - 103
13ALAALALYSLYSchain CCE14 - 11815 - 119
23ALAALALYSLYSchain GGI14 - 11815 - 119
14LYSLYSALAALAchain DDF24 - 12125 - 122
24LYSLYSALAALAchain HHJ28 - 12129 - 122
15DADADTDTchain IIA1 - 1461 - 146
25DADADTDTchain JJB147 - 2921 - 146

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P84233
#3: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P62799
#4: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#5: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P02281

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DNA chain / Protein/peptide , 2 types, 3 molecules IJK

#1: DNA chain DNA (146-MER)


Mass: 45054.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
#6: Protein/peptide C-terminal domain of Regulatory protein IE1


Mass: 1703.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 5 strain Towne / References: UniProt: Q6SWP6, UniProt: P03169*PLUS

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Non-polymers , 2 types, 234 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.64 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: sodium cacodylate, magnesium acetate, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.0308 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0308 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 52496 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.33 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.056 / Rrim(I) all: 0.144 / Χ2: 1.022 / Net I/av σ(I): 12.5 / Net I/σ(I): 5 / Num. measured all: 346849
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.60.61151380.8560.2560.6640.999100
2.9-3.026.40.45751920.910.1940.4970.992100
3.02-3.156.90.3652000.9540.1460.3891.003100
3.15-3.326.90.25351990.9690.1040.2741.011100
3.32-3.536.60.19252020.9780.0810.2091.018100
3.53-3.86.50.14452100.9870.0610.1561.03499.9
3.8-4.186.90.12352290.990.050.1331.047100
4.18-4.786.40.152800.990.0420.1091.002100
4.78-6.026.80.09653180.9920.0390.1041.036100
6.02-306.20.07655280.9840.0340.0831.07499.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1AOI

1aoi


Resolution: 2.809→30 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2615 4.99 %Random selection
Rwork0.1955 49744 --
obs0.1978 52359 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.06 Å2 / Biso mean: 60.7308 Å2 / Biso min: 15.14 Å2
Refinement stepCycle: final / Resolution: 2.809→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6174 5983 4 230 12391
Biso mean--40.77 34.99 -
Num. residues----1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812986
X-RAY DIFFRACTIONf_angle_d0.94718790
X-RAY DIFFRACTIONf_chiral_restr0.0432137
X-RAY DIFFRACTIONf_plane_restr0.0041368
X-RAY DIFFRACTIONf_dihedral_angle_d26.8035357
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A954X-RAY DIFFRACTION5.128TORSIONAL
12E954X-RAY DIFFRACTION5.128TORSIONAL
21B732X-RAY DIFFRACTION5.128TORSIONAL
22F732X-RAY DIFFRACTION5.128TORSIONAL
31C992X-RAY DIFFRACTION5.128TORSIONAL
32G992X-RAY DIFFRACTION5.128TORSIONAL
41D846X-RAY DIFFRACTION5.128TORSIONAL
42H846X-RAY DIFFRACTION5.128TORSIONAL
51I2912X-RAY DIFFRACTION5.128TORSIONAL
52J2912X-RAY DIFFRACTION5.128TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8094-2.86040.29611140.26032415252993
2.8604-2.91540.33611350.25825902725100
2.9154-2.97490.36021310.260526072738100
2.9749-3.03950.33551280.256626332761100
3.0395-3.11010.26151460.25325482694100
3.1101-3.18780.30071450.24225882733100
3.1878-3.27390.27131320.243725972729100
3.2739-3.37010.24121310.223626222753100
3.3701-3.47870.30171350.214326232758100
3.4787-3.60290.26431330.20926022735100
3.6029-3.74690.26751280.206526362764100
3.7469-3.91710.22681590.205226322791100
3.9171-4.12310.26161400.192426092749100
4.1231-4.38070.24341280.182426432771100
4.3807-4.71780.25521480.173526132761100
4.7178-5.19030.20821350.175426742809100
5.1903-5.93640.24181460.182526662812100
5.9364-7.46040.21571440.180726702814100
7.4604-30.12130.1571570.1332776293398

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