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- PDB-1zla: X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bo... -

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Basic information

Entry
Database: PDB / ID: 1zla
TitleX-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core
Components
  • Histone H4
  • Palindromic 146bp Human alpha-Satellite DNA fragment
  • Xenopus laevis-like histone H2A
  • histone H2B
  • histone H3
  • latent nuclear antigen
KeywordsSTRUCTURAL PROTEIN/DNA / Latency Associated Nuclear Antigen (LANA) / Kaposi's sarcoma Herpes Virus (KSHV) / Nucleosome core particle / chromatin / protein/protein interaction / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / host cell nucleus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / 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 ...Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / 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 H4, conserved site / Histone H4 signature. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / : / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 ...: / : / : / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Latent nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Expression vector pET3-H2A (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChodaparambil, J.V. / Barbera, A.J. / Kaye, K.M. / Luger, K.
CitationJournal: Science / Year: 2006
Title: The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA.
Authors: Barbera, A.J. / Chodaparambil, J.V. / Kelley-Clarke, B. / Joukov, V. / Walter, J.C. / Luger, K. / Kaye, K.M.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Palindromic 146bp Human alpha-Satellite DNA fragment
J: Palindromic 146bp Human alpha-Satellite DNA fragment
A: histone H3
B: Histone H4
C: Xenopus laevis-like histone H2A
D: histone H2B
E: histone H3
F: Histone H4
G: Xenopus laevis-like histone H2A
H: histone H2B
K: latent nuclear antigen


Theoretical massNumber of molelcules
Total (without water)201,53011
Polymers201,53011
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.162, 109.599, 182.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein histone H3 /


Mass: 15340.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: GenBank: 288992, UniProt: P84233*PLUS
#3: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H4 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: UniProt: P62799
#4: Protein Xenopus laevis-like histone H2A


Mass: 14181.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Expression vector pET3-H2A (others) / Gene: Histone H2A / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: GenBank: 30268540, UniProt: P06897*PLUS
#5: Protein histone H2B /


Mass: 13794.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H2B / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: GenBank: 296216, UniProt: P02281*PLUS

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DNA chain / Protein/peptide / Non-polymers , 3 types, 69 molecules IJK

#1: DNA chain Palindromic 146bp Human alpha-Satellite DNA fragment


Mass: 45054.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Alpha-Satellite DNA / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Strain (production host): HB 101
#6: Protein/peptide latent nuclear antigen


Mass: 2260.646 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminal 1-23 amino acid region of Latency associated Nuclear Antigen (LANA)protein of Kaposi's Sarcoma Herpesvirus (KSHV)
References: GenBank: 5669894, UniProt: Q9DUM3*PLUS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Manganese chloride11
2Potassium chloride11
3Potassium cacodylate11
4Potassium chloride12
5Potassium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2005 / Details: mirrors
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 48638 / Num. obs: 47855 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 15273.7 / Redundancy: 2.66 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.99
Reflection shellResolution: 2.9→2.97 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.64 / % possible all: 82.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1aoi

1aoi


Resolution: 2.9→50 Å / Cross valid method: Thorughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2183 -Random
Rwork0.222 ---
all-47855 --
obs-43460 90.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.211 Å20 Å20 Å2
2--8.106 Å20 Å2
3----3.895 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 5980 0 66 12168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.538
X-RAY DIFFRACTIONc_bond_d0.0129
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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