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- PDB-5hda: Crystal Structure of the BS69 coiled coil-MYND domains bound to a... -

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Basic information

Entry
Database: PDB / ID: 5hda
TitleCrystal Structure of the BS69 coiled coil-MYND domains bound to an EBNA2 PXLXP motif
Components
  • Epstein-Barr nuclear antigen 2
  • Zinc finger MYND domain-containing protein 11
KeywordsIMMUNE SYSTEM / BS69 / EBNA2 / MYND / zMYND11 / coiled-coil
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / symbiont-mediated suppression of host translation initiation / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / cell cycle / regulation of signal transduction ...symbiont-mediated perturbation of host cell cycle progression / host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / symbiont-mediated suppression of host translation initiation / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / cell cycle / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / methylated histone binding / negative regulation of extrinsic apoptotic signaling pathway / chromosome / transcription corepressor activity / chromatin organization / double-stranded DNA binding / defense response to virus / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / negative regulation of DNA-templated transcription / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / domain with conserved PWWP motif / PWWP domain ...: / : / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Epstein-Barr nuclear antigen 2 / Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3899 Å
AuthorsSong, J. / Harter, M.
CitationJournal: Plos Pathog. / Year: 2016
Title: BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2.
Authors: Harter, M.R. / Liu, C.D. / Shen, C.L. / Gonzalez-Hurtado, E. / Zhang, Z.M. / Xu, M. / Martinez, E. / Peng, C.W. / Song, J.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger MYND domain-containing protein 11
C: Zinc finger MYND domain-containing protein 11
B: Epstein-Barr nuclear antigen 2
D: Epstein-Barr nuclear antigen 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5818
Polymers32,3194
Non-polymers2624
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-75 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.456, 38.190, 82.690
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Zinc finger MYND domain-containing protein 11 / Adenovirus 5 E1A-binding protein / Bone morphogenetic protein receptor-associated molecule 1 / Protein BS69


Mass: 15187.502 Da / Num. of mol.: 2 / Fragment: UNP Residues 480-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND11, BRAM1, BS69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15326
#2: Protein/peptide Epstein-Barr nuclear antigen 2 / EBV nuclear antigen 2


Mass: 972.156 Da / Num. of mol.: 2 / Fragment: UNP Residues 381-389 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: P12978
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21% PEGMME 350, 0.1M Tris-HCl pH 8.0, 6% Methanol, Hanging Drop Vapor Diffusion, Temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3899→44.6497 Å / Num. obs: 14546 / % possible obs: 99.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3899→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3899→44.6 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 711 4.9 %
Rwork0.2221 --
obs0.2241 14519 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3899→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 4 107 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052101
X-RAY DIFFRACTIONf_angle_d0.8742801
X-RAY DIFFRACTIONf_dihedral_angle_d15.714827
X-RAY DIFFRACTIONf_chiral_restr0.034292
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3899-2.57440.3361520.26612656X-RAY DIFFRACTION97
2.5744-2.83350.28841110.25992768X-RAY DIFFRACTION100
2.8335-3.24340.29381350.24232781X-RAY DIFFRACTION100
3.2434-4.08590.26931420.21442788X-RAY DIFFRACTION100
4.0859-44.64970.22041710.1942815X-RAY DIFFRACTION98

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