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- PDB-3fd4: Crystal Structure of Epstein-Barr virus gp42 protein -

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Basic information

Entry
Database: PDB / ID: 3fd4
TitleCrystal Structure of Epstein-Barr virus gp42 protein
ComponentsGlycoprotein gp42
KeywordsVIRAL PROTEIN / C type lectin / herpesvirus / Virus entry / membrane fusion / Host-virus interaction / Lectin / Membrane / Transmembrane
Function / homology
Function and homology information


host cell membrane / carbohydrate binding / virion membrane / membrane
Similarity search - Function
Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKirschner, A. / Jardetzky, T.
CitationJournal: Structure / Year: 2009
Title: Structure of Epstein-Barr virus glycoprotein 42 suggests a mechanism for triggering receptor-activated virus entry.
Authors: Kirschner, A.N. / Sorem, J. / Longnecker, R. / Jardetzky, T.S.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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.end_auth_comp_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein gp42
B: Glycoprotein gp42


Theoretical massNumber of molelcules
Total (without water)43,2532
Polymers43,2532
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area16410 Å2
MethodPISA
2
A: Glycoprotein gp42


Theoretical massNumber of molelcules
Total (without water)21,6261
Polymers21,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Glycoprotein gp42


Theoretical massNumber of molelcules
Total (without water)21,6261
Polymers21,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.792, 67.469, 79.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHETYRTYRAA88 - 16756 - 135
21PHEPHETYRTYRBB88 - 16756 - 135
12TRPTRPSERSERAA174 - 221142 - 189
22TRPTRPSERSERBB174 - 221142 - 189

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Components

#1: Protein Glycoprotein gp42


Mass: 21626.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: BZLF2 / Plasmid: pbacgus-3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03205
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 38.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9.5
Details: 30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.72505
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72505 Å / Relative weight: 1
ReflectionResolution: 2.4→46.73 Å / Num. all: 14237 / Num. obs: 14139 / % possible obs: 99.4 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 4.4
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KG0

1kg0


Resolution: 2.4→46.73 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.268 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24226 629 4.5 %RANDOM
Rwork0.21548 ---
obs0.21666 13445 99.55 %-
all-14237 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.86 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å20 Å20 Å2
2---2.34 Å20 Å2
3---6.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 0 281 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222410
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9153293
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.135285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3722.963108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62115354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg38.216158
X-RAY DIFFRACTIONr_chiral_restr0.1160.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211856
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02546
X-RAY DIFFRACTIONr_nbd_refined0.1630.3430
X-RAY DIFFRACTIONr_nbd_other0.180.31572
X-RAY DIFFRACTIONr_nbtor_refined0.1830.51099
X-RAY DIFFRACTIONr_nbtor_other0.1590.51231
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.373
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7781.51432
X-RAY DIFFRACTIONr_mcbond_other0.7942582
X-RAY DIFFRACTIONr_mcangle_it4.34222338
X-RAY DIFFRACTIONr_scbond_it3.3083978
X-RAY DIFFRACTIONr_scangle_it4.9394.5955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1766 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.05
tight thermal0.470.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 45 -
Rwork0.26 951 -
obs--99.2 %

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