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- PDB-5w0k: Crystal structure of EBV gHgL/CL40/gp42 N-domain -

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Basic information

Entry
Database: PDB / ID: 5w0k
TitleCrystal structure of EBV gHgL/CL40/gp42 N-domain
Components
  • CL40 IgG heavy chain
  • CL40 IgG light chain
  • Envelope glycoprotein H
  • Envelope glycoprotein L
  • Glycoprotein 42
KeywordsVIRAL PROTEIN/Immune system / receptor binding / herpesvirus entry / Epstein-Barr Virus / membrane fusion / VIRAL PROTEIN / VIRAL PROTEIN-Immune system complex
Function / homology
Function and homology information


host cell membrane / host cell endosome membrane / host cell Golgi apparatus / carbohydrate binding / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal ...Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulins / Roll / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycoprotein 42 / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSathiyamoorthy, K. / Jardetzky, T.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119480 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076183 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA117794 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Inhibition of EBV-mediated membrane fusion by anti-gHgL antibodies.
Authors: Sathiyamoorthy, K. / Jiang, J. / Mohl, B.S. / Chen, J. / Zhou, Z.H. / Longnecker, R. / Jardetzky, T.S.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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.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
A: Envelope glycoprotein H
B: Envelope glycoprotein L
H: CL40 IgG heavy chain
L: CL40 IgG light chain
X: Glycoprotein 42
C: Envelope glycoprotein H
D: Envelope glycoprotein L
E: CL40 IgG heavy chain
F: CL40 IgG light chain
Y: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)273,70810
Polymers273,70810
Non-polymers00
Water0
1
A: Envelope glycoprotein H
B: Envelope glycoprotein L
H: CL40 IgG heavy chain
L: CL40 IgG light chain
X: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)136,8545
Polymers136,8545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Envelope glycoprotein H
D: Envelope glycoprotein L
E: CL40 IgG heavy chain
F: CL40 IgG light chain
Y: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)136,8545
Polymers136,8545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.380, 133.130, 254.130
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 C
12(chain B and resid 25 through 130)
22chain D
13(chain E and (resid 1 through 130 or resid 135 through 216))
23(chain H and resid 1 through 216)
14(chain F and resid 1 through 210)
24chain L
15(chain X and resid 51 through 81)
25chain Y

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUTYRTYRchain AAA20 - 6741 - 655
211LEULEUTYRTYRchain CCF20 - 6741 - 655
112ALAALAARGARG(chain B and resid 25 through 130)BB25 - 1302 - 107
212ALAALAARGARGchain DDG25 - 1302 - 107
113GLUGLUGLYGLY(chain E and (resid 1 through 130 or resid 135 through 216))EH1 - 1301 - 130
123THRTHRARGARG(chain E and (resid 1 through 130 or resid 135 through 216))EH135 - 216135 - 216
213GLUGLUARGARG(chain H and resid 1 through 216)HC1 - 2161 - 216
114ASPASPASNASN(chain F and resid 1 through 210)FI1 - 2101 - 210
214ASPASPASNASNchain LLD1 - 2101 - 210
115GLUGLUTRPTRP(chain X and resid 51 through 81)XE51 - 815 - 35
215GLUGLUTRPTRPchain YYJ51 - 815 - 35

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Envelope glycoprotein H / gH


Mass: 73225.008 Da / Num. of mol.: 2 / Fragment: UNP residues 20-679
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: gH, BXLF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L / gL


Mass: 12589.231 Da / Num. of mol.: 2 / Fragment: UNP residues 24-137
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: gL, BKRF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03212
#3: Antibody CL40 IgG heavy chain


Mass: 23347.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma / Cell line (production host): CL40 hybridoma / Production host: Mus musculus (house mouse)
#4: Antibody CL40 IgG light chain


Mass: 23601.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma / Cell line (production host): CL40 hybridoma / Production host: Mus musculus (house mouse)
#5: Protein/peptide Glycoprotein 42 / / gp42


Mass: 4090.565 Da / Num. of mol.: 2 / Fragment: UNP residues 47-81 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
References: UniProt: P03205

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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: 2.79 Å3/Da / Density % sol: 56 %
Description: Initial crystals appear as stacked plates in PEG3350 as growth precipitant, optimized crystals grew in PEG4000 as precipitant and are in the shape of a small and irregularly shaped rhombohedron
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryojet
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 3.1→48.19 Å / Num. obs: 60129 / % possible obs: 100 % / Redundancy: 14.9 % / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PHF, 2XQY

3phf

2xqy


Resolution: 3.1→22.763 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2991 2707 4.99 %
Rwork0.2416 51571 -
obs0.2445 54278 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.62 Å2 / Biso mean: 67.6934 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: final / Resolution: 3.1→22.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18663 0 0 0 18663
Num. residues----2410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319107
X-RAY DIFFRACTIONf_angle_d0.62725986
X-RAY DIFFRACTIONf_chiral_restr0.0422977
X-RAY DIFFRACTIONf_plane_restr0.0033279
X-RAY DIFFRACTIONf_dihedral_angle_d10.65111427
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7652X-RAY DIFFRACTION13.708TORSIONAL
12C7652X-RAY DIFFRACTION13.708TORSIONAL
21B1030X-RAY DIFFRACTION13.708TORSIONAL
22D1030X-RAY DIFFRACTION13.708TORSIONAL
31E2316X-RAY DIFFRACTION13.708TORSIONAL
32H2316X-RAY DIFFRACTION13.708TORSIONAL
41F2276X-RAY DIFFRACTION13.708TORSIONAL
42L2276X-RAY DIFFRACTION13.708TORSIONAL
51X317X-RAY DIFFRACTION13.708TORSIONAL
52Y317X-RAY DIFFRACTION13.708TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.15630.3751810.33151586166754
3.1563-3.21680.4034920.30761799189160
3.2168-3.28230.38731040.29881988209268
3.2823-3.35350.34691200.29632193231374
3.3535-3.43120.33161260.27112415254181
3.4312-3.51670.33221310.2752599273088
3.5167-3.61150.29441510.27692851300296
3.6115-3.71730.32111570.26929783135100
3.7173-3.83670.30631570.263529823139100
3.8367-3.97320.38561560.24129533109100
3.9732-4.13130.33571570.238829803137100
4.1313-4.31820.24841580.212630013159100
4.3182-4.54410.24321570.199829933150100
4.5441-4.82630.26631590.198530143173100
4.8263-5.19480.23671580.205329903148100
5.1948-5.71010.30281600.222830353195100
5.7101-6.51930.29241600.246330533213100
6.5193-8.15050.30251600.258430693229100
8.1505-22.76310.27581630.23083092325597

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