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- PDB-3fvc: Crystal structure of a trimeric variant of the Epstein-Barr virus... -

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Basic information

Entry
Database: PDB / ID: 3fvc
TitleCrystal structure of a trimeric variant of the Epstein-Barr virus glycoprotein B
ComponentsGlycoprotein GP110
KeywordsVIRAL PROTEIN / viral fusion protein / PH domains / fusion loops / Glycoprotein / Late protein / Membrane / Transmembrane
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / PH-domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsBackovic, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of a trimeric variant of the Epstein-Barr virus glycoprotein B
Authors: Backovic, M. / Longnecker, R. / Jardetzky, T.S.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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

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Assembly

Deposited unit
A: Glycoprotein GP110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2664
Polymers74,6021
Non-polymers6643
Water1629
1
A: Glycoprotein GP110
hetero molecules

A: Glycoprotein GP110
hetero molecules

A: Glycoprotein GP110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,79812
Polymers223,8073
Non-polymers1,9919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area38640 Å2
ΔGint-142 kcal/mol
Surface area81890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.800, 106.800, 210.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Glycoprotein GP110 / GP115


Mass: 74602.430 Da / Num. of mol.: 1 / Fragment: ectodomain / Mutation: W112H, Y113R, W193R, L194V, I195E, W196A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95 / Gene: BALF4, VGLB_EBV / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: P03188
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.81 Å3/Da / Density % sol: 74.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.1 M N-Cyclohexyl-3-aminopropanesulfonic acid (CAPS) pH 10.5 or 11.5, 1.40 M (NH4)2SO4 (AS) and 0.2 M Li2SO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2007
RadiationMonochromator: Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 23367 / % possible obs: 98.5 % / Redundancy: 8.3 %
Reflection shellHighest resolution: 3.2 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3 / % possible all: 91.6

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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
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GUM

2gum


Resolution: 3.2→26.61 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.854 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.993 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28292 2155 9.2 %RANDOM
Rwork0.24246 ---
obs0.24635 21144 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.778 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å21.39 Å20 Å2
2--2.79 Å20 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 3.2→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 42 9 4552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.956280
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8565553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64623.863233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.12915788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6331534
X-RAY DIFFRACTIONr_chiral_restr0.1090.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023507
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.30.31948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3540.53185
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1370.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.3171
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.07422813
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85334504
X-RAY DIFFRACTIONr_scbond_it1.10322014
X-RAY DIFFRACTIONr_scangle_it1.83731776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 98 -
Rwork0.243 1406 -
obs--89.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58740.00870.22340.7182-0.86254.2438-0.0070.5219-0.1549-0.4857-0.1299-0.09130.47480.56960.1369-0.21080.06420.0793-0.2077-0.0705-0.2825-42.353419.89958.3826
232.00896.76530.76726.2006-5.016625.46950.0932-0.3399-0.0335-0.6922-0.28180.1165-0.094-0.11410.188700-0.0001-0.0002-0.00020.0003-59.380254.6515-20.6882
30.16860.02331.03980.01850.24247.05440.05990.40960.2133-0.60350.0638-0.1639-1.2121-0.1021-0.12360.00030.0003-0.00070.001-0.00010.0016-60.36838.987261.0159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 533
2X-RAY DIFFRACTION2A534 - 620
3X-RAY DIFFRACTION3A621 - 680

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