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- PDB-6vlk: A varicella-zoster virus glycoprotein -

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Basic information

Entry
Database: PDB / ID: 6vlk
TitleA varicella-zoster virus glycoprotein
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / viral membrane glycoprotein
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 - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / TonB-dependent receptor (TBDR) proteins signature 1. / 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 - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / TonB-dependent receptor (TBDR) proteins signature 1. / 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 / Helix non-globular / Special / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesVaricella-zoster virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4529 Å
AuthorsXing, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI102546, P41GM103832, R01GM079429 and S10OD021600 United States
CitationJournal: Nat Commun / Year: 2020
Title: A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation.
Authors: Stefan L Oliver / Yi Xing / Dong-Hua Chen / Soung Hun Roh / Grigore D Pintilie / David A Bushnell / Marvin H Sommer / Edward Yang / Andrea Carfi / Wah Chiu / Ann M Arvin /
Abstract: Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells ...Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies.
History
DepositionJan 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / citation_author / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _citation.title / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 2, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein B
B: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0798
Polymers169,8452
Non-polymers3,2346
Water3,081171
1
A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,86912
Polymers254,7673
Non-polymers7,1019
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 area46620 Å2
ΔGint-57 kcal/mol
Surface area79770 Å2
MethodPISA
2
B: Envelope glycoprotein B
hetero molecules

B: Envelope glycoprotein B
hetero molecules

B: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,36812
Polymers254,7673
Non-polymers2,6009
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area41020 Å2
ΔGint-148 kcal/mol
Surface area77340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.318, 118.318, 749.026
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-971-

HOH

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Components

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Protein / Non-polymers , 2 types, 173 molecules AB

#1: Protein Envelope glycoprotein B / gB


Mass: 84922.445 Da / Num. of mol.: 2 / Mutation: W180G/Y185G/R491G/R493G/R494G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Varicella-zoster virus (strain Oka vaccine)
Strain: Oka vaccine / Gene: gB, ORF31 / Cell line (production host): 293s GNTI / Production host: Homo sapiens (human) / References: UniProt: Q4JR05
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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 / Feature type: SUBJECT OF INVESTIGATION
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

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Details

Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na acetate pH 4.6, 20% PEG 400, 6% ethylene glycol
PH range: 4.6-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→101.52 Å / Num. obs: 74955 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.8
Reflection shellResolution: 2.45→2.59 Å / Redundancy: 10 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 10367 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUM

2gum


Resolution: 2.4529→50.222 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 3772 5.04 %
Rwork0.1808 --
obs0.1832 74911 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4529→50.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9451 0 144 171 9766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089836
X-RAY DIFFRACTIONf_angle_d1.12313363
X-RAY DIFFRACTIONf_dihedral_angle_d18.6423694
X-RAY DIFFRACTIONf_chiral_restr0.0781526
X-RAY DIFFRACTIONf_plane_restr0.0041692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4529-2.4840.29151240.23812588X-RAY DIFFRACTION100
2.484-2.51670.31441370.23422611X-RAY DIFFRACTION100
2.5167-2.55110.28721470.23372572X-RAY DIFFRACTION100
2.5511-2.58760.31491450.22532596X-RAY DIFFRACTION100
2.5876-2.62620.2911530.21882606X-RAY DIFFRACTION100
2.6262-2.66720.23881370.20672578X-RAY DIFFRACTION100
2.6672-2.7110.26121440.21352595X-RAY DIFFRACTION100
2.711-2.75770.32491160.20662649X-RAY DIFFRACTION100
2.7577-2.80780.26341190.21722630X-RAY DIFFRACTION100
2.8078-2.86180.26961290.2072587X-RAY DIFFRACTION100
2.8618-2.92030.2831280.21932622X-RAY DIFFRACTION100
2.9203-2.98370.27421350.2152610X-RAY DIFFRACTION100
2.9837-3.05310.24571400.2112626X-RAY DIFFRACTION100
3.0531-3.12950.29891530.21452616X-RAY DIFFRACTION100
3.1295-3.21410.26311380.21632608X-RAY DIFFRACTION100
3.2141-3.30860.27891600.21362622X-RAY DIFFRACTION100
3.3086-3.41540.24631420.19772610X-RAY DIFFRACTION100
3.4154-3.53750.24911250.18912632X-RAY DIFFRACTION100
3.5375-3.6790.20931310.18532637X-RAY DIFFRACTION100
3.679-3.84640.24141350.17812665X-RAY DIFFRACTION100
3.8464-4.04910.19851300.16252629X-RAY DIFFRACTION100
4.0491-4.30270.21550.15152648X-RAY DIFFRACTION100
4.3027-4.63470.16091580.132638X-RAY DIFFRACTION100
4.6347-5.10070.1721470.142682X-RAY DIFFRACTION100
5.1007-5.83780.1981600.16052671X-RAY DIFFRACTION100
5.8378-7.35140.23561420.1792741X-RAY DIFFRACTION100
7.3514-50.2220.23161420.18162870X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -29.8876 Å / Origin y: 18.6589 Å / Origin z: -64.2573 Å
111213212223313233
T0.0607 Å2-0.0012 Å20.0015 Å2-0.1469 Å20.0025 Å2--0.0991 Å2
L0.0704 °2-0.02 °2-0.0843 °2-0.0284 °20.0343 °2--0.0924 °2
S-0.0025 Å °0.0098 Å °0.0201 Å °-0.0049 Å °0.0118 Å °-0.0032 Å °0.0704 Å °0.0153 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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