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- PDB-6bm8: Crystal structure of glycoprotein B from Herpes Simplex Virus type I -

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Basic information

Entry
Database: PDB / ID: 6bm8
TitleCrystal structure of glycoprotein B from Herpes Simplex Virus type I
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / fusogen / bitopic membrane protein
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Glycoprotein B / Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å
AuthorsCooper, R.S. / Heldwein, E.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI107171 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM115060 United States
Burroughs Welcome FundInvestigators in the Pathogenesis of Infectious Diseases United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis for membrane anchoring and fusion regulation of the herpes simplex virus fusogen gB.
Authors: Cooper, R.S. / Georgieva, E.R. / Borbat, P.P. / Freed, J.H. / Heldwein, E.E.
History
DepositionNov 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9825
Polymers93,5281
Non-polymers1,4534
Water00
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)284,94515
Polymers280,5853
Non-polymers4,36012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area44470 Å2
ΔGint-169 kcal/mol
Surface area96830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.597, 118.597, 800.576
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Envelope glycoprotein B / gB


Mass: 93528.438 Da / Num. of mol.: 1 / Fragment: residues 72-904
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Gene: UL27, gB, HHV1gp041 / Plasmid: pFastBac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A1Z0P7, UniProt: P10211*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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
#4: 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.: 2
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
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: 7.2 Å3/Da / Density % sol: 82.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 4000, 0.1 M Tris HCl pH 7.5, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.99→101.87 Å / Num. obs: 19003 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 164.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.072 / Rrim(I) all: 0.131 / Net I/σ(I): 7 / Num. measured all: 62145 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.99-4.373.31.22144770.5060.791.4699.1
9.77-101.872.90.02613920.9990.0190.03296.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASERphasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUM

2gum


Resolution: 4.1→101.87 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.94
RfactorNum. reflection% reflection
Rfree0.2855 1742 9.98 %
Rwork0.2686 --
obs0.2703 17450 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 318.74 Å2 / Biso mean: 190.5642 Å2 / Biso min: 106.87 Å2
Refinement stepCycle: final / Resolution: 4.1→101.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 95 0 5391
Biso mean--226.99 --
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065533
X-RAY DIFFRACTIONf_angle_d1.0117536
X-RAY DIFFRACTIONf_chiral_restr0.057842
X-RAY DIFFRACTIONf_plane_restr0.008976
X-RAY DIFFRACTIONf_dihedral_angle_d7.9653271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.1003-4.22090.35971390.36061244138396
4.2209-4.35710.35931430.34381295143899
4.3571-4.51290.33051420.323112911433100
4.5129-4.69360.2841470.302113101457100
4.6936-4.90720.40091440.29041308145299
4.9072-5.16590.30941450.28651305145099
5.1659-5.48950.30011420.30671272141497
5.4895-5.91330.37121460.30371322146899
5.9133-6.50830.32151470.287713141461100
6.5083-7.44980.24861490.25641342149199
7.4498-9.3850.2231460.23241323146997
9.385-101.90450.24991520.22821382153494

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