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- PDB-4bom: Structure of herpesvirus fusion glycoprotein B-bilayer complex re... -

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Basic information

Entry
Database: PDB / ID: 4bom
TitleStructure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction
ComponentsENVELOPE GLYCOPROTEIN B
KeywordsVIRAL PROTEIN / MEMBRANE PROXIMAL REGION / PROTEIN COAT / PSEUDO-ATOMIC VIRUS-HOST INTERACTION
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / 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
Envelope glycoprotein B
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 27 Å
AuthorsMaurer, U.E. / Zeev-Ben-Mordehai, Z. / Pandurangan, A.P. / Cairns, T.M. / Hannah, B.P. / Whitbeck, J.C. / Eisenberg, R.J. / Cohen, G.H. / Topf, M. / Huiskonen, J.T. / Grunewald, K.
CitationJournal: Structure / Year: 2013
Title: The structure of herpesvirus fusion glycoprotein B-bilayer complex reveals the protein-membrane and lateral protein-protein interaction.
Authors: Ulrike E Maurer / Tzviya Zeev-Ben-Mordehai / Arun Prasad Pandurangan / Tina M Cairns / Brian P Hannah / J Charles Whitbeck / Roselyn J Eisenberg / Gary H Cohen / Maya Topf / Juha T Huiskonen / Kay Grünewald /
Abstract: Glycoprotein B (gB) is a key component of the complex herpesvirus fusion machinery. We studied membrane interaction of two gB ectodomain forms and present an electron cryotomography structure of the ...Glycoprotein B (gB) is a key component of the complex herpesvirus fusion machinery. We studied membrane interaction of two gB ectodomain forms and present an electron cryotomography structure of the gB-bilayer complex. The two forms differed in presence or absence of the membrane proximal region (MPR) but showed an overall similar trimeric shape. The presence of the MPR impeded interaction with liposomes. In contrast, the MPR-lacking form interacted efficiently with liposomes. Lateral interaction resulted in coat formation on the membranes. The structure revealed that interaction of gB with membranes was mediated by the fusion loops and limited to the outer membrane leaflet. The observed intrinsic propensity of gB to cluster on membranes indicates an additional role of gB in driving the fusion process forward beyond the transient fusion pore opening and subsequently leading to fusion pore expansion.
History
DepositionMay 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Other
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Oct 24, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / diffrn_radiation ...citation / diffrn_radiation / diffrn_radiation_wavelength / em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant / em_software / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _em_entity_assembly.source / _em_entity_assembly.type / _em_software.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN B
B: ENVELOPE GLYCOPROTEIN B
C: ENVELOPE GLYCOPROTEIN B


Theoretical massNumber of molelcules
Total (without water)213,3773
Polymers213,3773
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein ENVELOPE GLYCOPROTEIN B / GB / GB-1 / GB1


Mass: 71125.688 Da / Num. of mol.: 3 / Fragment: GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724
Source method: isolated from a genetically manipulated source
Details: LIPOSOMES CONSISTING OF PHOSPHATIDYLCHOLINE AND CHOLESTEROL AT 1.7\:1 MOLAR RATIO WERE INCUBATED WITH GB AT PH 5.5 AT 37C FOR ONE HOUR
Source: (gene. exp.) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
Strain: KOS / Plasmid: PCW289 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda / References: UniProt: P06437

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: HUMAN HERPESVIRUS 1 ENVELOPED GLYCOPROTEIN GB ECTODOMAIN LACKING THE MEMBRANE PROXIMAL REGION BOUND TO LIPOSOMES
Type: COMPLEX / Source: RECOMBINANT
Source (natural)Organism: HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionName: PBS WITH SODIUM CITRATE / pH: 5.5 / Details: PBS WITH SODIUM CITRATE
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE-PROPANE / Details: LIQUID NITROGEN PROPANE MIXTURE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 17, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 67000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTilt angle max: 60 ° / Tilt angle min: -60 °
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 9

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Processing

EM software
IDNameCategory
1Flex-EMmodel fitting
2JSUBTOMO3D reconstruction
CTF correctionDetails: LOW PASS FILTER TO THE FIRST ZERO CROSSING OF THE CTF
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionMethod: SUBTOMOGRAM AVERAGING / Resolution: 27 Å / Num. of particles: 786 / Actual pixel size: 4.6 Å
Details: THE MISSING FUSION LOOP RESIDUES 261 AND 262 WERE MODELED IN ALL THE THREE CHAINS OF USING MODELLER BASED ON THE GB CRYSTAL STRUCTURE (PDB ID 2GUM) SUBMISSION BASED ON EXPERIMENTAL DATA FROM ...Details: THE MISSING FUSION LOOP RESIDUES 261 AND 262 WERE MODELED IN ALL THE THREE CHAINS OF USING MODELLER BASED ON THE GB CRYSTAL STRUCTURE (PDB ID 2GUM) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2380. (DEPOSITION ID: 11670).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--FLEXIBLE
Atomic model buildingPDB-ID: 3NWF

3nwf


Accession code: 3NWF / Source name: PDB / Type: experimental model
RefinementHighest resolution: 27 Å
Refinement stepCycle: LAST / Highest resolution: 27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14745 0 0 0 14745

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