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- PDB-3nw8: Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH -

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Entry
Database: PDB / ID: 3nw8
TitleGlycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / ENVELOPE GLYCOPROTEIN / MEMBRANE FUSION / Glycoprotein B / Herpesvirus 1 / HSV-1 / Membrane
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 / membrane / identical protein binding
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
MESO-ERYTHRITOL / Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75915 Å
AuthorsStampfer, S.D. / Lou, H. / Cohen, G.H. / Eisenberg, R.J. / Heldwein, E.E.
CitationJournal: J.Virol. / Year: 2010
Title: Structural basis of local, pH-dependent conformational changes in glycoprotein B from herpes simplex virus type 1.
Authors: Stampfer, S.D. / Lou, H. / Cohen, G.H. / Eisenberg, R.J. / Heldwein, E.E.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)319,82032
Polymers315,1894
Non-polymers4,63128
Water3,765209
1
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)239,18421
Polymers236,3923
Non-polymers2,79318
Water543
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 area41090 Å2
ΔGint-161 kcal/mol
Surface area80040 Å2
MethodPISA
2
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)240,61830
Polymers236,3923
Non-polymers4,22627
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 area42520 Å2
ΔGint-184 kcal/mol
Surface area79590 Å2
MethodPISA
3
C: Envelope glycoprotein B
hetero molecules

C: Envelope glycoprotein B
hetero molecules

C: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,22927
Polymers236,3923
Non-polymers3,83724
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 area41640 Å2
ΔGint-197 kcal/mol
Surface area79400 Å2
MethodPISA
4
D: Envelope glycoprotein B
hetero molecules

D: Envelope glycoprotein B
hetero molecules

D: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,42718
Polymers236,3923
Non-polymers3,03615
Water543
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 area40630 Å2
ΔGint-168 kcal/mol
Surface area80110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.985, 117.985, 321.537
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
Envelope glycoprotein B / gB / gB-1 / gB1


Mass: 78797.203 Da / Num. of mol.: 4 / Fragment: Ectodomain (UNP residues 30 to 730) / Mutation: Y179S
Source method: isolated from a genetically manipulated source
Details: Y179S mutation
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: KOS / Gene: gB, UL27 / Plasmid: pVT-Bac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P06437

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Sugars , 2 types, 13 molecules

#2: 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.: 2
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
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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

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Non-polymers , 4 types, 224 molecules

#4: Chemical
ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT HSV-1 STRAIN KOS SEQUENCE IN THE UNP DATABASE CONTAINS THREE MUTATIONS RELATIVE ...AUTHORS STATE THAT HSV-1 STRAIN KOS SEQUENCE IN THE UNP DATABASE CONTAINS THREE MUTATIONS RELATIVE TO SEQUENCES OF OTHER STRAINS OF HSV-1 AND HSV-2. THEIR SEQUENCE WAS DERIVED FROM THE SEQUENCE OF HSV-1 KOS GB FROM PLASMID PKBXX (S. PERSON) AND DOES NOT CONTAIN THESE MUTATIONS.

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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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.75903→48.6897 Å / Num. all: 128895 / Num. obs: 118749 / % possible obs: 92.1285 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.9
Reflection shellResolution: 2.76→2.81 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.38 / % possible all: 83

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NWA

3nwa


Resolution: 2.75915→48.6897 Å / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 5778 5.31 %RANDOM
Rwork0.2015 ---
obs0.2037 108812 84.4257 %-
all-128885 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.125 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.241 Å20 Å2-0 Å2
2--5.241 Å2-0 Å2
3----10.4819 Å2
Refinement stepCycle: LAST / Resolution: 2.75915→48.6897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19454 0 295 209 19958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320244
X-RAY DIFFRACTIONf_angle_d0.60127487
X-RAY DIFFRACTIONf_dihedral_angle_d13.2797411
X-RAY DIFFRACTIONf_chiral_restr0.0423037
X-RAY DIFFRACTIONf_plane_restr0.0023562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7593-2.8040.35421280.30613815X-RAY DIFFRACTION63
2.804-2.8519000.30244286X-RAY DIFFRACTION71
2.8519-2.90310.33685620.28063862X-RAY DIFFRACTION64
2.9031-2.9583000.27454544X-RAY DIFFRACTION74
2.9583-3.01790.33314530.27024139X-RAY DIFFRACTION69
3.0179-3.08260.3117840.26294654X-RAY DIFFRACTION76
3.0826-3.1532000.25464782X-RAY DIFFRACTION79
3.1532-3.23080.27436100.24944241X-RAY DIFFRACTION70
3.2308-3.3167000.2464983X-RAY DIFFRACTION82
3.3167-3.41240.26466030.22884437X-RAY DIFFRACTION73
3.4124-3.52030.2787520.21635077X-RAY DIFFRACTION84
3.5203-3.6433000.20655239X-RAY DIFFRACTION86
3.6433-3.78550.24326670.19884632X-RAY DIFFRACTION76
3.7855-3.9528000.19015382X-RAY DIFFRACTION88
3.9528-4.15430.21426960.17724826X-RAY DIFFRACTION79
4.1543-4.40440.217730.15635623X-RAY DIFFRACTION93
4.4044-4.7281000.13965768X-RAY DIFFRACTION94
4.7281-5.17460.1997190.15435034X-RAY DIFFRACTION84
5.1746-5.8583000.17895889X-RAY DIFFRACTION96
5.8583-7.15480.23047340.20915091X-RAY DIFFRACTION84

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