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- PDB-3nwf: Glycoprotein B from Herpes simplex virus type 1, low-pH -

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Basic information

Entry
Database: PDB / ID: 3nwf
TitleGlycoprotein B from Herpes simplex virus type 1, low-pH
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / Coiled-Coil / 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: 3 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 1.2Dec 21, 2011Group: Derived calculations
Revision 1.3Dec 28, 2011Group: Derived calculations
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B
D: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,53015
Polymers315,4934
Non-polymers2,03711
Water1,36976
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)239,04618
Polymers236,6203
Non-polymers2,42615
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 area36200 Å2
ΔGint-188 kcal/mol
Surface area77230 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)237,6509
Polymers236,6203
Non-polymers1,0306
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 area36440 Å2
ΔGint-188 kcal/mol
Surface area77500 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)238,61112
Polymers236,6203
Non-polymers1,9919
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 area35780 Å2
ΔGint-175 kcal/mol
Surface area78470 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)237,2846
Polymers236,6203
Non-polymers6643
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 area35750 Å2
ΔGint-176 kcal/mol
Surface area78600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.802, 117.802, 318.324
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 78873.297 Da / Num. of mol.: 4 / Fragment: Ectodomain (UNP residues 30 to 730)
Source method: isolated from a genetically manipulated source
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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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: Chemical ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 13, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 2.8→50.3672 Å / Num. all: 121632 / Num. obs: 112550 / % possible obs: 92.533 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.98
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.98 / % possible all: 68

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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: 3→41.5354 Å / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 4724 5.12 %RANDOM
Rwork0.1972 ---
obs0.1994 92349 93.3412 %-
all-98937 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.636 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→41.5354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19109 0 129 76 19314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319737
X-RAY DIFFRACTIONf_angle_d0.65826847
X-RAY DIFFRACTIONf_dihedral_angle_d14.297110
X-RAY DIFFRACTIONf_chiral_restr0.0452978
X-RAY DIFFRACTIONf_plane_restr0.0023492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04780.38412100.2943101X-RAY DIFFRACTION68
3.0478-3.0988000.28553749X-RAY DIFFRACTION81
3.0988-3.15330.3881420.27143714X-RAY DIFFRACTION83
3.1533-3.2120.30375350.25393527X-RAY DIFFRACTION77
3.212-3.2752000.2424192X-RAY DIFFRACTION90
3.2752-3.3437000.23954202X-RAY DIFFRACTION93
3.3437-3.41840.25256900.22223500X-RAY DIFFRACTION77
3.4184-3.5002000.21544347X-RAY DIFFRACTION94
3.5002-3.5905000.21254375X-RAY DIFFRACTION96
3.5905-3.69080.27054800.19953942X-RAY DIFFRACTION86
3.6908-3.80340.28532570.19984170X-RAY DIFFRACTION90
3.8034-3.9311000.19054278X-RAY DIFFRACTION94
3.9311-4.07790.2505620.17834287X-RAY DIFFRACTION94
4.0779-4.24940.23056520.183695X-RAY DIFFRACTION81
4.2494-4.454000.15414498X-RAY DIFFRACTION98
4.454-4.7047000.14254489X-RAY DIFFRACTION98
4.7047-5.02350.21627490.15553703X-RAY DIFFRACTION81
5.0235-5.4511000.17754503X-RAY DIFFRACTION98
5.4511-6.0754000.19674531X-RAY DIFFRACTION99
6.0754-7.14220.23617510.20313778X-RAY DIFFRACTION82

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