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- PDB-3nwa: Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH -

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Basic information

Entry
Database: PDB / ID: 3nwa
TitleGlycoprotein B from Herpes simplex virus type 1, W174R mutant, 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 / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
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 / 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 ...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 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-domain like / 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: 2.2629 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 1.2Jul 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_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 1.3Sep 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)316,87313
Polymers315,3774
Non-polymers1,4959
Water33,6341867
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)237,92912
Polymers236,5333
Non-polymers1,3969
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 area38720 Å2
ΔGint-163 kcal/mol
Surface area76790 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)237,5639
Polymers236,5333
Non-polymers1,0306
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 area39410 Å2
ΔGint-162 kcal/mol
Surface area77550 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)237,5639
Polymers236,5333
Non-polymers1,0306
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 area38450 Å2
ΔGint-151 kcal/mol
Surface area77860 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)237,5639
Polymers236,5333
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 area38590 Å2
ΔGint-151 kcal/mol
Surface area76190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.090, 117.090, 321.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-1057-

HOH

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Components

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


Mass: 78844.281 Da / Num. of mol.: 4 / Fragment: Ectodomain (UNP residues 30 to 730) / Mutation: W174R
Source method: isolated from a genetically manipulated source
Details: W174R 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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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


Mass: 122.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1867 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 7% PEG 4000, 0.5M NaCl, 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: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2629→48.3517 Å / Num. all: 229990 / Num. obs: 227148 / % possible obs: 98.7643 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.57
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.06 / % possible all: 72

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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 2GUM

2gum


Resolution: 2.2629→47.3159 Å / Cross valid method: THROUGHOUT / σ(F): 0.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.227 10883 5.43 %RANDOM
Rwork0.1724 ---
obs0.1757 200267 87.0779 %-
all-229986 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.934 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9812 Å2-0 Å2-0 Å2
2--5.9812 Å2-0 Å2
3----11.9624 Å2
Refinement stepCycle: LAST / Resolution: 2.2629→47.3159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19557 0 96 1867 21520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720172
X-RAY DIFFRACTIONf_angle_d1.00427379
X-RAY DIFFRACTIONf_dihedral_angle_d15.2527406
X-RAY DIFFRACTIONf_chiral_restr0.0662994
X-RAY DIFFRACTIONf_plane_restr0.0043575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2916-2.32970.32425770.27226992X-RAY DIFFRACTION65
2.3297-2.37050.30775690.26747358X-RAY DIFFRACTION70
2.3705-2.41440.3026000.2567624X-RAY DIFFRACTION71
2.4144-2.4616000.25258413X-RAY DIFFRACTION79
2.4616-2.51280.2986040.24097956X-RAY DIFFRACTION74
2.5128-2.56860.29226290.23548054X-RAY DIFFRACTION75
2.5686-2.6296000.22778932X-RAY DIFFRACTION83
2.6296-2.69690.28426270.22298465X-RAY DIFFRACTION80
2.6969-2.77170.26746650.21268625X-RAY DIFFRACTION80
2.7717-2.85550.24161670.20659244X-RAY DIFFRACTION86
2.8555-2.95050.26935010.19619149X-RAY DIFFRACTION86
2.9505-3.05960.24996830.18879083X-RAY DIFFRACTION85
3.0596-3.18670.21487060.17339278X-RAY DIFFRACTION87
3.1867-3.3381000.161910217X-RAY DIFFRACTION95
3.3381-3.5230.20727340.14569593X-RAY DIFFRACTION90
3.523-3.75720.20347410.13719645X-RAY DIFFRACTION90
3.7572-4.0695000.126810391X-RAY DIFFRACTION97
4.0695-4.52080.17467440.11179716X-RAY DIFFRACTION91
4.5208-5.27640.18917470.12139584X-RAY DIFFRACTION90
5.2764-7.10180.21967440.1729582X-RAY DIFFRACTION89

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