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3nwd

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH

Method: X-RAY DIFFRACTION Dmax: 278.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein B

Human herpesvirus 1

UniProt P06437

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 3 其他Polymer 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 30–730 Fragment：Ectodomain (UNP residues 30 to 730) Mutation：Y179S 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.88 Å R-free 0.283
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 30–730 Fragment：Ectodomain (UNP residues 30 to 730) Mutation：Y179S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.88 Å R-free 0.283
3 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 30–730 Fragment：Ectodomain (UNP residues 30 to 730) Mutation：Y179S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MRY MESO-ERYTHRITOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.88 Å R-free 0.283
4 Other combination Homooligomer Protein × 3 其他Polymer 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 30–730 Fragment：Ectodomain (UNP residues 30 to 730) Mutation：Y179S 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.88 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3NWD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GUM Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I Deposited 2006-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 103–730（628 aa） Fragment：residues 103-730
Chain B 103–730（628 aa） Fragment：residues 103-730
Chain C 103–730（628 aa） Fragment：residues 103-730
Not recorded NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8% PEG 6000, 0.1 M Na Hepes, 15% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.275
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：Y179S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MRY MESO-ERYTHRITOL × 6 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.76 Å R-free 0.242
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：Y179S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 MRY MESO-ERYTHRITOL × 12 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.76 Å R-free 0.242
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：Y179S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MRY MESO-ERYTHRITOL × 9 NA SODIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.76 Å R-free 0.242
3NW8 Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH Deposited 2010-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：Y179S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MRY MESO-ERYTHRITOL × 3 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.76 Å R-free 0.242
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：W174R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.26 Å R-free 0.227
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：W174R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.26 Å R-free 0.227
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：W174R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.26 Å R-free 0.227
3NWA Glycoprotein B from Herpes simplex virus type 1, W174R mutant, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：W174R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.26 Å R-free 0.227
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MRY MESO-ERYTHRITOL × 3 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.249
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.249
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain C 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.249
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG 4000, 0.3M NaCl, and 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.249
3WV0 O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha Deposited 2014-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 50–56（7 aa） Fragment：O-glycan with attached peptide, UNP residues 50-56
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2 M ammonium sulfate 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.299
3WV0 O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha Deposited 2014-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 50–56（7 aa） Fragment：O-glycan with attached peptide, UNP residues 50-56
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.2 M ammonium sulfate 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.299
4BOM Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction Deposited 2013-05-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 103–724（622 aa） Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724
Chain B 103–724（622 aa） Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724
Chain C 103–724（622 aa） Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer PBS WITH SODIUM CITRATE；pH 5.5；PBS WITH SODIUM CITRATE
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；LIQUID NITROGEN PROPANE MIXTURE
Resolution 27.00 Å
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 61–730（670 aa） Fragment：ectodomain
Mutation：A504P, R505G, Q507G, N511G NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.255
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 61–730（670 aa） Fragment：ectodomain
Mutation：A504P, R505G, Q507G, N511G NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.255
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain C 61–730（670 aa） Fragment：ectodomain
Mutation：A504P, R505G, Q507G, N511G NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MRY MESO-ERYTHRITOL × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.255
4HSI Glycoprotein B from Herpes simplex virus type 1, A504P/R505G/Q507G/N511G mutant, low-pH Deposited 2012-10-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 61–730（670 aa） Fragment：ectodomain
Mutation：A504P, R505G, Q507G, N511G NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；15% PEG 4000, 0.2 M NaCl, 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.255
4L1R Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant, low-pH Deposited 2013-06-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：A549T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；15% PEG 4000, 0.3 M NaCl, 0.1 M Sodium Citrate, pH 5.5, vapor diffusion, hanging drop, temperature 296K
Resolution 3.03 Å R-free 0.243
4L1R Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant, low-pH Deposited 2013-06-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 30–730（701 aa） Fragment：Ectodomain (UNP residues 30 to 730)
Mutation：A549T NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；15% PEG 4000, 0.3 M NaCl, 0.1 M Sodium Citrate, pH 5.5, vapor diffusion, hanging drop, temperature 296K
Resolution 3.03 Å R-free 0.243
5XO2 Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II Deposited 2017-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 50–56（7 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate
Resolution 2.20 Å R-free 0.262
5XO2 Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II Deposited 2017-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 50–56（7 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate
Resolution 2.20 Å R-free 0.262
7UHZ Post-fusion ectodomain of HSV-1 gB in complex with BMPC-23 Fab Deposited 2022-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 103–730（628 aa）
Chain B 103–730（628 aa）
Chain C 103–730（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UI0 Post-fusion ectodomain of HSV-1 gB in complex with HSV010-13 Fab Deposited 2022-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 103–730（628 aa）
Chain B 103–730（628 aa）
Chain C 103–730（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8KFA Cryo-EM structure of HSV-1 gB with D48 Fab complex Deposited 2023-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 111–725（615 aa）
Chain B 111–725（615 aa）
Chain C 111–725（615 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å

12 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GB_HHV1K
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–703； UniProt 30–730 Author chain B； PDBConstruct 3–703； UniProt 30–730 Author chain C； PDBConstruct 3–703； UniProt 30–730 Author chain D； PDBConstruct 3–703； UniProt 30–730

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3nwd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3nwd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3nwd
Deposition date deposition_date2010-07-09
Structure title titleGlycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH
Keywords keywordsCoiled-Coil, ENVELOPE GLYCOPROTEIN, MEMBRANE FUSION, VIRAL PROTEIN, Glycoprotein B, Herpesvirus 1, HSV-1, Membrane; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron104.80 Å
Forward intensity I(0) i01125240000.00
Molecular weight molecular_weight274740.0 kDa
Excluded volume excluded_volume340650 ų
Envelope volume envelope_volume818900 ų
Hydration-shell volume shell_volume82399 ų
Envelope diameter envelope_diameter388.7 Å
Shell Rg shell_rg60.81 Å
Envelope Rg envelope_rg102.40 Å
Shape Rg shape_rg104.80 Å
Total Rg total_rg103.80 Å
Total atoms total_atoms19367
Residues n_residues2410
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax278.0 Å
Rg (real space) rg_real93.52 Å
Rg uncertainty (real space) rg_real_error1.53 Å
I(0) (real space) i0_real1.0750e+09
I(0) uncertainty (real space) i0_real_error2.3870e+07
Rg (reciprocal space) rg_reciprocal89.86 Å
I(0) (reciprocal space) i0_reciprocal1087000000.0000
Solution quality estimate total_estimate0.9039
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary92.7 Å
Skewness Skewness skewness0.407
Kurtosis Kurtosis kurtosis-0.631
Angular range angular_range— – 0.0750 Å−1
Current regularization parameter α current_alpha0.5993
Highest regularization parameter α highest_alpha65210000.0000
Real-space data points n_real_points16
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.948; Stabil: 0.973; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.028
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3nwda_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamilye.76.1 — Viral glycoprotein ectodomain-like
Family Family familye.76.1.1 — Glycoprotein B-like
Domain ID domain_idd3nwdb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamilye.76.1 — Viral glycoprotein ectodomain-like
Family Family familye.76.1.1 — Glycoprotein B-like
Domain ID domain_idd3nwdc_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamilye.76.1 — Viral glycoprotein ectodomain-like
Family Family familye.76.1.1 — Glycoprotein B-like
Domain ID domain_idd3nwdd_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamilye.76.1 — Viral glycoprotein ectodomain-like
Family Family familye.76.1.1 — Glycoprotein B-like

CATH v4.4 (16 domains)

Domain ID domain_id3nwdA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily1230 —
Domain ID domain_id3nwdA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1890 —
Domain ID domain_id3nwdA03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily100 —
Domain ID domain_id3nwdA05
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily3280 —
Domain ID domain_id3nwdB01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily1230 —
Domain ID domain_id3nwdB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1890 —
Domain ID domain_id3nwdB03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily100 —
Domain ID domain_id3nwdB05
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily3280 —
Domain ID domain_id3nwdC01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily1230 —
Domain ID domain_id3nwdC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1890 —
Domain ID domain_id3nwdC03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily100 —
Domain ID domain_id3nwdC05
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily3280 —
Domain ID domain_id3nwdD01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily1230 —
Domain ID domain_id3nwdD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1890 —
Domain ID domain_id3nwdD03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily100 —
Domain ID domain_id3nwdD05
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily3280 —
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8. Citations (1)

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9. Files and Curves (10)