8kfa

Cryo-EM structure of HSV-1 gB with D48 Fab complex

Method: ELECTRON MICROSCOPY D_max: 170.7 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein B

Human herpesvirus 1 (strain KOS)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 111–725 Chain B； UniProt 111–725 Chain C； UniProt 111–725	Not recorded	D48 heavy chain × 3 D48 light chain × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.04 Å

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 8KFA	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 oligomeric state 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 103–730（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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination 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 × 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
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 × 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
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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：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
3NWD Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 × 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
3NWF Glycoprotein B from Herpes simplex virus type 1, low-pH Deposited 2010-07-09	Different construct Different mutation/modification Different oligomeric state 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 oligomeric state 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 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 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

12 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GB_HHV1K
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–615； UniProt 111–725 Author chain B； PDBConstruct 1–615； UniProt 111–725 Author chain C； PDBConstruct 1–615； UniProt 111–725

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8kfa
Deposition date deposition_date	2023-08-15
Structure title title	Cryo-EM structure of HSV-1 gB with D48 Fab complex
Keywords keywords	HSV-1 gB, fab, neutralizing antibody, complex, Cryo-EM, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	50.93 Å
Radius of gyration Rg (electron density) rg_electron	50.62 Å
Forward intensity I(0) i0	1019920000.00
Molecular weight molecular_weight	263570.0 kDa
Excluded volume excluded_volume	328090 Å³
Envelope volume envelope_volume	468260 Å³
Hydration-shell volume shell_volume	77251 Å³
Envelope diameter envelope_diameter	169.0 Å
Shell Rg shell_rg	53.39 Å
Envelope Rg envelope_rg	49.99 Å
Shape Rg shape_rg	50.62 Å
Total Rg total_rg	50.74 Å
Total atoms total_atoms	18665
Residues n_residues	2421
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	170.7 Å
Rg (real space) rg_real	50.84 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	1.0200e+09
I(0) uncertainty (real space) i0_real_error	1.9390e+07
Rg (reciprocal space) rg_reciprocal	51.00 Å
I(0) (reciprocal space) i0_reciprocal	1020000000.0000
Solution quality estimate total_estimate	0.8698
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	71.6 Å
Skewness Skewness skewness	0.196
Kurtosis Kurtosis kurtosis	-0.387
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	83200000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.836

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	D48 heavy chain
Molecular weight formula_weight	24742.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,D,E
Atom count atom_count	18665

EVQLVETGGGVVRPGRSLRLSCTTSGFSFSGSAMHWVRQAPGKGLEWVAVISHDGNIIQYHDSVKGRFTISRDNSKNVLLLQMNSLRVDDTAMYYCARDVWLLPATISYAFDFWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVGSHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	D48 light chain
Molecular weight formula_weight	23476.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,F,G

VIWMTQSPPSLSASIGDTVTITCRASQGISNSIAWYQRRPGKAPELLVYAAYRLQSGVPSRLSGSGSGAEYTLTIKNMQPEDFATYYCQQYYDNPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein B
Molecular weight formula_weight	70337.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

ANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPNPTPPPPGASANASVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHA

来源 Source

来源生物 organism	Human herpesvirus 1 (strain KOS)
NCBI Class编号 ncbi_taxonomy_id	10306
宿主生物 host_organism	Homo sapiens

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.04 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	168888

fit	/app/data/saxs_computation/kf/8kfa/8kfa.fit
pddf	/app/data/pr_computation/kf/8kfa/8kfa.pr.out
profile	/app/data/saxs_computation/kf/8kfa/8kfa.dat

Cryo-EM structure of HSV-1 gB with D48 Fab complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)