4bom

Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction

Method: ELECTRON MICROSCOPY D_max: 184.7 Å Quality: GOOD

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

ENVELOPE GLYCOPROTEIN B

HUMAN HERPESVIRUS 1

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 103–724 Chain B； UniProt 103–724 Chain C； UniProt 103–724	Fragment：GLYCOPROTEIN B ECTODOMAIN, RESIDUES 103-724	No other associated polymer	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

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 4BOM	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 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 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 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 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 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 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 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 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 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 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 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 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 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
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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 30 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 1–622； UniProt 103–724 Author chain B； PDBConstruct 1–622； UniProt 103–724 Author chain C； PDBConstruct 1–622； UniProt 103–724

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bom
Deposition date deposition_date	2013-05-21
Structure title title	Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction
Keywords keywords	VIRAL PROTEIN, MEMBRANE PROXIMAL REGION, PROTEIN COAT, PSEUDO-ATOMIC VIRUS-HOST INTERACTION; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	51.70 Å
Radius of gyration Rg (electron density) rg_electron	52.01 Å
Forward intensity I(0) i0	667586000.00
Molecular weight molecular_weight	209070.0 kDa
Excluded volume excluded_volume	259460 Å³
Envelope volume envelope_volume	392240 Å³
Hydration-shell volume shell_volume	66914 Å³
Envelope diameter envelope_diameter	176.7 Å
Shell Rg shell_rg	49.74 Å
Envelope Rg envelope_rg	51.46 Å
Shape Rg shape_rg	52.00 Å
Total Rg total_rg	51.95 Å
Total atoms total_atoms	14745
Residues n_residues	1824
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

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

Maximum dimension Dmax dmax	184.7 Å
Rg (real space) rg_real	52.10 Å
Rg uncertainty (real space) rg_real_error	2.57 Å
I(0) (real space) i0_real	6.6760e+08
I(0) uncertainty (real space) i0_real_error	1.5330e+07
Rg (reciprocal space) rg_reciprocal	51.35 Å
I(0) (reciprocal space) i0_reciprocal	666900000.0000
Solution quality estimate total_estimate	0.8051
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.2 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.460
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	53050000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.822

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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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	1

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

Resolution resolution	27.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	27.00 Å
Resolution测定方法 resolution_method	SUBTOMOGRAM AVERAGING
颗粒数 num_particles	786

Description description	ENVELOPE GLYCOPROTEIN B
Molecular weight formula_weight	71125.7 kDa
Source method src_method	man
Copy count entity_count	3

Structure of herpesvirus fusion glycoprotein B-bilayer complex revealing the protein-membrane and lateral protein-protein interaction

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

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	14745

来源生物 organism	HUMAN HERPESVIRUS 1
通用名 common_name	HUMAN HERPES SIMPLEX VIRUS 1
NCBI Class编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	Spodoptera frugiperda

fit	/app/data/saxs_computation/bo/4bom/4bom.fit
pddf	/app/data/pr_computation/bo/4bom/4bom.pr.out
profile	/app/data/saxs_computation/bo/4bom/4bom.dat