8tnt

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2

Method: X-RAY DIFFRACTION D_max: 213.7 Å Quality: GOOD

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

Envelope glycoprotein H

Epstein-Barr virus

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 19–674	Not recorded	Envelope glycoprotein L × 1 （P03212） Glycoprotein 42 × 1 （P03205） 769C2 light chain × 1 769C2 heavy chain × 1 F-2-1 light chain × 1 F-2-1 heavy chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；280 K；20mM Tris pH7.5, 150mM NaCl, 4% Tacsimate pH 7.0, and 10% PEG 3,350	Resolution 3.15 Å R-free 0.287

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 8TNT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 1 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 3 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 5 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 20–672（653 aa） Fragment：EXTRACELLULAR DOMAIN (unp residue 20-672)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
5T1D Crystal structure of EBV gHgL/gp42/E1D1 complex Deposited 2016-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 20–674（655 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1 M Tris pH 8.0, 0.18 M Potassium Citrate, 12 % PEG 6000	Resolution 3.10 Å R-free 0.265
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 20–679（660 aa） Fragment：UNP residues 20-679	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000	Resolution 3.10 Å R-free 0.299
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 20–679（660 aa） Fragment：UNP residues 20-679	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000	Resolution 3.10 Å R-free 0.299
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 18–674（657 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 18–674（657 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 18–674（657 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 18–674（657 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7S07 Crystal structure of Epstein-Barr virus glycoprotein gH/gL/gp42-peptide in complex with human neutralizing antibodies 769B10 and 769C2 Deposited 2021-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 18–674（657 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris pH6.5, 20% PEG3350, 7.5% Glycerol, 0.7% Dioxane	Resolution 3.29 Å R-free 0.291
7S1B Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7 Deposited 2021-09-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 18–674（657 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 24% PEG3350, 7.5% Glycerol	Resolution 3.03 Å R-free 0.288
8TNN Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10 Deposited 2023-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 17–674（658 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350	Resolution 3.36 Å R-free 0.281
8TNN Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10 Deposited 2023-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 17–674（658 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350	Resolution 3.36 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	GH_EBVB9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–656； UniProt 19–674

Envelope glycoprotein L

Epstein-Barr virus

UniProt P03212

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain B； UniProt 24–135	Not recorded	Envelope glycoprotein H × 1 （P03231） Glycoprotein 42 × 1 （P03205） 769C2 light chain × 1 769C2 heavy chain × 1 F-2-1 light chain × 1 F-2-1 heavy chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；280 K；20mM Tris pH7.5, 150mM NaCl, 4% Tacsimate pH 7.0, and 10% PEG 3,350	Resolution 3.15 Å R-free 0.287

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8TNT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 2 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 4 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 6 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
3PHF Crystal Structure of the Epstein-Barr virus gH and gL complex Deposited 2010-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 24–131（108 aa） Fragment：EXTRACELLULAR DOMAIN (unp residues 24-131)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；24% PEG 1000, 0.1M Sodium Citrate, 0.2M NDSB256-4T , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.58 Å R-free 0.313
5T1D Crystal structure of EBV gHgL/gp42/E1D1 complex Deposited 2016-08-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 24–135（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1 M Tris pH 8.0, 0.18 M Potassium Citrate, 12 % PEG 6000	Resolution 3.10 Å R-free 0.265
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 24–137（114 aa） Fragment：UNP residues 24-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000	Resolution 3.10 Å R-free 0.299
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 24–137（114 aa） Fragment：UNP residues 24-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000	Resolution 3.10 Å R-free 0.299
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–132（109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 24–132（109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 24–132（109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7CZE Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2 Deposited 2020-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 24–132（109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350	Resolution 3.00 Å R-free 0.285
7S07 Crystal structure of Epstein-Barr virus glycoprotein gH/gL/gp42-peptide in complex with human neutralizing antibodies 769B10 and 769C2 Deposited 2021-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 27–124（98 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris pH6.5, 20% PEG3350, 7.5% Glycerol, 0.7% Dioxane	Resolution 3.29 Å R-free 0.291
7S1B Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7 Deposited 2021-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 24–137（114 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 24% PEG3350, 7.5% Glycerol	Resolution 3.03 Å R-free 0.288
8TNN Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10 Deposited 2023-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 24–135（112 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350	Resolution 3.36 Å R-free 0.281
8TNN Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10 Deposited 2023-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 24–135（112 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350	Resolution 3.36 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	GL_EBVB9
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–112； UniProt 24–135

Glycoprotein 42

Epstein-Barr virus

UniProt P03205

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain C； UniProt 33–223	Not recorded	Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） 769C2 light chain × 1 769C2 heavy chain × 1 F-2-1 light chain × 1 F-2-1 heavy chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；280 K；20mM Tris pH7.5, 150mM NaCl, 4% Tacsimate pH 7.0, and 10% PEG 3,350	Resolution 3.15 Å R-free 0.287

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8TNT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KG0 Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor HLA-DR1 Deposited 2001-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 86–221（136 aa） Fragment：Extracellular Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；300 K；PEG 4000, Ammonium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.65 Å R-free 0.247
3FD4 Crystal Structure of Epstein-Barr virus gp42 protein Deposited 2008-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 33–223（191 aa） Chain B 33–223（191 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；298 K；30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION	Resolution 2.40 Å R-free 0.242
3FD4 Crystal Structure of Epstein-Barr virus gp42 protein Deposited 2008-11-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–223（191 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；298 K；30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION	Resolution 2.40 Å R-free 0.242
3FD4 Crystal Structure of Epstein-Barr virus gp42 protein Deposited 2008-11-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–223（191 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；298 K；30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION	Resolution 2.40 Å R-free 0.242
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain X 47–81（35 aa） Fragment：UNP residues 47-81	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000	Resolution 3.10 Å R-free 0.299
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain Y 47–81（35 aa） Fragment：UNP residues 47-81	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.25 M sodium sulfate, 0.1 M Bis-tris propane pH 8.5, 20 % (w/v) PEG 4000	Resolution 3.10 Å R-free 0.299
8TNN Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10 Deposited 2023-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 33–223（191 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350	Resolution 3.36 Å R-free 0.281
8TNN Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10 Deposited 2023-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 33–223（191 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350	Resolution 3.36 Å R-free 0.281
8TOO Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12 Deposited 2023-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 85–223（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350	Resolution 2.60 Å R-free 0.275
8TOO Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12 Deposited 2023-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 85–223（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350	Resolution 2.60 Å R-free 0.275
8TOO Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12 Deposited 2023-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 85–223（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350	Resolution 2.60 Å R-free 0.275
8TOO Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12 Deposited 2023-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 85–223（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350	Resolution 2.60 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	GP42_EBVB9
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–191； UniProt 33–223

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	8tnt
Deposition date deposition_date	2023-08-02
Structure title title	Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2
Keywords keywords	Viral Protein, Antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	60.80 Å
Radius of gyration Rg (electron density) rg_electron	62.02 Å
Forward intensity I(0) i0	546725000.00
Molecular weight molecular_weight	195010.0 kDa
Excluded volume excluded_volume	244100 Å³
Envelope volume envelope_volume	367790 Å³
Hydration-shell volume shell_volume	57198 Å³
Envelope diameter envelope_diameter	230.4 Å
Shell Rg shell_rg	49.86 Å
Envelope Rg envelope_rg	63.05 Å
Shape Rg shape_rg	62.00 Å
Total Rg total_rg	61.69 Å
Total atoms total_atoms	13731
Residues n_residues	1810
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	213.7 Å
Rg (real space) rg_real	62.00 Å
Rg uncertainty (real space) rg_real_error	2.20 Å
I(0) (real space) i0_real	5.4660e+08
I(0) uncertainty (real space) i0_real_error	1.0900e+07
Rg (reciprocal space) rg_reciprocal	59.74 Å
I(0) (reciprocal space) i0_reciprocal	544700000.0000
Solution quality estimate total_estimate	0.7721
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.1 Å
Skewness Skewness skewness	0.646
Kurtosis Kurtosis kurtosis	-0.149
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0006
Highest regularization parameter α highest_alpha	19130000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.611; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.698; Smooth: 0.504

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	72687.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13731

SLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

来源 Source

来源生物 organism	Epstein-Barr virus
NCBI Class编号 ncbi_taxonomy_id	10376
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	12475.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHR

来源 Source

来源生物 organism	Epstein-Barr virus
NCBI Class编号 ncbi_taxonomy_id	10376
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Glycoprotein 42
Molecular weight formula_weight	21626.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNS

来源 Source

来源生物 organism	Epstein-Barr virus
NCBI Class编号 ncbi_taxonomy_id	10376
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	769C2 light chain
Molecular weight formula_weight	22842.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

QSVLTQPASVSGSLGQSVTISCTGTSSDVGGYDYVSWYQQHPGKALKLMIFEVNNRPSGVSTRFSGSKSGNTASLTISGLQAEDEADYYCNSYSTTTTWVFGGGTSLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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 5 Entity 5 polymer

Description description	769C2 heavy chain
Molecular weight formula_weight	24670.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYAMDWVRQAPGKGLEWVSLISSRSSNIYYSDSVKGRFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREAGGFHSHFDMWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

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 6 Entity 6 polymer

Description description	F-2-1 light chain
Molecular weight formula_weight	23723.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCLHSRDLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	F-2-1 heavy chain
Molecular weight formula_weight	24759.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

EVKLLESGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTSSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGDWWYFDVWGAGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	117.317 Å
Unit-cell length b length_b	85.172 Å
Unit-cell length c length_c	119.714 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	46.320 Å
R factor r_factor	0.2562
R_work r_work	0.2545
R_free r_free	0.2866

fit	/app/data/saxs_computation/tn/8tnt/8tnt.fit
pddf	/app/data/pr_computation/tn/8tnt/8tnt.pr.out
profile	/app/data/saxs_computation/tn/8tnt/8tnt.dat

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2

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

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein L

State in the Current Structure

Other States of the Same Protein in the Database

Glycoprotein 42

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

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

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

Entity 8 Entity 8 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)