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5t1d

Crystal structure of EBV gHgL/gp42/E1D1 complex

Method: X-RAY DIFFRACTION Dmax: 178.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein H

Epstein-Barr virus (strain B95-8)

UniProt P03231

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 2 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 20–674 Not recorded Envelope glycoprotein L × 1 （P03212） Glycoprotein 42 × 1 （P0C6Z5） E1D1 IgG2a heavy chain × 1 E1D1 IgG2a light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 5T1D 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31 Different construct Different oligomeric state 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 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 oligomeric state 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 oligomeric state 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
8TNT Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 19–674（656 aa）
Not recorded 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

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 1–655； UniProt 20–674

Envelope glycoprotein L

Epstein-Barr virus (strain B95-8)

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 Other combination Heteromer Protein × 5 其他Polymer 2 PDB declaration: pentameric（5） Consistent with protein copy count Chain B； UniProt 24–135 Not recorded Envelope glycoprotein H × 1 （P03231） Glycoprotein 42 × 1 （P0C6Z5） E1D1 IgG2a heavy chain × 1 E1D1 IgG2a light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 5T1D 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
5W0K Crystal structure of EBV gHgL/CL40/gp42 N-domain Deposited 2017-05-31 Different construct Different oligomeric state 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 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 oligomeric state 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 oligomeric state 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
8TNT Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2 Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 24–135（112 aa）
Not recorded 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

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 (strain GD1)

UniProt P0C6Z5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 2 PDB declaration: pentameric（5） Consistent with protein copy count Chain C； UniProt 33–223 Not recorded Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） E1D1 IgG2a heavy chain × 1 E1D1 IgG2a light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 5T1D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C5V An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus Deposited 2018-01-16 Different oligomeric state Different ligand/ion Different experimental method 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 × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 47–79（33 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 47–79（33 aa） Fragment：Residues 47-79
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
7YOY Cryo-EM structure of EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3 (localized refinement) Deposited 2022-08-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 88–223（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8KHR Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1 Deposited 2023-08-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 34–223（190 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9IVJ Cryo-EM structure of EBV gH/gL/gp42 in complex with fab 4G12 Deposited 2024-07-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 34–223（190 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GP42_EBVG
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

SAXS profile for 5t1d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5t1d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5t1d
Deposition date deposition_date2016-08-18
Structure title titleCrystal structure of EBV gHgL/gp42/E1D1 complex
Keywords keywordsreceptor binding, herpesvirus entry, Epstein-Barr Virus, membrane fusion, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.22 Å
Radius of gyration Rg (electron density) rg_electron52.97 Å
Forward intensity I(0) i0325394000.00
Molecular weight molecular_weight150800.0 kDa
Excluded volume excluded_volume189390 ų
Envelope volume envelope_volume266440 ų
Hydration-shell volume shell_volume48025 ų
Envelope diameter envelope_diameter191.9 Å
Shell Rg shell_rg46.25 Å
Envelope Rg envelope_rg53.34 Å
Shape Rg shape_rg52.95 Å
Total Rg total_rg52.79 Å
Total atoms total_atoms21034
Residues n_residues1356
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax178.8 Å
Rg (real space) rg_real52.98 Å
Rg uncertainty (real space) rg_real_error2.52 Å
I(0) (real space) i0_real3.2540e+08
I(0) uncertainty (real space) i0_real_error6.8020e+06
Rg (reciprocal space) rg_reciprocal51.57 Å
I(0) (reciprocal space) i0_reciprocal324800000.0000
Solution quality estimate total_estimate0.7192
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.8 Å
Skewness Skewness skewness0.649
Kurtosis Kurtosis kurtosis-0.344
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15570000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.535; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.598; Smooth: 0.143
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5t1dh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5t1dl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5t1dl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id5t1dA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
Homologous superfamily homologous superfamily20 — Herpesvirus glycoprotein H, domain D-II
Domain ID domain_id5t1dB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology390 — SAND domain
Homologous superfamily homologous superfamily20 — Viral glycoprotein L
Domain ID domain_id5t1dH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5t1dH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5t1dL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5t1dL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)