← Back to search
8sm0

Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350

Method: X-RAY DIFFRACTION Dmax: 97.6 Å Quality: GOOD
▼

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

Complement receptor type 2

Homo sapiens

UniProt P20023

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 21–149 Fragment：first two amino-terminal domains Envelope glycoprotein gp350 × 1 （P03200） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5 Resolution 1.68 Å R-free 0.241

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 8SM0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GHQ CR2-C3D COMPLEX STRUCTURE Deposited 2001-01-11 Different construct Different mutation/modification 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 21–153（133 aa） Fragment：SEQUENCE DATABASE RESIDUES 21-153
Chain C 21–153（133 aa） Fragment：SEQUENCE DATABASE RESIDUES 21-153
Not recorded ZN ZINC ION × 2 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 2.04 Å R-free 0.239
1LY2 Crystal structure of unliganded human CD21 SCR1-SCR2 (Complement receptor type 2) Deposited 2002-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–149（130 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K
Resolution 1.80 Å R-free 0.234
1W2R Solution structure of CR2 SCR 1-2 by X-ray scattering Deposited 2004-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–153（133 aa）
Not recorded No recorded non-water small molecule SOLUTION SCATTERING mmCIF provides none of the parsed conditions Resolution not provided
1W2S Solution structure of CR2 SCR 1-2 in its complex with C3d by X-ray scattering Deposited 2004-07-08 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–153（133 aa）
Not recorded No recorded non-water small molecule SOLUTION SCATTERING mmCIF provides none of the parsed conditions Resolution not provided
2ATY Complement receptor chimaeric conjugate CR2-Ig Deposited 2005-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–153（133 aa）
Chain B 21–153（133 aa）
Not recorded No recorded non-water small molecule SOLUTION SCATTERING mmCIF provides none of the parsed conditions Resolution not provided
2GSX Complement Receptor Type 2 Deposited 2006-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–971（951 aa）
Not recorded No recorded non-water small molecule SOLUTION SCATTERING mmCIF provides none of the parsed conditions Resolution not provided
3OED The structure of the complex between complement receptor CR2 and its ligand complement fragment C3d Deposited 2010-08-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–153（134 aa） Fragment：CR2 (unp residues 20-153)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；100 mM HEPES, 20% Poly Ethylene Glycol 6000, 200 mM CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Resolution 3.16 Å R-free 0.259
3OED The structure of the complex between complement receptor CR2 and its ligand complement fragment C3d Deposited 2010-08-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 20–153（134 aa） Fragment：CR2 (unp residues 20-153)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；100 mM HEPES, 20% Poly Ethylene Glycol 6000, 200 mM CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Resolution 3.16 Å R-free 0.259
8ZNI Structure of Epstein-Barr virus major glycoprotein gp350 in complex with the receptor CR2 Deposited 2024-05-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–971（971 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CR2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–129； UniProt 21–149

Envelope glycoprotein gp350

Human herpesvirus 4

UniProt P03200

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 1–425 Not recorded Complement receptor type 2 × 1 （P20023） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5 Resolution 1.68 Å R-free 0.241

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 8SM0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SGN Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–425（425 aa）
Not recorded EDO 1,2-ETHANEDIOL × 23 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.72M ammonium sulfate, 0.1M Tris pH 8.0
Resolution 2.20 Å R-free 0.237
8SIC Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine Deposited 2023-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–425（425 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；18% PEG 8000, 0.22 M sodium acetate, 0.1 M sodium cacodylate pH 6.5
Resolution 2.76 Å R-free 0.295
8SIC Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine Deposited 2023-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–425（425 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；18% PEG 8000, 0.22 M sodium acetate, 0.1 M sodium cacodylate pH 6.5
Resolution 2.76 Å R-free 0.295
8SM1 CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350 Deposited 2023-04-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–425（425 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5
Resolution 3.29 Å R-free 0.298
9MA0 Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11 Deposited 2025-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–470（470 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.33 Å
9MA7 Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9 Deposited 2025-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–470（470 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.14 Å

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

View Construct and Data Evidence
UniProt name GP350_EBVB9
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 1–425； UniProt 1–425

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 8sm0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8sm0
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8sm0
Deposition date deposition_date2023-04-25
Structure title titleCrystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350
Keywords keywordsVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier28.32 Å
Radius of gyration Rg (electron density) rg_electron27.68 Å
Forward intensity I(0) i060977400.00
Molecular weight molecular_weight60259.0 kDa
Excluded volume excluded_volume75057 ų
Envelope volume envelope_volume96903 ų
Hydration-shell volume shell_volume30104 ų
Envelope diameter envelope_diameter103.3 Å
Shell Rg shell_rg33.94 Å
Envelope Rg envelope_rg27.89 Å
Shape Rg shape_rg27.66 Å
Total Rg total_rg28.38 Å
Total atoms total_atoms8289
Residues n_residues529
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
▼

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

Maximum dimension Dmax dmax97.6 Å
Rg (real space) rg_real28.41 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real6.0980e+07
I(0) uncertainty (real space) i0_real_error8.6760e+05
Rg (reciprocal space) rg_reciprocal28.39 Å
I(0) (reciprocal space) i0_reciprocal60980000.0000
Solution quality estimate total_estimate0.8704
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.424
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13420000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.957
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)