Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350. Determined by X-ray diffraction at 1.68 Å resolution. Released 1 May 2024.
Explore 8SM0 in 3D Show helices and sheets RCSB PDB PDBe
8SM0 contains 14 α-helices and 50 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 1 |
| α-helix | 6-8 | 3 | |
| β-strand | 12-14 | 3 | 2 |
| β-strand | 21 | 1 | 1 |
| α-helix | 22 | 1 | |
| β-strand | 26-28 | 3 | 3 |
| β-strand | 29-31 | 3 | 2 |
| β-strand | 36-38 | 3 | 4 |
| β-strand | 42-44 | 3 | 3 |
| β-strand | 45-46 | 2 | 5 |
| β-strand | 54-55 | 2 | 5 |
| β-strand | 61-63 | 3 | 4 |
| β-strand | 70-71 | 2 | 6 |
| α-helix | 72-74 | 3 | |
| β-strand | 79-83 | 5 | 7 |
| β-strand | 88-89 | 2 | 6 |
| β-strand | 93-98 | 6 | 7 |
| β-strand | 103-105 | 3 | 8 |
| β-strand | 109-112 | 4 | 7 |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 122-124 | 3 | |
| β-strand | 125-127 | 3 | 8 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 10-16 | 7 | 9 |
| β-strand | 25-30 | 6 | 10 |
| β-strand | 44-54 | 11 | 9 |
| β-strand | 57-68 | 12 | 9 |
| β-strand | 75-76 | 2 | 10 |
| β-strand | 80-82 | 3 | 9 |
| α-helix | 88-91 | 4 | |
| β-strand | 92-98 | 7 | 10 |
| β-strand | 101-107 | 7 | 10 |
| β-strand | 123-133 | 11 | 9 |
| α-helix | 138 | 1 | |
| β-strand | 139-151 | 13 | 9 |
| α-helix | 152 | 1 | |
| α-helix | 156-159 | 4 | |
| β-strand | 166-167 | 2 | 11 |
| β-strand | 172-175 | 4 | 11 |
| β-strand | 178-180 | 3 | 11 |
| β-strand | 181-187 | 7 | 12 |
| β-strand | 196 | 1 | 13 |
| β-strand | 197-204 | 8 | 11 |
| β-strand | 207-213 | 7 | 11 |
| β-strand | 218 | 1 | 13 |
| α-helix | 221-222 | 2 | |
| β-strand | 224-229 | 6 | 12 |
| β-strand | 230-232 | 3 | 11 |
| α-helix | 236-237 | 2 | |
| α-helix | 240-241 | 2 | |
| β-strand | 242-247 | 6 | 12 |
| β-strand | 260-267 | 8 | 12 |
| α-helix | 273-275 | 3 | |
| β-strand | 279-286 | 8 | 11 |
| β-strand | 297-305 | 9 | 11 |
| α-helix | 315-316 | 2 | |
| β-strand | 318-324 | 7 | 14 |
| β-strand | 329-333 | 5 | 15 |
| α-helix | 334-336 | 3 | |
| β-strand | 346-352 | 7 | 14 |
| β-strand | 365-367 | 3 | 14 |
| β-strand | 379-383 | 5 | 15 |
| β-strand | 389-393 | 5 | 15 |
| β-strand | 401-409 | 9 | 14 |
| β-strand | 415-423 | 9 | 14 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Complement receptor type 2 | C | protein | 129 | Homo sapiens | P20023 (AlphaFold model) |
| Envelope glycoprotein gp350 | G | protein | 431 | Human herpesvirus 4 | P03200 (AlphaFold model) |
>8SM0_1 Complement receptor type 2 (chains C) ISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAP KCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGP TRLPTCVSV
>8SM0_2 Envelope glycoprotein gp350 (chains G) MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQ LDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEE QQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLD VTLPLSLPTSAQDSNFSVKTEMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVP SGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQ SNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTET DFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVI FSKAPHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 12 |
Water and common crystallization additives (SO4) are not listed.
Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350. Joyce, M.G., Bu, W., Chen, W.H. et al. Immunity (2025) 58:295. DOI 10.1016/j.immuni.2025.01.010 · PubMed
Other PDB entries of the same protein (UniProt P20023 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 8SM0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.