9LOY
Cryo-EM structure of SARS-CoV-2 JN.1 spike glycoprotein in complex with F61R2-780 Fab
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B, C (A, B, C) | Spike glycoprotein | polymer | 1200 | 133286.1 | 3 | UniProt (P0DTC2) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, F (E, H) | F61R2-780 heavy chain | polymer | 117 | 12993.5 | 2 | Homo sapiens | ||
| 3 | E, G (F, I) | F61R2-780 light chain | polymer | 106 | 11449.7 | 2 | Homo sapiens | ||
| 4 | AA, BA, CA, DA, EA... (C, A, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 25 | Chemie (NAG) |
Sequence modifications
A, B, C: 4 - 1208 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Ile 22 | Thr 19 | variant |
| Thr 24 | Arg 21 | conflict |
| - | Leu 24 | deletion |
| - | Pro 25 | deletion |
| - | Pro 26 | deletion |
| Ser 27 | Ala 27 | conflict |
| Leu 50 | Ser 50 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Phe 127 | Val 127 | conflict |
| Asp 142 | Gly 142 | variant |
| - | Tyr 145 | deletion |
| Ser 157 | Phe 157 | conflict |
| Gly 158 | Arg 158 | conflict |
| - | Asn 211 | deletion |
| Ile 212 | Leu 212 | conflict |
| Gly 213 | Val 213 | variant |
| Phe 216 | Leu 216 | conflict |
| Asn 245 | His 245 | conflict |
| Asp 264 | Ala 264 | conflict |
| Val 332 | Ile 332 | conflict |
| His 339 | Gly 339 | variant |
| Thr 356 | Lys 356 | conflict |
| Phe 371 | Ser 371 | variant |
| Pro 373 | Ser 373 | variant |
| Phe 375 | Ser 375 | variant |
| Ala 376 | Thr 376 | variant |
| Lys 403 | Arg 403 | conflict |
| Asn 405 | Asp 405 | variant |
| Ser 408 | Arg 408 | variant |
| Asn 417 | Lys 417 | variant |
| Lys 440 | Asn 440 | variant |
| His 445 | Val 445 | conflict |
| Ser 446 | Gly 446 | variant |
| Asp 450 | Asn 450 | conflict |
| Trp 452 | Leu 452 | conflict |
| Ser 455 | Leu 455 | conflict |
| Lys 460 | Asn 460 | variant |
| Asn 477 | Ser 477 | variant |
| Lys 478 | Thr 478 | variant |
| Lys 481 | Asn 481 | conflict |
| - | Val 483 | deletion |
| Lys 484 | Glu 484 | variant |
| Pro 486 | Phe 486 | variant |
| Arg 498 | Gln 498 | variant |
| Tyr 501 | Asn 501 | variant |
| His 505 | Tyr 505 | variant |
| Lys 554 | Glu 554 | conflict |
| Val 570 | Ala 570 | conflict |
| Gly 614 | Asp 614 | variant |
| Ser 621 | Pro 621 | conflict |
| Tyr 655 | His 655 | variant |
| Lys 679 | Asn 679 | variant |
| Arg 681 | Pro 681 | variant |
| Gly 682 | Arg 682 | conflict |
| Ser 683 | Arg 683 | conflict |
| Ser 685 | Arg 685 | conflict |
| Lys 764 | Asn 764 | variant |
| Tyr 796 | Asp 796 | variant |
| Pro 817 | Phe 817 | engineered mutation |
| Pro 892 | Ala 892 | engineered mutation |
| Pro 899 | Ala 899 | engineered mutation |
| Phe 939 | Ser 939 | conflict |
| Pro 942 | Ala 942 | engineered mutation |
| His 954 | Gln 954 | variant |
| Lys 969 | Asn 969 | variant |
| Pro 986 | Lys 986 | engineered mutation |
| Pro 987 | Val 987 | engineered mutation |
| Leu 1143 | Pro 1143 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 7 |
| Total formula weight | 448744.7 | |
| Non-Polymers* | Number of molecules | 25 |
| Total formula weight | 5530.2 | |
| All* | Total formula weight | 454274.9 |
