9ELN
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (one RBD up state)
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 | 1199 | 133213.0 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, H, I, J, K... (D, H, I, J, K...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 7 | In PDB GlyTouCan (G42666HT) | |||
| 3 | E, F, G, L, N... (E, F, G, L, N...) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 7 | In PDB GlyTouCan (G15407YE) | |||
| 4 | AA, BA, CA, DA, EA... (A, B, C) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 21 | 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 |
| - | Ala 27 | deletion |
| Ser 27 | Tyr 28 | conflict |
| Tyr 28 | Thr 29 | conflict |
| Thr 29 | Asn 30 | conflict |
| Asn 30 | Ser 31 | conflict |
| Leu 50 | Ser 50 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Phe 127 | Val 127 | conflict |
| Asp 143 | Gly 142 | variant |
| - | Tyr 144 | 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 | conflict |
| Pro 892 | Ala 892 | conflict |
| Pro 899 | Ala 899 | conflict |
| Phe 939 | Ser 939 | conflict |
| Pro 942 | Ala 942 | conflict |
| His 954 | Gln 954 | variant |
| Lys 969 | Asn 969 | variant |
| Pro 986 | Lys 986 | conflict |
| Pro 987 | Val 987 | conflict |
| Leu 1104 | Val 1104 | conflict |
| Leu 1143 | Pro 1143 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 399639.1 | |
| Branched | Number of molecules | 14 |
| Total formula weight | 7076.6 | |
| Non-Polymers* | Number of molecules | 21 |
| Total formula weight | 4645.4 | |
| All* | Total formula weight | 411361.1 |
