8IFY
Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2
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 | 1127 | 125148.0 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, E (E, F) | Angiotensin-converting enzyme | polymer | 661 | 76530.5 | 2 | UniProt (A0A6J0Z472) Pfam (PF01401) | Odocoileus virginianus (white-tailed deer) | |
| 3 | F, G, H, I, J... (G, H, I, J, K...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 14 | In PDB GlyTouCan (G42666HT) | |||
| 4 | AA, BA, CA, DA, EA... (B, C, E, F, A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 25 | Chemie (NAG) | |||
| 5 | NA, TA (E, F) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
A, B, C: 30 - 1145 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Gln 19 | - | expression tag |
| Cys 20 | - | expression tag |
| Val 21 | - | expression tag |
| Asn 22 | - | expression tag |
| Leu 23 | - | expression tag |
| Ile 24 | - | expression tag |
| Thr 25 | - | expression tag |
| Arg 26 | - | expression tag |
| Thr 27 | - | expression tag |
| Gln 28 | - | expression tag |
| Ser 29 | - | expression tag |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Asp 142 | Gly 142 | variant |
| Gly 213 | Val 213 | variant |
| Asp 339 | Gly 339 | variant |
| Phe 371 | Ser 371 | variant |
| Pro 373 | Ser 373 | variant |
| Phe 375 | Ser 375 | variant |
| Ala 376 | Thr 376 | variant |
| Asn 405 | Asp 405 | variant |
| Ser 408 | Arg 408 | variant |
| Asn 417 | Lys 417 | variant |
| Lys 440 | Asn 440 | variant |
| Arg 452 | Leu 452 | variant |
| Asn 477 | Ser 477 | variant |
| Lys 478 | Thr 478 | variant |
| Ala 484 | Glu 484 | variant |
| Val 486 | Phe 486 | variant |
| Arg 498 | Gln 498 | variant |
| Tyr 501 | Asn 501 | variant |
| His 505 | Tyr 505 | variant |
| Gly 614 | Asp 614 | variant |
| Tyr 655 | His 655 | variant |
| Lys 679 | Asn 679 | variant |
| His 681 | Pro 681 | variant |
| 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 |
| 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 |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 528505.1 | |
| Branched | Number of molecules | 14 |
| Total formula weight | 5941.6 | |
| Non-Polymers* | Number of molecules | 27 |
| Total formula weight | 5661.0 | |
| All* | Total formula weight | 540107.7 |
