8Y6A
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 and S309 Fab
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A | Angiotensin-converting enzyme 2 | polymer | 603 | 69982.6 | 1 | UniProt (Q9BYF1) Pfam (PF01401) In PDB | Homo sapiens (human) | ACE-related carboxypeptidase,Angiotensin-converting enzyme homolog,ACEH,Metalloprotease MPROT15 |
2 | B | Spike protein S1 | polymer | 228 | 26123.6 | 1 | UniProt (P0DTC2) Pfam (PF09408) In PDB | Severe acute respiratory syndrome coronavirus 2 | |
3 | C | heavy chain of S309 Fab | polymer | 230 | 24573.5 | 1 | Homo sapiens | ||
4 | D | light chain of S309 Fab | polymer | 214 | 23204.7 | 1 | Homo sapiens | ||
5 | E | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 748.7 | 1 | In PDB GlyTouCan (G81315DD) | |||
6 | F, H | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 2 | In PDB GlyTouCan (G15407YE) | |||
7 | G | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
8 | A, B | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 3 | Chemie (NAG) | |||
9 | A | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) |
Sequence modifications
A: 19 - 615 (UniProt: Q9BYF1)
B: 319 - 541 (UniProt: P0DTC2)
PDB | External Database | Details |
---|---|---|
His 616 | - | expression tag |
His 617 | - | expression tag |
His 618 | - | expression tag |
His 619 | - | expression tag |
His 620 | - | expression tag |
His 621 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Val 332 | Ile 332 | variant |
His 339 | Gly 339 | variant |
Thr 356 | Lys 356 | variant |
Phe 371 | Ser 371 | variant |
Pro 373 | Ser 373 | variant |
Phe 375 | Ser 375 | variant |
Ala 376 | Thr 376 | variant |
Lys 403 | Arg 403 | variant |
Asn 405 | Asp 405 | variant |
Ser 408 | Arg 408 | variant |
Asn 417 | Lys 417 | variant |
Lys 440 | Asn 440 | variant |
His 445 | Val 445 | variant |
Ser 446 | Gly 446 | variant |
Asp 450 | Asn 450 | variant |
Trp 452 | Leu 452 | variant |
Lys 460 | Asn 460 | variant |
Asn 477 | Ser 477 | variant |
Lys 478 | Thr 478 | variant |
Lys 481 | Asn 481 | variant |
- | 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 |
His 542 | - | expression tag |
His 543 | - | expression tag |
His 544 | - | expression tag |
His 545 | - | expression tag |
His 546 | - | expression tag |
His 547 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 4 |
Total formula weight | 143884.4 | |
Branched | Number of molecules | 4 |
Total formula weight | 2346.2 | |
Non-Polymers* | Number of molecules | 4 |
Total formula weight | 729.0 | |
All* | Total formula weight | 146959.6 |