Cryo-Em Structure of Sars-Cov-2 Spike Protein in complex with Double Nabs 3E2 and 1C4 (Local Refinement)
| PDB | 8iv8 |
| Species | MUS MUSCULUS |
| Method | ELECTRON MICROSCOPY |
| Resolution | 3.92Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Kappa |
| Has constant region | False |
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Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV5 |
| Light subgroup | IGKV4 |
| Species | MUS MUSCULUS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 52A | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 82A | 82B | 82C | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 100A | 100B | 100C | 100D | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| E | V | M | L | V | E | S | G | G | G | V | V | K | P | G | G | S | L | K | L | S | C | A | A | S | G | F | S | F | S | T | Y | A | M | S | W | I | R | Q | T | P | E | K | S | L | E | W | V | A | A | I | S | S | G | G | T | N | T | Y | Y | P | G | S | V | K | G | R | F | T | I | S | R | D | K | A | M | N | T | L | Y | L | Q | L | S | S | L | R | S | E | D | T | A | M | Y | Y | C | V | R | H | S | G | N | Y | V | D | S | V | M | D | Y | W | G | Q | G | T | S | V | T | V | S | S |
Light chain
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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| Q | I | V | L | T | Q | S | P | A | I | M | S | A | S | L | G | E | E | I | T | L | T | C | S | V | S | S | S | V | S | D | M | H | W | Y | Q | Q | K | S | G | T | S | P | K | V | F | I | Y | S | T | S | N | L | A | S | G | V | P | S | R | F | S | G | S | G | S | G | T | F | Y | S | L | T | I | S | S | V | E | A | E | D | A | A | Y | Y | Y | C | H | Q | W | S | S | W | T | F | G | G | G | T | K | L | E | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | G |
| Antigen type | protein |
| Antigen name | spike protein s1 |
| Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
| Antigen sequence | ESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFSFSTY |
| CDRH2 | SSGGTN |
| CDRH3 | HSGNYVDSVMDY |
| CDRL1 | SVSSSVSDMH |
| CDRL2 | STSNLAS |
| CDRL3 | HQWSSWT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -59.09° |
| HC1 | 72.67° |
| HC2 | 118.58° |
| LC1 | 116.81° |
| LC2 | 83.23° |
| dc | 16.54Å |
| Fv Details | |
|---|---|
| Heavy chain | C |
| Light chain | D |
| Heavy subgroup | IGHV9 |
| Light subgroup | IGKV5 |
| Species | MUS MUSCULUS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 52A | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 82A | 82B | 82C | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 100A | 100B | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| Q | I | Q | L | V | Q | S | G | P | E | L | K | K | P | G | E | T | V | K | I | S | C | K | A | S | G | Y | T | F | T | D | Y | G | L | N | W | V | K | Q | A | P | G | K | G | L | K | W | M | G | W | I | N | T | Y | S | G | E | P | T | Y | N | D | E | F | R | G | R | F | A | F | S | L | E | T | S | T | I | T | A | Y | L | K | I | N | N | L | K | N | E | D | T | A | T | Y | F | C | A | R | G | G | N | W | D | W | Y | F | D | V | W | G | A | G | T | T | V | T | V | S | S |
Light chain
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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| D | I | V | L | T | Q | S | P | A | T | L | S | V | T | P | G | D | N | V | S | L | S | C | R | A | S | Q | I | I | S | N | N | L | H | W | Y | Q | Q | K | S | H | E | S | P | R | L | L | I | K | Y | A | S | Q | S | I | S | G | I | P | S | R | F | S | G | S | G | S | G | T | D | F | T | L | S | I | N | S | V | E | T | E | D | F | G | M | Y | F | C | Q | Q | S | N | T | W | P | L | T | C | G | S | G | T | K | L | E | L | N |
| Antigen Details | |
|---|---|
| Antigen chains | G |
| Antigen type | protein |
| Antigen name | spike protein s1 |
| Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
| Antigen sequence | ESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYTFTDY |
| CDRH2 | NTYSGE |
| CDRH3 | GGNWDWYFDV |
| CDRL1 | RASQIISNNLH |
| CDRL2 | YASQSIS |
| CDRL3 | QQSNTWPLT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -58.32° |
| HC1 | 74.16° |
| HC2 | 113.35° |
| LC1 | 121.67° |
| LC2 | 83.24° |
| dc | 16.69Å |
Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]
SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]
Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link]
