Cryo-Em Structure of Hiv-1 Bg505Ds-Sosip.664 Env Trimer Bound to Dj85-C.01 Fab
| PDB | 8tl2 |
| Species | HOMO SAPIENS |
| Method | ELECTRON MICROSCOPY |
| Resolution | 3.2Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Kappa |
| Has constant region | True |
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Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | G |
| Light chain | H |
| Heavy subgroup | IGHV4 |
| Light subgroup | IGKV1 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| 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 | 31A | 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 | 100E | 100F | 100G | 100H | 100I | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| Q | V | Q | L | Q | E | S | G | P | G | L | V | K | P | S | E | T | L | S | L | T | C | A | V | S | G | V | S | I | S | G | N | Y | Y | W | N | W | I | R | Q | S | P | G | K | G | L | E | W | I | G | N | I | H | G | N | T | A | A | T | V | Y | N | P | S | L | G | S | R | V | T | F | S | R | D | T | S | K | N | Q | F | S | L | R | L | D | S | V | T | A | A | D | T | A | V | Y | F | C | A | T | L | Y | E | F | R | V | Y | M | G | E | R | I | S | Y | H | D | Y | W | G | Q | G | L | L | V | T | V | S | A |
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 | Q | M | T | Q | S | P | S | S | L | S | A | S | V | G | D | R | V | T | I | S | C | R | A | S | Q | D | I | S | S | D | L | N | W | Y | Q | Q | K | P | G | K | P | P | Q | L | L | I | Y | F | A | S | N | L | Q | S | G | V | P | S | R | F | S | G | S | G | A | G | T | E | F | T | L | T | I | N | S | L | Q | A | E | D | F | A | S | Y | F | C | L | Q | Y | Q | S | Y | P | W | T | F | G | Q | G | T | M | V | D | L | K |
| Antigen Details | |
|---|---|
| Antigen chains | B,A |
| Antigen type | protein |
| Antigen name | bg505 ds-sosip transmembrane protein gp41; bg505 ds-sosip surface protein gp120 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GVSISGNY |
| CDRH2 | HGNTAA |
| CDRH3 | LYEFRVYMGERISYHDY |
| CDRL1 | RASQDISSDLN |
| CDRL2 | FASNLQS |
| CDRL3 | LQYQSYPWT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -57.83° |
| HC1 | 73.83° |
| HC2 | 118.4° |
| LC1 | 118.24° |
| LC2 | 82.66° |
| dc | 16.76Å |
| Fv Details | |
|---|---|
| Heavy chain | K |
| Light chain | L |
| Heavy subgroup | IGHV4 |
| Light subgroup | IGKV1 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| 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 | 31A | 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 | 100E | 100F | 100G | 100H | 100I | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| Q | V | Q | L | Q | E | S | G | P | G | L | V | K | P | S | E | T | L | S | L | T | C | A | V | S | G | V | S | I | S | G | N | Y | Y | W | N | W | I | R | Q | S | P | G | K | G | L | E | W | I | G | N | I | H | G | N | T | A | A | T | V | Y | N | P | S | L | G | S | R | V | T | F | S | R | D | T | S | K | N | Q | F | S | L | R | L | D | S | V | T | A | A | D | T | A | V | Y | F | C | A | T | L | Y | E | F | R | V | Y | M | G | E | R | I | S | Y | H | D | Y | W | G | Q | G | L | L | V | T | V | S | A |
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 | Q | M | T | Q | S | P | S | S | L | S | A | S | V | G | D | R | V | T | I | S | C | R | A | S | Q | D | I | S | S | D | L | N | W | Y | Q | Q | K | P | G | K | P | P | Q | L | L | I | Y | F | A | S | N | L | Q | S | G | V | P | S | R | F | S | G | S | G | A | G | T | E | F | T | L | T | I | N | S | L | Q | A | E | D | F | A | S | Y | F | C | L | Q | Y | Q | S | Y | P | W | T | F | G | Q | G | T | M | V | D | L | K |
| Antigen Details | |
|---|---|
| Antigen chains | F,D,E |
| Antigen type | protein |
| Antigen name | bg505 ds-sosip transmembrane protein gp41; bg505 ds-sosip surface protein gp120 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GVSISGNY |
| CDRH2 | HGNTAA |
| CDRH3 | LYEFRVYMGERISYHDY |
| CDRL1 | RASQDISSDLN |
| CDRL2 | FASNLQS |
| CDRL3 | LQYQSYPWT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -58.24° |
| HC1 | 73.83° |
| HC2 | 117.73° |
| LC1 | 118.63° |
| LC2 | 82.3° |
| dc | 16.93Å |
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]
