Table 5.
HIV-1 bNAbs with insertions in L4 and/or H4
| Gene | PDB Chains | Length | DE loop sequence | Antibody/Germline |
|---|---|---|---|---|
| Heavy | 4toyH 4tvpD* 5cezD* 5fyjD* 5fykD* 5fylD* 5t3sD* 5u7oD* 5u7mD* 5um8D* 5utfD* 5utyD* 5v7jD* 5w6dD* 5wduH,M,U* 6ce0D* 6ch7D 6ch8D 6ch9D 6ck9D* 6de7D* 6ieqD 6mcoD 6mtjD 6mdtD 6mtnD 6mu6D 6mu7D 6mu8D 6mufD 6mugD 6nm6E 6nnfD 6nnjD | 16 | TDTEVPVTSFTSTGAA RDT----------SISTA |
35O22 IGHV1-18*01 |
| Heavy | 4jb9H | 15 | RLFSQDLYYPDRGTA RDT----------SISTA |
VRC06 IGHV1-2*02 |
| Heavy | 3se8H 4cc8F,H,I 5jxaH 6cde5,Q,q* 6cdi8,Q,q* 6cue7,Q,q 6cuf8,Q,q 6e5pI,O,V 6mpg8,Q,q 6mphQ,f,g 6n1vQ,f,g 6n1w8,Q,q 6nf2C,N,V 6osy8,F,P 6ot1J,S,q 6v8zC,I,O | 15 | RQLSQDPDDPDWGVA RDTSIST----------A |
VRC03 IGHV1-2*02 |
| Heavy | 4s1qH | 15 | RQLSQDPDDPDWGIA RDTSIST----------A |
VRC01.H03 + 06.D-001739 IGHV1-2*02 |
| Heavy | 6nm6U | 15 | RQLSQDPDDPDWGIA RDTSIST----------A |
N6 FR3-03 IGHV1-2*02 |
| Heavy | 6nnfU | 15 | RQLSQDPDDPDWGTA RDTSIST----------A |
VRC01 FR303 IGHV1-2*02 |
| Heavy | 4xnzB,E,H | 15 | RQLSQDPDDPDWGVA RDTSIST----------A |
VRC06B IGHV1-2*02 |
| Heavy | 4p9hH 4p9mH 5a7xN,P,R 5a8hF,L,R. 5c7kE 5cjxA,D,H 5js9E 5jsaE 5thrP,R,T 5viyK,M,I. 5vj6M,O,Q 6cm3P,R,T 6eduP,R,T 6nqdC,G,K | 12 | AVDLTGSSPPIS ADESTST------S |
8ANC195 IGHV1-69*01 |
| Heavy | 4jpvH 4lsvH 5v8lG,H,I 5v8mH,R,S | 12 | RHASWDFDTYSF RDTSIST----------A |
3BNC117 IGHV1-2*02 |
| Heavy | 3rpiA,H 4gw4A,H | 12 | RQASWDFDTYSF RDTSIST----------A |
3BNC60 IGHV1-2*02 |
| Lambda | 4jy6A,C | 9 | PDFRPGTTA -----NSGNTA |
PGT123 IGLV3-21*01 |
| Lambda | 4fq2L 6ccbE,L 6ck9L* 5ceyA,C 5cezL* 5t3xL 5t3zL 5v7jL* 5w6dL* 6mtjL* 6mtnL* 6mu6L* 6mu7L* 6mu8L* 6mufL* 6mugL* 6nm6L* 6nnfL* 6nnjL* | 9 | PDINFGTRA -----NSGNTA |
10–1074 IGLV3-21*01 |
| Lambda | 4r26L 4r2gC,I,M 5t3sL* 5um8L* 6ce0L* 6ieqL* 6mcoL* 6mdtL* | 9 | PDINFGTTA -----NSGNTA |
PGT124 IGLV3-21*01 |
| Lambda | 5cexC | 9 | PDSNFGTTA -----NSGNTA |
32H + 109L IGLV3-21*01 |
| Lambda | 4fq1L 4fqcL 4jy4A | 9 | PDSPFGTTA -----NSGNTA |
PGT121 IGLV3-21*01 |
| Lambda | 3jcbB 3jccB 4jy5L 4ncoG,K,C 4tvpL* 5d9qL,E,M 5fyjL* 5fykL* 5fylL* 5i8hJ,L 5u7mL* 5u7oL* 5utfL* 5utyL* 5wduB,K,S* 6b0nL 6cdeN,8,n* 6cdiN,6,n* 6cue6,n,N* 6cuf6,n,N* 6de7L* 6nf2F,T,K* 6osyD,N,6* 6ot1R,I,n* | 9 | PGSTFGTTA -----NSGNTA |
PGT122 IGLV3-21*01 |
The table lists all of the antibody structures in the PDB with insertions in L4 or H4 related to bNAbs along with their sequences, germline, and bNAb lineage. Entries with an asterisk (*) represent structures with insertions in both the light and heavy chains. There is only one other antibody with an inserted DE loop in the PDB: the engineered nanobody toward Higb2 toxin in cholera (PDBID 5mje, DE sequence RDSAEDSAKNTV). It is not listed in the Table. The amino acid sequences of the inserted DE loop in the PDB and the germline were aligned by locating the insertion in their DNA sequences.