5V6L: Rabbit Anti-HIV-1 gp120 V3 Fab 10A37

Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A37 in complex with V3 peptide JR-FL. Determined by X-ray diffraction at 2.55 Å resolution. Released 17 Jan 2018.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Oryctolagus cuniculus, Human immunodeficiency virus 1
Chains: 6
Atoms: 6,849
Mol. weight: 96.56 kDa
Released: 17 Jan 2018

Explore 5V6L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V6L contains 37 α-helices and 88 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	17-25	9	6
β-strand	34-39	7	8
β-strand	46-52	7	8
β-strand	57-59	3	8
β-strand	64	1	6
β-strand	67-70	4	6
β-strand	76-82	7	6
α-helix	84-86	3
β-strand	88-95	8	8
α-helix	98-100	3
β-strand	100D-103	4	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	131-132	2
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
β-strand	191-197	7	11
α-helix	198-200	3
β-strand	202-208	7	11

Chain I: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	11-12	2	18
β-strand	17-24	8	17
β-strand	34-39	7	19
β-strand	46-52	7	19
β-strand	57-59	3	19
β-strand	67-71	5	17
β-strand	76-82	7	17
α-helix	84-86	3
β-strand	88-95	8	19
α-helix	98-100	3
β-strand	100D-103	4	19
β-strand	107-109	3	19
β-strand	110-111	2	18
α-helix	115-116	2
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
α-helix	131-132	2
β-strand	135-145	11	21
β-strand	146	1	20
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-170	2	21
β-strand	176-185	10	21
α-helix	189-190	2
β-strand	191-197	7	11
α-helix	198-200	3
β-strand	202-208	7	11

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	95A-95C	3
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	125-127	3
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-149	6	5
β-strand	152-154	3	5
β-strand	158-162	5	4
α-helix	163-166	4
β-strand	172-181	10	4
α-helix	182-186	5
β-strand	190-197	8	5
β-strand	200-207	8	5
α-helix	208-210	3

Chain M: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	10-14	5	13
β-strand	18-25	8	12
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-76	7	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	95A-95C	3
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	125-127	3
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	144-149	6	16
β-strand	152-153	2	16
α-helix	154	1
β-strand	158-162	5	15
α-helix	163-166	4
β-strand	172-181	10	15
α-helix	182-186	5
β-strand	190-197	8	16
β-strand	200-207	8	16
α-helix	208-210	3

Chains P and Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	315-320	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37	L, M	protein	215	Oryctolagus cuniculus
Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37	H, I	protein	220	Oryctolagus cuniculus
Envelope glycoprotein, v3 region	P, Q	protein	23	Human immunodeficiency virus 1	P20871

Sequence of entity 1 (L, M), FASTA

>5V6L_1 Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37 (chains L, M)
ALVMTQTPSSVSAAVGGTVTINCQASEDIQRNLAWYQQKPGQRPKFLIYGVSNLESGVPS
RFKGSGSGTEYTLTISDLECDDAATYYCQSALYTSATDICAFGGGTEVVVKGDPVAPTVL
IFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSS
TLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

Sequence of entity 2 (H, I), FASTA

>5V6L_2 Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37 (chains H, I)
QEQLVESGGGLVKPGGTLTLTCTASGFSFSSGFFMCWVRQAPGKGLEWIGCIYGGSNDNT
YYANWAKGRFTISKTSSTTVTLQMTSRTAADTATYFCARDAGTSGYIAYNLWGPGTLVTV
SSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQ
SSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAPS

Sequence of entity 3 (P, Q), FASTA

>5V6L_3 Envelope glycoprotein, v3 region (chains P, Q)
NNTRKSIHIGPGRAFYTTGEIIG

Primary citation

Increased epitope complexity correlated with antibody affinity maturation and a novel binding mode revealed by structures of rabbit antibodies against the third variable loop (V3) of HIV-1 gp120. Pan, R., Qin, Y., Banasik, M. et al. J Virol (2018). DOI 10.1128/JVI.01894-17 · PubMed

Other PDB entries of the same protein (UniProt P20871), best resolution first:

9MMJ 1.78 Å, Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the…
5V6M 1.9 Å, Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in complex with V3 peptide ConB
4R2G 3.28 Å, Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4
1CE4 Conformational model for the consensus V3 loop of the envelope protein GP120 of HIV-1
2ESX The structure of the V3 region within gp120 of JR-FL HIV-1 strain (minimized average…
2ESZ The structure of the V3 region within gp120 of JR-FL HIV-1 strain (ensemble)

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