5V6M: Rabbit Anti-HIV-1 gp120 V3 Fab 10A3

Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in complex with V3 peptide ConB. Determined by X-ray diffraction at 1.9 Å resolution. Released 17 Jan 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Oryctolagus cuniculus, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,980
Mol. weight: 47.4 kDa
Ligands: CA
Released: 17 Jan 2018

Explore 5V6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V6M contains 18 α-helices and 43 β-strands across 3 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
β-strand	33-39	7	7
β-strand	45-52	8	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-73	7	6
β-strand	76-81	6	6
α-helix	84-86	3
β-strand	88-94	7	7
β-strand	98-99	2	7
β-strand	103-107	5	7
α-helix	111-112	2
β-strand	113	1	8
α-helix	114-115	2
β-strand	116-120	5	9
α-helix	121-123	3
β-strand	131-141	11	9
β-strand	142	1	8
β-strand	147-150	4	10
α-helix	151-153	3
β-strand	155	1	10
β-strand	159-161	3	9
α-helix	162-164	3
β-strand	165-166	2	9
β-strand	172-181	10	9
α-helix	182-184	3
β-strand	190-196	7	10
α-helix	197-199	3
β-strand	201-207	7	10

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	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	84-91	8	2
β-strand	96-98	3	2
β-strand	102-107	6	2
β-strand	116	1	3
α-helix	117-118	2
β-strand	119-123	5	4
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	4
β-strand	145	1	3
β-strand	150-155	6	5
β-strand	158-159	2	5
α-helix	160	1
β-strand	164-168	5	4
α-helix	169-172	4
β-strand	178-187	10	4
α-helix	188-191	4
β-strand	196-202	7	5
β-strand	210-215	6	5

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	307-309	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3	L	protein	219	Oryctolagus cuniculus
Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3	H	protein	213	Oryctolagus cuniculus
Envelope glycoprotein gp120 V3 peptide of Con B sequence	P	protein	15	Human immunodeficiency virus 1	P20871

Sequence of entity 1 (L), FASTA

>5V6M_1 Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3 (chains L)
AQVLTQTPSSVSAAVGGTVTIKCQSSQSVYPNNNLGWYQQKPGQPPKLLIYEASTLASGV
PSRFKGSGSGTQFTLTISDLECDDAATYYCLGAYDFTVAEGAAFGGGTEVVVKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (H), FASTA

>5V6M_2 Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3 (chains H)
QEQLEESGGGLVQPEGSLTLTCKASGFSFSAIAMCWVRQAPGKGLEWIGCIATDTGSTYY
ANWAKGRFTISNPSSTTVTLQMTSLTAADTATYFCARNFYLWGPGTLVTVSSASTKGPSV
FPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV
VTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (P), FASTA

>5V6M_3 Envelope glycoprotein gp120 V3 peptide of Con B sequence (chains P)
NNTRKSIHIGPGRAF

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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…
5V6L 2.55 Å, Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A37 in complex with V3 peptide JR-FL
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)

Browse structure collections

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