4JO3: Rabbit mAb R20 Fab

Crystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus B gp120. Determined by X-ray diffraction at 2.6 Å resolution. Released 31 Jul 2013.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Oryctolagus cuniculus, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,039
Mol. weight: 96.42 kDa
Released: 31 Jul 2013

Explore 4JO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JO3 contains 31 α-helices and 92 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	33-39	8	9
β-strand	46-52	7	9
β-strand	57-59	3	9
β-strand	64	1	7
β-strand	67-71	5	7
β-strand	76-81	6	7
α-helix	84-86	3
β-strand	88-100B	15	9
β-strand	100E-103	12	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	131-133	3
β-strand	136-145	10	5
β-strand	146	1	10
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-184	9	5
β-strand	191-197	7	11
α-helix	198-200	3
β-strand	202-208	7	11

Chain I: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
β-strand	34-39	7	19
β-strand	46-52	7	19
β-strand	57-59	3	19
β-strand	64	1	17
β-strand	67-73	7	17
β-strand	76-81	6	17
α-helix	84-86	3
β-strand	88-100C	16	19
β-strand	100E-103	12	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
β-strand	136-145	10	21
β-strand	146	1	20
β-strand	151-154	4	22
α-helix	155-157	3
β-strand	159	1	22
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-170	2	21
β-strand	176-184	9	21
β-strand	191-197	7	22
α-helix	198-200	3
β-strand	202-208	7	22

Chain L: 9 helices, 22 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	84-90	7	2
β-strand	98	1	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	1
β-strand	120	1	5
α-helix	121	1
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-149	6	6
β-strand	152-154	3	6
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	6
β-strand	200-207	8	6
α-helix	208-210	3

Chain M: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	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
β-strand	98	1	13
β-strand	102-107	6	13
β-strand	111	1	14
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	144-149	6	16
β-strand	152-153	2	16
β-strand	158-162	5	15
α-helix	163-166	4
β-strand	172-181	10	15
α-helix	182-187	6
β-strand	190-197	8	16
β-strand	200-207	8	16
α-helix	208-210	3

Chains P and Q: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	324-325	2	9
α-helix	326-328	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain	L, M	protein	214	Oryctolagus cuniculus
monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain	H, I	protein	227	Oryctolagus cuniculus
gp120	P, Q	protein	15	Human immunodeficiency virus 1	P35961

Sequence of entity 1 (L, M), FASTA

>4JO3_1 monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain (chains L, M)
DIVMTQTPASVSAAVGGTVTINCQASETISNYLAWYQQKPGQPPKLLIYKASTLASGVSS
RFKGSGSGTEYTLTISGVQCDDAATYYCQQGYSISDIDNSFGGGTEVVVKGDPVAPTVLI
FPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSST
LTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

Sequence of entity 2 (H, I), FASTA

>4JO3_2 monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain (chains H, I)
QSLEESGGDLVKPGASLTLTCTASGFSFTNNYYMCWVRQAPGKGLEWIACIYGGGRDIVF
YATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARENFDAVGVGGGTYSTDYYFDLW
GPGTLVIVSSGQPKAPSVFPLAPCCGDTPSATVTLGCLVKGYLPEPVTVTWNSGTLTNGV
RTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAP

Sequence of entity 3 (P, Q), FASTA

>4JO3_3 gp120 (chains P, Q)
TTGEIIGDIRQAHCN

Primary citation

Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans. Pan, R., Sampson, J.M., Chen, Y. et al. J Virol (2013) 87:10221-10231. DOI 10.1128/JVI.00843-13 · PubMed

Other PDB entries of the same protein (UniProt P35961), best resolution first:

4JZZ 1.49 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4JZW 1.78 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4KA2 1.79 Å, Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120
4RWY 2.13 Å, Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131…
4K0A 2.13 Å, Crystal structure of CD4-mimetic miniprotein M48U7 in complex with HIV-1 YU2 gp120
4LAJ 2.14 Å, Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic…
1YYM 2.2 Å, crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120…
2NY7 2.3 Å, HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing…
2I60 2.4 Å, Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1…
4DVR 2.5 Å, Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
1YYL 2.75 Å, crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2…
1G9N 2.9 Å, HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

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