3MNV: Non-neutralizing HIV antibody 13H11 Fab fragment

Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Nov 2010.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 7,087
Mol. weight: 97.4 kDa
Released: 17 Nov 2010

Explore 3MNV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MNV contains 39 α-helices and 89 β-strands across 4 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 A: 9 helices, 23 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	30-30A	2	3
β-strand	30F-31	2	3
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	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-188	6
β-strand	191-197	7	6
β-strand	205-210	6	6

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
α-helix	33	1
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-178	2	10
β-strand	185-194	10	10
α-helix	195-197	3
β-strand	207-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	30-30A	2	14
β-strand	30F-31	2	14
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	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-154	2	17
α-helix	155	1
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-197	7	17
β-strand	205-210	6	17

Chain D: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
α-helix	7	1
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	57-59	3	19
α-helix	61-63	3
β-strand	67-72	6	18
α-helix	73-75	3
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-93	6	19
β-strand	103	1	19
β-strand	107-111	5	19
α-helix	115-116	2
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
β-strand	137-147	11	21
β-strand	148	1	20
β-strand	153-157	4	22
α-helix	162-164	3
β-strand	166	1	22
β-strand	171-173	3	21
α-helix	174-176	3
β-strand	177-178	2	21
β-strand	185-194	10	21
α-helix	195-197	3
β-strand	207-212	6	22
α-helix	213-215	3
β-strand	217-222	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Anti-HIV-1 antibody 13H11 light chain	A, C	protein	224	Mus musculus, Homo sapiens	Q8TCD0 (AlphaFold model)
Anti-HIV-1 antibody 13H11 heavy chain	B, D	protein	219	Mus musculus, Homo sapiens	Q6N089 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3MNV_1 ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN (chains A, C)
RLDIQLTQSPSSLAMSGGQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFAS
IRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAA
PSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDST
YSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGS

Sequence of entity 2 (B, D), FASTA

>3MNV_2 ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN (chains B, D)
LQIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQVPGKGLKWMGWINTETGEPT
YADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGWLHWGLGTTLTVSSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
SVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Primary citation

Crystal structure of a non-neutralizing antibody to the HIV-1 gp41 membrane-proximal external region. Nicely, N.I., Dennison, S.M., Spicer, L. et al. Nat Struct Mol Biol (2010) 17:1492-1494. DOI 10.1038/nsmb.1944 · PubMed

Other PDB entries of the same protein (UniProt Q8TCD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
4NWT 1.75 Å, Crystal structure of the anti-human NGF Fab APE1531
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
4NUG 1.86 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT151
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3PGF 2.1 Å, Crystal structure of maltose bound MBP with a conformationally specific synthetic…
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)

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