3MNZ: Gp41 MPER-derived peptide

Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide bearing Ala substitutions in a helical conformation. Determined by X-ray diffraction at 1.8 Å resolution. Released 17 Nov 2010.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Human immunodeficiency virus 1, Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,992
Mol. weight: 50.59 kDa
Released: 17 Nov 2010

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

Secondary structure: helices and β-sheets

3MNZ contains 19 α-helices and 47 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 A: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-7	4	2
β-strand	10-13	4	3
β-strand	19-25	7	2
β-strand	30-30A	2	4
β-strand	30F-31	2	4
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	85-90	6	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	102-106	5	3
β-strand	111	1	5
α-helix	112-113	2
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-155	3	7
β-strand	159-163	5	6
α-helix	164-167	4
β-strand	173-182	10	6
α-helix	183-187	5
β-strand	191-197	7	7
β-strand	205-210	6	7

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	32	1	1
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-94	7	9
β-strand	102-103	2	9
β-strand	107-111	5	9
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	137-147	11	11
β-strand	148	1	10
β-strand	153-157	4	12
α-helix	162-164	3
β-strand	166	1	12
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177-178	2	11
β-strand	185-194	10	11
α-helix	195-197	3
β-strand	207-212	6	12
α-helix	213-215	3
β-strand	217-222	6	12

Chain P: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	657-667	11
β-strand	670	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
gp41 MPER-derived peptide	P	protein	21	Human immunodeficiency virus 1	P04578 (AlphaFold model)
Anti-HIV-1 antibody 13H11 light chain	A	protein	224	Mus musculus, Homo sapiens	Q8TCD0 (AlphaFold model)
Anti-HIV-1 antibody 13H11 heavy chain	B	protein	219	Mus musculus, Homo sapiens	S6B291 (AlphaFold model)

Sequence of entity 1 (P), FASTA

>3MNZ_1 gp41 MPER-derived peptide (chains P)
AQAKNAQELLELDKWASLWNX

Sequence of entity 2 (A), FASTA

>3MNZ_2 ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN (chains A)
RLDIQLTQSPSSLAMSGGQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFAS
IRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAA
PSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDST
YSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGS

Sequence of entity 3 (B), FASTA

>3MNZ_3 ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN (chains B)
LQIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQVPGKGLKWMGWINTETGEPT
YADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGWLHWGLGTTLTVSSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
SVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Primary citation

Crystal Structure of a Non-Neutralizing HIV-1 gp41 Envelope Antibody Demonstrates Neutralization Mechanism of gp41 Antibodies. Nicely, N.I., Dennison, S.M., Kelsoe, G. et al. To be published.

Other PDB entries of the same protein (UniProt P04578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8F3A 1.2 Å, HIV-1 gp41 coiled-coil pocket IQN17
6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
9ARN 1.41 Å, Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal…
1DF4 1.45 Å, Interactions between HIV-1 GP41 core and detergents and their implications for membrane…
6BXP 1.45 Å, Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
7EKB 1.45 Å, Crystal structure of 4E10 modified with pyrene acetamide
5X08 1.49 Å, Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with…
6JQK 1.5 Å, Structure of C34M/N36
5TKK 1.55 Å, Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex…
6PDR 1.55 Å, Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion…

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