6UBI: N123-VRC34.05 HIV neutralizing antibody

N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519. Determined by X-ray diffraction at 1.9 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,527
Mol. weight: 97.01 kDa
Released: 18 Mar 2020

Explore 6UBI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UBI contains 30 α-helices and 85 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: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	64	1	1
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	98	1	3
β-strand	100A	1	3
β-strand	100E-103	4	2
β-strand	107-111	5	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	136-145	10	5
β-strand	146	1	4
β-strand	151-154	4	6
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
α-helix	186-188	3
β-strand	195-200	6	6
β-strand	205-210	6	6

Chains B and E: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
β-strand	98	1	8
β-strand	102-106	5	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	9
β-strand	145-150	6	10
β-strand	153-154	2	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-186	4
β-strand	191-197	7	10
β-strand	205-210	6	10

Chain D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7	1
β-strand	10-12	3	12
β-strand	18-25	8	11
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	57-59	3	12
α-helix	61-63	3
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-95	8	12
α-helix	98-100	3
β-strand	100E-103	4	12
β-strand	107-111	5	12
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-185	10	14
α-helix	186-188	3
β-strand	189	1	16
β-strand	192	1	16
β-strand	195-200	6	15
β-strand	205-210	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VRC34.05 heavy chain	A, D	protein	229	Homo sapiens	P0DOX5 (AlphaFold model)
VRC34.05 light chain	B, E	protein	212	Homo sapiens	Q6GMX0 (AlphaFold model)
HIV fusion peptide 512-519	C, F	protein	8	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6UBI_1 VRC34.05 heavy chain (chains A, D)
SQYLAQSGSEVKKPGASVKVSCRLHGDKFGAHYIHWVRQAPGQGLEWLGFFHPGTGDAVS
AQKFQGRISLTRDTSISTGYLEVRRLSSDDTAVYYCARDKTYSDEATGMDIWGQGTTVIV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (B, E), FASTA

>6UBI_2 VRC34.05 light chain (chains B, E)
DIKLTQSPAFLSASVGERVTFTCRASQDIRHELVWYQQKPGRGPKLLIYYGSTLEGGVPS
RFSGRRSGTEFTVTISSLQPEDVGTYYCQQLNSFPLTFGGGTTVDIRRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 3 (C, F), FASTA

>6UBI_3 HIV fusion peptide 512-519 (chains C, F)
AVGIGAVF

Primary citation

VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage. Shen, C.H., DeKosky, B.J., Guo, Y. et al. Cell Host Microbe (2020) 27:531. DOI 10.1016/j.chom.2020.01.027 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…
8ECQ 2.0 Å, Bovine Fab 2G3

Browse structure collections

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