6UCF: N123-VRC34_pI4 HIV neutralizing antibody

N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519. Determined by X-ray diffraction at 1.29 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 1.29 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 4,065
Mol. weight: 48.53 kDa
Released: 18 Mar 2020

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

Secondary structure: helices and β-sheets

6UCF contains 20 α-helices and 44 β-strands across 2 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: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
α-helix	98-100	3
β-strand	100E-103	4	7
β-strand	107-111	5	7
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
α-helix	128-130	3
β-strand	132	1	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	186-188	3
β-strand	195-200	6	10
α-helix	201-203	3
β-strand	205-210	6	10

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	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
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N123-VRC34_pI4 light chain	L	protein	213	Homo sapiens	Q6GMX0 (AlphaFold model)
N123-VRC34_pI4 heavy chain	H	protein	229	Homo sapiens
HIV fusion peptide	A	protein	8	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6UCF_1 N123-VRC34_pI4 light chain (chains L)
DIQLTQSPSFLSASVGDRVTITCRASQGVRNELAWYQQKPGKAPNLLIYYASTLQSGVPS
RFSASGSGTHFTLTVSSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (H), FASTA

>6UCF_2 N123-VRC34_pI4 heavy chain (chains H)
QEVLVQSGAEVKKPGASVKVSCRAFGYTFTGNALHWVRQAPGQGLEWLGWINPHSGDTTT
SQKFQGRVYMTRDKSINTAYLDVTRLTSDDTAIYYCARDKYYGNEAVGMDVWGQGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (A), FASTA

>6UCF_3 HIV fusion peptide (chains A)
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 Q6GMX0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
2D7T 1.7 Å, Crystal structure of human anti polyhydroxybutyrate antibody Fv
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
3BN9 2.17 Å, Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2
8CWK 2.37 Å, Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)
5O1R 2.86 Å, human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B
5VOB 3.02 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
1BEY 3.25 Å, Antibody to campath-1H humanized FAB
6B70 3.7 Å, Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy…
5VOC 3.99 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low…
6B7Z 6.5 Å, Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11 heavy chain…

Browse structure collections

About this viewer

MolViewer shows 6UCF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.