6UCE: N123-VRC34_pI3 HIV neutralizing antibody

N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519. Determined by X-ray diffraction at 1.38 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 1.38 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 4,147
Mol. weight: 49.03 kDa
Released: 18 Mar 2020

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

Secondary structure: helices and β-sheets

6UCE contains 16 α-helices and 43 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	2
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
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	2
α-helix	98-100	3
β-strand	100E-103	4	2
β-strand	107-111	5	2
β-strand	117	1	7
α-helix	118-119	2
β-strand	120-124	5	8
β-strand	135-145	11	8
β-strand	146	1	7
β-strand	151-154	4	9
β-strand	159	1	9
β-strand	163-165	3	8
α-helix	166-168	3
β-strand	169-170	2	8
β-strand	176-185	10	8
α-helix	186-188	3
β-strand	194-200	7	9
α-helix	201-203	3
β-strand	205-211	7	9

Chain L: 8 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	62-65	4	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	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	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N123-VRC34_pI3 light chain	L	protein	214	Homo sapiens	Q6GMX0 (AlphaFold model)
N123-VRC34_pI3 heavy chain	H	protein	233	Homo sapiens
HIV fusion peptide	C	protein	8	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6UCE_1 N123-VRC34_pI3 light chain (chains L)
DIQLTQSPSFLSASVGDRVTITCRASQGISNELAWYQQKPGKAPNLLIYYASTLQSGVPS
RFSASGSGTHFTLTISSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>6UCE_2 N123-VRC34_pI3 heavy chain (chains H)
QEVLVQSGAEVKKPGASVKVSCKAFGYTFTGNPMHWVRQAPGQGLEWMGWINPHSGDTTT
AQKFQGRVYMTRDKSINTAYLDVTRLTSDDTAIYYCARDKYYGNEAVGMDVWGQGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLF

Sequence of entity 3 (C), FASTA

>6UCE_3 HIV fusion peptide (chains C)
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:

6UCF 1.29 Å, N123-VRC34_pI4 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…

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