6UOE: 3-25 Fab germline-reversion variant

3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide. Determined by X-ray diffraction at 1.8 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Human betaherpesvirus 5
Chains: 3
Atoms: 4,091
Mol. weight: 49.91 kDa
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6UOE contains 18 α-helices and 46 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 H: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
β-strand	100C-100D	2	4
β-strand	100H-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	5
α-helix	118-119	2
β-strand	120-124	5	6
α-helix	128-130	3
β-strand	131-132	2	6
β-strand	135-145	11	6
β-strand	146	1	5
β-strand	151-154	4	7
α-helix	155-157	3
β-strand	163-165	3	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-185	10	6
α-helix	186-188	3
β-strand	195-200	6	7
α-helix	201-203	3
β-strand	205-210	6	7

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
β-strand	205-210	6	12

Chain P: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	72-74	3
β-strand	76-77	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-25 Fab heavy chain	H	protein	229	Homo sapiens	P0DOX5 (AlphaFold model)
3-25 Fab light chain	L	protein	215	Homo sapiens	P0DOX7 (AlphaFold model)
Envelope glycoprotein B	P	protein	15	Human betaherpesvirus 5	P06473

Sequence of entity 1 (H), FASTA

>6UOE_1 3-25 Fab heavy chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSNHGLHWVRQAPGKGLEWVAVVSKDGTNEHY
ADSVRGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREGYCGDDRCYSGQPDYWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 2 (L), FASTA

>6UOE_2 3-25 Fab light chain (chains L)
EIVLTQSPATLSLSPGERATLSCRASQSVGRYLAWYQQKPGQAPRLLIYDSSNRATGVPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSHWPPLTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (P), FASTA

>6UOE_3 Envelope glycoprotein B (chains P)
HRANETIYNTTLKYG

Primary citation

Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step. Ye, X., Su, H., Wrapp, D. et al. PLoS Pathog (2020) 16:e1008736-e1008736. DOI 10.1371/journal.ppat.1008736 · 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…
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
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
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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