5VJO: PDB entry 5VJO

Complex between HyHEL10 Fab fragment heavy chain mutant I29F and Pekin duck egg lysozyme isoform I (DEL-I). Determined by X-ray diffraction at 2.43 Å resolution. Released 11 Apr 2018.

Method: X-ray diffraction
Resolution: 2.43 Å
Organisms: Mus musculus, Anas platyrhynchos
Chains: 6
Atoms: 8,226
Mol. weight: 121.78 kDa
Released: 11 Apr 2018

Explore 5VJO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VJO contains 38 α-helices and 104 β-strands across 6 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.

Chains A and C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	18-24	7	1
α-helix	29-31	3
β-strand	34-40	7	3
β-strand	44-51	8	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	87-89	3
β-strand	91-97	7	3
β-strand	103	1	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	135-145	11	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	169-171	3	5
β-strand	174-184	11	5
β-strand	194-199	6	6
β-strand	204-209	6	6

Chain B: 5 helices, 21 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
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	153-155	3	11
β-strand	159-163	5	10
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-198	8	11
β-strand	201-210	10	11

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	14
β-strand	19-25	7	18
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	19
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	144-150	7	21
β-strand	153-155	3	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-198	8	21
α-helix	204	1
β-strand	205-210	6	21

Chains E and F: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	22
α-helix	5-14	10
β-strand	20	1	23
β-strand	23	1	23
α-helix	25-36	12
β-strand	39	1	22
β-strand	43-45	3	24
β-strand	51-53	3	24
β-strand	58-59	2	24
β-strand	65	1	25
β-strand	79	1	25
α-helix	80-84	5
α-helix	89-99	11
α-helix	104-107	4
α-helix	109-114	6
α-helix	121-124	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HyHEL10 heavy chain Fab fragment carrying I29F mutation.	A, C	protein	213	Mus musculus	P01868 (AlphaFold model)
HyHEL10 light chain Fab fragment	B, D	protein	211	Mus musculus	A0A125T904 (AlphaFold model)
lysozyme isoform I (DEL-I)	E, F	protein	129	Anas platyrhynchos	P00705 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5VJO_1 HyHEL10 heavy chain Fab fragment carrying I29F mutation. (chains A, C)
DVQLQESGPSLVKPSQTLSLTCSVTGDSFTSDYWSWIRKFPGNRLEYMGYVSYSGSTYYN
PSLKSRISITRDTSKNQYYLDLNSVTTEDTATYYCANWDGDYWGQGTLVTVSAAKTTPPS
VYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 2 (B, D), FASTA

>5VJO_2 HyHEL10 light chain Fab fragment (chains B, D)
DIVLTQSPATLSVTPGNSVSLSCRASQSIGNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 3 (E, F), FASTA

>5VJO_3 lysozyme isoform I (DEL-I) (chains E, F)
KVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESSFNTQATNRNTDGSTDYGILQINS
RWWCDDGKTPGSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDV
SKWIRGCRL

Primary citation

Germinal center antibody mutation trajectories are determined by rapid self/foreign discrimination. Burnett, D.L., Langley, D.B., Schofield, P. et al. Science (2018) 360:223-226. DOI 10.1126/science.aao3859 · PubMed

Other PDB entries of the same protein (UniProt P01868 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1P7K 1.75 Å, Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to…
1SEQ 1.78 Å, Fab MNAC13
1KEL 1.9 Å, Catalytic antibody 28B4 FAB fragment complexed with hapten…
1R3J 1.9 Å, potassium channel KcsA-Fab complex in high concentration of Tl+
2FD6 1.9 Å, Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor…
5VJQ 1.9 Å, Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin…
1GPO 1.95 Å, Crystal structure of the rationally designed antibody M41 as a FAB fragment
3ZO0 1.99 Å, Mouse IgG2a in complex with mouse TRIM21 PRYSPRY
1BM3 2.0 Å, Immunoglobulin OPG2 FAB-peptide complex
1FNS 2.0 Å, Crystal structure of the von willebrand factor (VWF) A1 domain I546V mutant in complex…
1OPG 2.0 Å, OPG2 FAB fragment
1P2C 2.0 Å, crystal structure analysis of an anti-lysozyme antibody

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