5OCY: ACPA E4

Crystal structure of ACPA E4 in complex with CII-C-48-CIT. Determined by X-ray diffraction at 2.6 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,376
Mol. weight: 48.45 kDa
Released: 4 Jul 2018

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

Secondary structure: helices and β-sheets

5OCY contains 15 α-helices and 49 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 C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	4

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
α-helix	17	1
β-strand	18-25	8	1
β-strand	34-40	7	3
β-strand	46-52	7	3
β-strand	58-60	3	3
α-helix	65-67	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	3
β-strand	102	1	4
β-strand	106-110	5	3
β-strand	114-116	3	3
β-strand	117-118	2	2
α-helix	121-122	2
β-strand	124	1	5
α-helix	125-126	2
β-strand	127-131	5	6
β-strand	142-152	11	6
β-strand	153	1	5
β-strand	158-162	5	7
β-strand	169-172	4	6
α-helix	173-175	3
β-strand	176-178	3	6
β-strand	181-191	11	6
β-strand	201-206	6	7
β-strand	211-216	6	7

Chain L: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	8
β-strand	5	1	9
β-strand	9-12	4	10
β-strand	18-23	6	9
α-helix	28-31	4
β-strand	35-39	5	10
β-strand	46-49	4	10
β-strand	50	1	11
β-strand	54	1	11
α-helix	55-56	2
β-strand	63-67	5	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	85-93	9	10
β-strand	98-101	4	10
β-strand	102	1	8
β-strand	105-109	5	10
β-strand	115	1	12
α-helix	116-117	2
β-strand	118-122	5	13
α-helix	123-125	3
α-helix	126-129	4
β-strand	134-143	10	13
β-strand	144	1	12
β-strand	149-154	6	14
β-strand	157-158	2	14
α-helix	159	1
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	169-170	2	13
β-strand	176-184	9	13
α-helix	186-191	6
β-strand	194-201	8	14
β-strand	204-211	8	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ACPA E4 Fab fragment - heavy chain	H	protein	220	Homo sapiens
ACPA E4 Fab fragment - light chain	L	protein	216	Homo sapiens
Cii-C-48-cit	C	protein	18	Homo sapiens	P02458 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5OCY_1 ACPA E4 Fab fragment - heavy chain (chains H)
QVQLEESGPGLVRPSETLSLSCTVSGFPMSESYFWGWIRQSPGKGLEWLGSVIHTGTTYY
RPSLESRLTIAMDPSKNQVSLSLTSVTVADSAMYYCVRIRGGSSNWLDPWGPGIVVTASS
AKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSG
LYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKIEPR

Sequence of entity 2 (L), FASTA

>5OCY_2 ACPA E4 Fab fragment - light chain (chains L)
QSVWTQPPSVSAAPGQKVTISCSGDDSILRSAFVSWYQQVPGSAPKLVIFDDRQRPSGIP
ARFSGSNSGTTATLDIAGLQRGDEADYYCAAWNGRLSAFVFGSGTKLTVLGQPKSSPSVT
LFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASS
YLTLTARAWERHSSYSCQVTHEGHTVEKSLSRADCS

Sequence of entity 3 (C), FASTA

>5OCY_3 CII-C-48-CIT (chains C)
CEAGEPGERGLKGHRGCA

Primary citation

Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies. Ge, C., Xu, B., Liang, B. et al. Arthritis Rheumatol (2019) 71:210-221. DOI 10.1002/art.40698 · PubMed

Other PDB entries of the same protein (UniProt P02458 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HG7 1.0 Å, Crystal structure of a collagen II fragment containing the binding site of PEDF and…
5NIR 1.74 Å, Crystal structure of collagen 2A vWC domain
5OCX 1.75 Å, Crystal structure of ACPA E4 in complex with CII-C-13-CIT
7NZE 2.05 Å, Crystal structure of HLA-DR4 in complex with a human collagen type II peptide
6NIX 2.1 Å, Crystal structure of Immune Receptor
2SEB 2.5 Å, X-ray crystal structure of HLA-DR4 complexed with a peptide from human collagen II
6BIN 2.5 Å, HLA-DRB1 in complex with Type II collagen peptide
5MV4 2.9 Å, ACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen type II…
2FSE 3.1 Å, Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1…
1U5M Structure of a Chordin-like Cysteine-rich Repeat (VWC module) from Collagen IIA

Browse structure collections

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