5MV4: ACC1 Fab fragment

ACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen type II (ptm23). Determined by X-ray diffraction at 2.9 Å resolution. Released 19 Jul 2017.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Mus musculus
Chains: 24
Atoms: 27,296
Mol. weight: 410.47 kDa
Released: 19 Jul 2017

Explore 5MV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MV4 contains 143 α-helices and 352 β-strands across 16 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, C, I, L and R: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	44-51	8	2
α-helix	54-56	3
β-strand	60-62	3	2
α-helix	64-66	3
β-strand	70-75	6	1
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-100	7	2
β-strand	105-106	2	2
β-strand	110-114	5	2
α-helix	118-119	2
β-strand	120	1	3
α-helix	121-122	2
β-strand	123-127	5	4
α-helix	128-130	3
β-strand	138-148	11	4
β-strand	149	1	3
β-strand	154-157	4	5
α-helix	158-160	3
β-strand	166-168	3	4
α-helix	169-171	3
β-strand	172-174	3	4
β-strand	177-187	11	4
β-strand	197-202	6	5
α-helix	203-205	3
β-strand	207-212	6	5
α-helix	214-217	4

Chains B, D, G, J, M, P, S and V: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	2
β-strand	19-25	7	6
β-strand	30-31	2	7
β-strand	34-35	2	7
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
α-helix	59	1
β-strand	66-71	6	6
β-strand	74-79	6	6
α-helix	84-86	3
β-strand	88-94	7	2
α-helix	100	1
β-strand	101-102	2	2
β-strand	106-111	6	2
β-strand	115	1	8
β-strand	118-122	5	9
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	9
β-strand	144	1	8
β-strand	148-154	7	10
β-strand	157-159	3	10
β-strand	163-167	5	9
α-helix	168-171	4
β-strand	177-186	10	9
α-helix	187-192	6
β-strand	195-202	8	10
β-strand	205-214	10	10

Chain F: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-40	7	22
β-strand	44-51	8	22
α-helix	54-56	3
β-strand	60-62	3	22
α-helix	64-66	3
β-strand	70-75	6	21
β-strand	80-85	6	21
α-helix	90-92	3
β-strand	94-100	7	22
β-strand	105-106	2	22
β-strand	110-114	5	22
α-helix	118-119	2
β-strand	120	1	23
α-helix	121-122	2
β-strand	123-127	5	24
α-helix	128-131	4
β-strand	139-148	10	24
β-strand	149	1	23
β-strand	154-157	4	25
α-helix	158-160	3
β-strand	166-168	3	24
α-helix	169-171	3
β-strand	172-174	3	24
β-strand	177-186	10	24
β-strand	197-202	6	25
α-helix	203-205	3
β-strand	207-212	6	25
α-helix	214-217	4

Chain O: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	49
β-strand	10-12	3	50
β-strand	18-25	8	49
α-helix	29-31	3
β-strand	34-40	7	50
β-strand	44-51	8	50
α-helix	54-56	3
β-strand	60-62	3	50
α-helix	64-66	3
β-strand	70-75	6	49
β-strand	80-85	6	49
α-helix	90-92	3
β-strand	94-100	7	50
β-strand	105-106	2	50
β-strand	110-114	5	50
α-helix	118-119	2
β-strand	120	1	51
α-helix	121-122	2
β-strand	123-127	5	52
α-helix	128-131	4
β-strand	138-148	11	52
β-strand	149	1	51
β-strand	154-157	4	53
α-helix	158-160	3
β-strand	166-168	3	52
α-helix	169-171	3
β-strand	172-174	3	52
β-strand	177-187	11	52
β-strand	197-202	6	53
α-helix	203-205	3
β-strand	207-212	6	53
α-helix	214-217	4

Chain U: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	68
β-strand	10-12	3	69
β-strand	18-25	8	68
α-helix	29-31	3
β-strand	34-40	7	69
β-strand	44-51	8	69
α-helix	54-56	3
β-strand	60-62	3	69
α-helix	64-66	3
β-strand	70-75	6	68
β-strand	80-85	6	68
α-helix	90-92	3
β-strand	94-100	7	69
β-strand	105-106	2	69
β-strand	110-114	5	69
α-helix	118-119	2
β-strand	120	1	70
α-helix	121-122	2
β-strand	123-127	5	71
β-strand	138-148	11	71
β-strand	149	1	70
β-strand	154-157	4	72
α-helix	158-160	3
β-strand	166-168	3	71
α-helix	169-171	3
β-strand	172-174	3	71
β-strand	177-187	11	71
β-strand	197-202	6	72
α-helix	203-205	3
β-strand	207-212	6	72
α-helix	214-217	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ACC1 antibody Fab fragment, heavy chain	A, C, F, I, L, O, R, U	protein	218	Mus musculus
ACC1 antibody Fab fragment, light chain	B, D, G, J, M, P, S, V	protein	218	Mus musculus
synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen…	E, H, K, N, Q, T, W, X	protein	46	Mus musculus	P02458 (AlphaFold model)

Sequence of entity 1 (A, C, F, I, L, O, R, U), FASTA

>5MV4_1 ACC1 antibody Fab fragment, heavy chain (chains A, C, F, I, L, O, R, U)
EVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKVNNHAT
NYAESVKGRFTISRDDSRSVVYLQMNNLKPEDTGIYYCTGLTFDYWGQGTTLTVSSAKTT
APSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLLSGLYTL
SSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRGP

Sequence of entity 2 (B, D, G, J, M, P, S, V), FASTA

>5MV4_2 ACC1 antibody Fab fragment, light chain (chains B, D, G, J, M, P, S, V)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISSMNWFQQKAGQPPKFLIYAASKQGS
GVPARFSGSGSGTDFSLIIHPVEEDDTAVYFCQQSKGVPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (E, H, K, N, Q, T, W, X), FASTA

>5MV4_3 synthetic peptide containing the citrullinated collagen type II epitope CII616-639,Collagen alpha-1(II) chain,synthetic peptide containing the citrullinated collagen type II epitope CII616-639 (chains E, H, K, N, Q, T, W, X)
GPPGPPGPPGPPGPPGARGAPGERGETGPPGPAGFAGPPGPPGPPG

Primary citation

Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage. Ge, C., Tong, D., Liang, B. et al. JCI Insight (2017) 2. DOI 10.1172/jci.insight.93688 · 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
5OCY 2.6 Å, Crystal structure of ACPA E4 in complex with CII-C-48-CIT
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

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