6YXK: ACPA 3F3

Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74. Determined by X-ray diffraction at 2.0 Å resolution. Released 12 May 2021.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,762
Mol. weight: 50.27 kDa
Ligands: NAG
Released: 12 May 2021

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

Secondary structure: helices and β-sheets

6YXK contains 19 α-helices and 47 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 A: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-12	4	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	46-52	7	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-101	10	2
β-strand	106	1	3
β-strand	112-113	2	2
β-strand	117-121	5	2
α-helix	124-126	3
β-strand	127	1	4
α-helix	128-129	2
β-strand	130-134	5	5
α-helix	135-137	3
β-strand	145-155	11	5
β-strand	156	1	4
β-strand	161-164	4	6
α-helix	165-167	3
β-strand	169	1	6
β-strand	173-175	3	5
α-helix	176-178	3
β-strand	179-180	2	5
β-strand	186-195	10	5
α-helix	196-198	3
β-strand	205-210	6	6
α-helix	211-213	3
β-strand	215-220	6	6

Chain B: 8 helices, 23 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	30-31	2	9
β-strand	36-37	2	9
β-strand	39-44	6	8
β-strand	51-55	5	8
β-strand	59-60	2	8
α-helix	61	1
β-strand	68-73	6	7
β-strand	76-81	6	7
α-helix	86-88	3
β-strand	90-96	7	8
β-strand	104	1	8
β-strand	107-111	5	8
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	150-155	6	12
β-strand	158-159	2	12
α-helix	160	1
β-strand	164-168	5	11
α-helix	169-172	4
β-strand	178-187	10	11
α-helix	188-191	4
β-strand	196-202	7	12
β-strand	210-215	6	12

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ACPA 3F3 Fab fragment - heavy chain	A	protein	223	Homo sapiens
ACPA 3F3 Fab fragment - light chain	B	protein	218	Homo sapiens
Citrullinated Vimentin (59-74)	C	protein	16	Homo sapiens	P08670 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YXK_1 ACPA 3F3 Fab fragment - heavy chain (chains A)
VQLVQPGAEVMQPGASMKVPCETSGYIFNDYYLHWVRQAPGLGLEWMGWIAPKTGVTKFA
QKFQGRVNMTADSSVNTSYLEMTGLTFDDTAVYFCARGTYLPVDESAAFDVWGLGTDVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLFSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 2 (B), FASTA

>6YXK_2 ACPA 3F3 Fab fragment - light chain (chains B)
DIEMTQYPDSLAVFLGERATVNCKSSQSVLHWGNDKNYFAWYQQKRGQAPKLLISSSSAR
ESGVPDRFSGSGSGTDFNLTISSLQAEDVAVYFCQQYYEAPYTFGQGTRLEIKTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGC

Sequence of entity 3 (C), FASTA

>6YXK_3 Citrullinated Vimentin (59-74) (chains C)
GVYATRSSAVRLRSSV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation. Kissel, T., Ge, C., Hafkenscheid, L. et al. Sci Adv (2022) 8:eabm1759-eabm1759. DOI 10.1126/sciadv.abm1759 · PubMed

Other PDB entries of the same protein (UniProt P08670 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GK7 1.4 Å, Human vimentin coil 1A fragment (1A)
4YPC 1.44 Å, Trimeric crystal structure of vimentin coil1B fragment
4MD5 1.65 Å, Immune Receptor
3SWK 1.7 Å, Crystal structure of vimentin coil1B fragment
4MDJ 1.7 Å, Immune Receptor
3G1E 1.83 Å, X-ray crystal structure of coil 1A of human vimentin
1GK6 1.9 Å, Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)
6ATF 1.9 Å, HLA-DRB1*1402 in complex with Vimentin59-71
6ATI 1.98 Å, HLA-DRB1*1402 in complex with Vimentin-64Cit59-71
4MDI 2.0 Å, Immune Receptor
4YV3 2.0 Å, Trimeric crystal structure of vimentin coil1B fragment
4MD0 2.19 Å, Immune Receptor

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