6YXK | pdb_00006yxk

Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	C1-set_4	e6yxkB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e6yxkB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
A	V-set_8	e6yxkA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e6yxkA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Light Chain	IGKV4	Kappa	citrullinated vimentin (59-74)	SAbDab (2025-11-07)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Citrullinated Vimentin (59-74)	protein binding binding protein domain specific binding RNA binding double-stranded RNA binding nucleic acid binding scaffold protein binding keratin filament binding intermediate filament binding structural molecule activity structural constituent of eye lens structural constituent of cytoskeleton molecular adaptor activity identical protein binding	developmental process multicellular organismal process epithelium development cellular developmental process sensory organ development eye development animal organ development cell development visual system development tissue development lens fiber cell development epithelial cell differentiation multicellular organism development epithelial cell development cell differentiation developmental process multicellular organismal process epithelium development cellular developmental process sensory organ development eye development animal organ development cell development visual system development tissue development lens fiber cell development epithelial cell differentiation multicellular organism development epithelial cell development cell differentiation anatomical structure development camera-type eye development lens fiber cell differentiation cellular process sensory system development lens development in camera-type eye system development regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to stimulus response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of neuron projection development regulation of cellular component organization cell projection organization neuron projection development cellular component organization neurogenesis neuron differentiation cellular component organization or biogenesis negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization astrocyte differentiation glial cell development astrocyte development central nervous system development gliogenesis glial cell differentiation cellular response to nitrogen compound cellular response to muramyl dipeptide response to muramyl dipeptide response to nitrogen compound Bergmann glial cell differentiation immune response defense response response to type II interferon response to cytokine defense response to symbiont cellular response to type II interferon response to peptide immune system process defense response to other organism response to stress innate immune response cellular response to cytokine stimulus collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of collagen metabolic process positive regulation of collagen biosynthetic process collagen metabolic process intermediate filament organization intermediate filament-based process organelle organization supramolecular fiber organization cytoskeleton organization intermediate filament cytoskeleton organization	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix anchoring junction cell junction membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix anchoring junction cell junction focal adhesion cell-substrate junction extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle polymeric cytoskeletal fiber intracellular membraneless organelle intermediate filament cytoskeleton cytoskeleton membraneless organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex cytoplasm cytosol cell leading edge intracellular vesicle phagocytic vesicle cytoplasmic vesicle endocytic vesicle cell periphery plasma membrane membrane peroxisome microbody microtubule organizing center microtubule cytoskeleton axon cell projection neuron projection plasma membrane bounded cell projection
B	ACPA 3F3 Fab fragment - light chain	-	-	-
A	ACPA 3F3 Fab fragment - heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR018039	Intermediate filament protein, conserved site	Conserved Site
C	IPR050405	Intermediate filament structural protein	Family
C	IPR039008	Intermediate filament, rod domain	Domain
C	IPR006821	Intermediate filament head, DNA-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P08670	cataract 30 synovial sarcoma cataract pulverulent cataract cirrhosis of liver motor neuron disease Neoplasm Metastasis acute coronary syndrome lateral sclerosis breast carcinoma carcinosarcoma retinal disease nephrosis amyotrophic lateral sclerosis type 1 prostate cancer cataract 30 synovial sarcoma cataract pulverulent cataract cirrhosis of liver motor neuron disease Neoplasm Metastasis acute coronary syndrome lateral sclerosis breast carcinoma carcinosarcoma retinal disease nephrosis amyotrophic lateral sclerosis type 1 prostate cancer malignant mesothelioma Sjogren syndrome ulcerative colitis Duchenne muscular dystrophy neurodegenerative disease osteoarthritis susceptibility 1 glioblastoma ovarian cancer astrocytic tumor invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm breast cancer cancer pituitary cancer malignant ependymoma cystic fibrosis subependymal giant cell astrocytoma myopathy Emery-Dreifuss muscular dystrophy pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor ischemia reperfusion injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia lung cancer primitive neuroectodermal tumor malignant glioma malignant pancreatic neoplasm medulloblastoma Down syndrome drug-induced liver injury essential tremor osteoarthritis gastric carcinoma osteosarcoma anterior horn disease pancreatic intraductal papillary-mucinous carcinoma Becker muscular dystrophy juvenile dermatomyositis peritoneal neoplasm breast fibroadenoma limb-girdle muscular dystrophy pilocytic astrocytoma lung carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	CIR	Parent Component: ARG RESID: AA0214 PSI-MOD : L-citrulline MOD:00219

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.