6YN1

Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
EA [auth e]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
JA [auth j]	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
Z	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
AA [auth a]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
B	SCOP2 Family	Nucleosome core histones	8106031	4000793	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Core histone-like	8106032	3001387	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
FA [auth f]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
KA [auth k]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
BA [auth b]	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
GA [auth g]	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
LA [auth l]	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Core histone-like	8070525	3001387	SCOP2B (2022-06-29)
CA [auth c]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
HA [auth h]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
MA [auth m]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00125,PF16211	e6yn1A1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
EA [auth e]	PF00125,PF16211	e6yn1e1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
F	PF00125,PF16211	e6yn1F1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
JA [auth j]	PF00125,PF16211	e6yn1j1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
K	PF00125,PF16211	e6yn1K1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
P	PF00125,PF16211	e6yn1P1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
U	PF00125,PF16211	e6yn1U1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
Z	PF00125,PF16211	e6yn1Z1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
AA [auth a]	PF00125	e6yn1a1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
B	PF00125	e6yn1B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
FA [auth f]	PF00125	e6yn1f1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
G	PF00125	e6yn1G1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
KA [auth k]	PF00125	e6yn1k1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
L	PF00125	e6yn1L1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
Q	PF00125	e6yn1Q1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
V	PF00125	e6yn1V1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
BA [auth b]	PF00125	e6yn1b1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
C	PF00125	e6yn1C1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
GA [auth g]	PF00125	e6yn1g1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
H	PF00125	e6yn1H1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
LA [auth l]	PF00125	e6yn1l1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
M	PF00125	e6yn1M1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
R	PF00125	e6yn1R1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
W	PF00125	e6yn1W1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
CA [auth c]	PF15511	e6yn1c1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
D	PF15511	e6yn1D1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
HA [auth h]	PF15511	e6yn1h1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
I	PF15511	e6yn1I1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
MA [auth m]	PF15511	e6yn1m1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
N	PF15511	e6yn1N1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
S	PF15511	e6yn1S1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
X	PF15511	e6yn1X1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
AA [auth a], B, FA [auth f], G, KA [auth k], AA [auth a], B, FA [auth f], G, KA [auth k], L, Q, V	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
BA [auth b], C, GA [auth g], H, LA [auth l], BA [auth b], C, GA [auth g], H, LA [auth l], M, R, W	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	Histone H2A	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
AA [auth a], B, FA [auth f], G, KA [auth k], AA [auth a], B, FA [auth f], G, KA [auth k], L, Q, V	Histone H2B	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
BA [auth b], C, GA [auth g], H, LA [auth l], BA [auth b], C, GA [auth g], H, LA [auth l], M, R, W	Histone H3	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
DA [auth d], E, IA [auth i], J, NA [auth n], DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	Aprataxin and PNK-like factor	protein binding binding histone binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid protein binding binding histone binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity protein carrier chaperone histone chaperone activity molecular carrier activity 3'-5' exonuclease activity exonuclease activity ADP-D-ribose modification-dependent protein binding modification-dependent protein binding poly-ADP-D-ribose binding carbohydrate derivative binding DNA-(apurinic or apyrimidinic site) endonuclease activity protein folding chaperone cation binding ion binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling protein-containing complex organization protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis protein localization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling protein-containing complex organization protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis protein localization localization protein localization to chromatin cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization regulation of epithelial to mesenchymal transition developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation animal organ development regulation of cell differentiation mesenchyme development tissue development epithelial to mesenchymal transition cell differentiation anatomical structure development mesenchymal cell differentiation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process multicellular organismal process regulation of DNA recombination regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response cell activation involved in immune response regulation of primary metabolic process nucleobase-containing compound metabolic process multicellular organism development organic substance biosynthetic process leukocyte mediated immunity regulation of immune system process somatic diversification of immune receptors regulation of nucleobase-containing compound metabolic process somatic recombination of immunoglobulin genes involved in immune response system development immune response regulation of adaptive immune response cellular metabolic process DNA recombination regulation of cellular metabolic process primary metabolic process DNA metabolic process regulation of B cell mediated immunity immune effector process somatic diversification of immunoglobulins regulation of gene expression organic cyclic compound metabolic process regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus B cell mediated immunity regulation of immune response regulation of macromolecule biosynthetic process metabolic process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process isotype switching immune system development immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response cellular biosynthetic process somatic cell DNA recombination lymphocyte activation leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains organic substance metabolic process regulation of immunoglobulin mediated immune response leukocyte activation involved in immune response regulation of B cell activation regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process production of molecular mediator of immune response regulation of isotype switching B cell activation cell activation regulation of macromolecule metabolic process gene expression adaptive immune response immunoglobulin mediated immune response macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of lymphocyte mediated immunity regulation of immunoglobulin production immune system process somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process single strand break repair DNA repair positive regulation of biological process DNA ligation positive regulation of metabolic process regulation of DNA ligation positive regulation of DNA ligation positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of DNA metabolic process double-strand break repair double-strand break repair via nonhomologous end joining	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	IPR009072	Histone-fold	Homologous Superfamily
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	IPR007125	Histone H2A/H2B/H3	Domain
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	IPR002119	Histone H2A	Family
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	IPR032454	Histone H2A, C-terminal domain	Domain
A, EA [auth e], F, JA [auth j], K, A, EA [auth e], F, JA [auth j], K, P, U, Z	IPR032458	Histone H2A conserved site	Conserved Site
AA [auth a], B, FA [auth f], G, KA [auth k], AA [auth a], B, FA [auth f], G, KA [auth k], L, Q, V	IPR009072	Histone-fold	Homologous Superfamily
AA [auth a], B, FA [auth f], G, KA [auth k], AA [auth a], B, FA [auth f], G, KA [auth k], L, Q, V	IPR007125	Histone H2A/H2B/H3	Domain
AA [auth a], B, FA [auth f], G, KA [auth k], AA [auth a], B, FA [auth f], G, KA [auth k], L, Q, V	IPR000558	Histone H2B	Family
BA [auth b], C, GA [auth g], H, LA [auth l], BA [auth b], C, GA [auth g], H, LA [auth l], M, R, W	IPR009072	Histone-fold	Homologous Superfamily
BA [auth b], C, GA [auth g], H, LA [auth l], BA [auth b], C, GA [auth g], H, LA [auth l], M, R, W	IPR007125	Histone H2A/H2B/H3	Domain
BA [auth b], C, GA [auth g], H, LA [auth l], BA [auth b], C, GA [auth g], H, LA [auth l], M, R, W	IPR000164	Histone H3/CENP-A	Family
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	IPR009072	Histone-fold	Homologous Superfamily
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	IPR001951	Histone H4	Family
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	IPR035425	CENP-T/Histone H4, histone fold	Domain
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	IPR019809	Histone H4, conserved site	Conserved Site
CA [auth c], D, HA [auth h], I, MA [auth m], CA [auth c], D, HA [auth h], I, MA [auth m], N, S, X	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
DA [auth d], E, IA [auth i], J, NA [auth n], DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	IPR019406	Aprataxin and PNK-like factor, PBZ domain	Domain
DA [auth d], E, IA [auth i], J, NA [auth n], DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	IPR041388	PNK, FHA domain	Domain
DA [auth d], E, IA [auth i], J, NA [auth n], DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
DA [auth d], E, IA [auth i], J, NA [auth n], DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	IPR039253	Aprataxin and PNK-like factor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
DA [auth d], E, IA [auth i], J, NA [auth n], DA [auth d], E, IA [auth i], J, NA [auth n], O, T, Y	Pharos: Q8IW19	celiac disease osteosarcoma lung carcinoma vascular disease nicotine dependence