3LEL

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3leld_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
H	d3lelh_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
N	d3leln_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
R	d3lelr_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
A	d3lela_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
E	d3lele_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
K	d3lelk_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
O	d3lelo_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
F	d3lelf_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
L	d3lell_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
P	d3lelp_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
B	d3lelb_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
C	d3lelc_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
G	d3lelg_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
M	d3lelm_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
Q	d3lelq_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
G	SCOP2 Family	Nucleosome core histones	8067125	4000793	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Core histone-like	8067126	3001387	SCOP2 (2022-06-29)
M	SCOP2B Superfamily	Core histone-like	8067126	3001387	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Core histone-like	8067126	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)
D	Histone	e3lelD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
H	Histone	e3lelH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
N	Histone	e3lelN1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
R	Histone	e3lelR1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
A	Histone	e3lelA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E	Histone	e3lelE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
K	Histone	e3lelK1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
O	Histone	e3lelO1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
F	Histone_1	e3lelF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
L	Histone_1	e3lelL1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
P	Histone_1	e3lelP1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
B	Histone_1	e3lelB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
C	Histone_1	e3lelC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
G	Histone_1	e3lelG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
M	Histone_1	e3lelM1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
Q	Histone_1	e3lelQ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
H	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
N	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
R	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
E	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
K	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
O	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
F	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
L	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
P	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
B	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
C	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
G	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
M	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
Q	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, H, N, R	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
A, E, K, O	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
B, F, L, P	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
C, G, M, Q	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
C, G, M, Q	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H, N, R	Histone H2B 1.1	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
A, E, K, O	Histone H3.2	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 membrane-enclosed lumen 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 membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, F, L, P	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
C, G, M, Q	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
I, S	147-MER DNA	-	-	-
J, T	147-MER DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H, N, R	IPR009072	Histone-fold	Homologous Superfamily
D, H, N, R	IPR007125	Histone H2A/H2B/H3	Domain
D, H, N, R	IPR000558	Histone H2B	Family
A, E, K, O	IPR009072	Histone-fold	Homologous Superfamily
A, E, K, O	IPR007125	Histone H2A/H2B/H3	Domain
A, E, K, O	IPR000164	Histone H3/CENP-A	Family
B, F, L, P	IPR009072	Histone-fold	Homologous Superfamily
B, F, L, P	IPR001951	Histone H4	Family
B, F, L, P	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F, L, P	IPR019809	Histone H4, conserved site	Conserved Site
B, F, L, P	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C, G, M, Q	IPR009072	Histone-fold	Homologous Superfamily
C, G, M, Q	IPR007125	Histone H2A/H2B/H3	Domain
C, G, M, Q	IPR002119	Histone H2A	Family
C, G, M, Q	IPR032454	Histone H2A, C-terminal domain	Domain
C, G, M, Q	IPR032458	Histone H2A conserved site	Conserved Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.