4RIQ | pdb_00004riq

Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
X [auth Z]	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Dpy-30/Rlla-like	8104118	3001874	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)
X [auth Z]	C2	e4riqZ1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
V	C2	e4riqV1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
T	C2	e4riqT1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
S	C2	e4riqS1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
Q	C2	e4riqQ1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
P	C2	e4riqP1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
N	C2	e4riqN1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
M	C2	e4riqM1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
K	C2	e4riqK1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
J	C2	e4riqJ1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
H	C2	e4riqH1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
G	C2	e4riqG1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
E	C2	e4riqE1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
D	C2	e4riqD1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
B	C2	e4riqB1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)
A	C2	e4riqA1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: C2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X [auth Z]	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
V	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
T	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
S	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
Q	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
P	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
N	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
M	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
K	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
J	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
H	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
G	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
E	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
D	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
B	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)
A	1.20.890.10	Mainly Alpha	Up-down Bundle	cAMP-dependent Protein Kinase, Chain A	cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D, E, G, A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, X [auth Z]	PF05186	Dpy-30 motif (Dpy-30)	Dpy-30 motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	Set1/Ash2 histone methyltransferase complex subunit ASH2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding beta-catenin binding protein binding cation binding transition metal ion binding zinc ion binding ion binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding beta-catenin binding protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process response to hormone response to endogenous stimulus response to chemical response to estrogen developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen Set1C/COMPASS complex MLL1/2 complex MLL3/4 complex MLL1 complex
A, B, D, E, G, A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, X [auth Z]	Protein dpy-30 homolog	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	localization cellular localization transport establishment of localization in cell cellular process intracellular transport establishment of localization vesicle-mediated transport endosomal transport regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic localization cellular localization transport establishment of localization in cell cellular process intracellular transport establishment of localization vesicle-mediated transport endosomal transport regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm protein-containing complex histone methyltransferase complex membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm organelle lumen methyltransferase complex nuclear lumen Set1C/COMPASS complex MLL1/2 complex MLL3/4 complex MLL1 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR053835	Set1/Ash2 histone methyltransferase complex subunit ASH2-like, winged-helix	Domain
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR001870	B30.2/SPRY domain	Domain
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR049455	Set1/Ash2 histone methyltransferase complex subunit ASH2-like, PHD zinc finger	Domain
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR037353	Histone methyltransferase complex subunit ASH2	Family
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	IPR003877	SPRY domain	Domain
A, B, D, E, G, A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, X [auth Z]	IPR037856	Sdc1/DPY30	Family
A, B, D, E, G, A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, X [auth Z]	IPR007858	Dpy-30 motif	Conserved Site
A, B, D, E, G, A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, X [auth Z]	IPR049629	DPY30/SDC1, dimerization/docking domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, I, L, O, C, F, I, L, O, R, U, W [auth X]	Pharos: Q9UBL3	hypertensive disorder osteosarcoma
A, B, D, E, G, A, B, D, E, G, H, J, K, M, N, P, Q, S, T, V, X [auth Z]	Pharos: Q9C005	androgenetic alopecia ovarian cancer breast cancer hereditary spastic paraplegia 4

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.