6PI7

Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment and the PIWIL1 peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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	Tudor/PWWP/MBT domain-like	8039785	3000404	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8039785	3000404	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	KOG2279	e6pi7A1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: KOG2279	ECOD (1.6)
A	TUDOR	e6pi7A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)
D	KOG2279	e6pi7D2	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: KOG2279	ECOD (1.6)
D	TUDOR	e6pi7D1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: TUDOR	ECOD (1.6)
B	C1-set_4	e6pi7B2	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	e6pi7B1	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)
E	C1-set_4	e6pi7E1	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)
E	V-set	e6pi7E2	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)
C	V-set_8	e6pi7C1	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)
C	C1-set_1	e6pi7C2	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)
F	V-set_8	e6pi7F2	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)
F	C1-set_1	e6pi7F1	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)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, E	Antibody Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKV1-1302, IGKV1D-1302, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202432-0)
C, F	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202432-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E	Light Chain	IGKV1	Kappa	tudor and kh domain-containing protein	SAbDab (2024-08-16)
C, F	Heavy Chain	IGHV3	-	tudor and kh domain-containing protein	SAbDab (2024-08-16)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Tudor and KH domain-containing protein	RNA binding binding organic cyclic compound binding nucleic acid binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation fertilization regulation of cellular process cellular biosynthetic process piRNA processing negative regulation of biological process RNA metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation fertilization regulation of cellular process cellular biosynthetic process piRNA processing negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organelle fission meiotic cell cycle male meiotic nuclear division meiotic cell cycle process cellular component organization nuclear division organelle organization meiotic nuclear division cellular component organization or biogenesis cell cycle cell cycle process multicellular organismal process blastoderm segmentation cellular developmental process anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process cell development cellular process involved in reproduction in multicellular organism female gamete generation embryo development oocyte development tripartite regional subdivision cellular component biogenesis embryonic axis specification multicellular organism development cellular component assembly anterior/posterior axis specification cell differentiation anatomical structure development cell maturation P granule organization embryonic pattern specification oocyte axis specification oocyte construction oogenesis oocyte anterior/posterior axis specification developmental maturation cytoplasm organization regionalization pole plasm assembly anatomical structure maturation maternal determination of anterior/posterior axis, embryo germ cell development oocyte differentiation axis specification	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm ribonucleoprotein granule pole plasm intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle P granule cytoplasmic ribonucleoprotein granule germ plasm ribonucleoprotein granule pole plasm intracellular non-membrane-bounded organelle supramolecular complex non-membrane-bounded organelle pi-body piP-body
B, E	Uncharacterized protein	-	-	-
C, F	Fab antigen-binding fragment	-	-	-
G	Piwi-like protein 1	mRNA cap binding complex binding protein-containing complex binding binding RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding mRNA binding protein binding kinase binding enzyme binding protein kinase binding regulatory RNA binding piRNA binding mRNA cap binding complex binding protein-containing complex binding binding RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding mRNA binding protein binding kinase binding enzyme binding protein kinase binding regulatory RNA binding piRNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of biological process retrotransposon silencing negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling retrotransposon silencing by heterochromatin formation cellular component organization or biogenesis negative regulation of macromolecule metabolic process retrotransposition heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of metabolic process piRNA-mediated retrotransposon silencing by heterochromatin formation transposition negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing negative regulation of gene expression regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process piRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic spermatid development spermatid differentiation cellular developmental process cell development cellular process involved in reproduction in multicellular organism cell differentiation anatomical structure development germ cell development sperm DNA condensation nucleus organization organelle organization spermatid nucleus differentiation primary piRNA processing piRNA processing RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process RNA processing nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulatory ncRNA processing meiotic cell cycle cell cycle	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle dense body intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle pole plasm intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle dense body chromatoid body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR002999	Tudor domain	Domain
A, D	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A, D	IPR004087	K Homology domain	Domain
A, D	IPR047382	Tudor and KH domain-containing protein, first type I K homology domain	Domain
A, D	IPR047381	Tudor and KH domain-containing protein, second type I K homology domain	Domain
A, D	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A, D	IPR047380	Tudor domain-containing protein 2-like, tudor domain	Domain
A, D	IPR050621	Tudor domain-containing	Family
A, D	IPR004088	K Homology domain, type 1	Domain
G	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
G	IPR014811	Argonaute, linker 1 domain	Domain
G	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
G	IPR031320	GAGE	Domain
G	IPR003100	PAZ domain	Domain
G	IPR036085	PAZ domain superfamily	Homologous Superfamily
G	IPR003165	Piwi domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: Q9Y2W6	allergic rhinitis breast cancer inflammatory bowel disease malignant ependymoma ulcerative colitis astrocytic tumor breast carcinoma invasive ductal breast carcinoma malignant mesothelioma attention deficit hyperactivity disorder, inattentive type heart disease lung carcinoma myocardial infarction
G	Pharos: Q96J94	Drug abuse substance dependence drug dependence malignant colon neoplasm substance abuse substance-related disorder

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 R01GM133198.