3ZEF | pdb_00003zef

Crystal structure of Prp8:Aar2 complex: second crystal form at 3.1 Angstrom resolution

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)
B	d3zefb2	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	automated matches	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3zefb3	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3zefb4	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	automated matches	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3zefb1	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Splicing factor Prp8 RT domain	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3zefb5	Artifacts	Tags	Tags	Tags	N-terminal Tags	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth D]	d3zefd2	All alpha proteins	alpha-alpha superhelix	U5 small nuclear riboprotein particle assembly factor Aar2 C-terminal domain-like	U5 small nuclear riboprotein particle assembly factor Aar2 C-terminal domain-like	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth D]	d3zefd1	All beta proteins	U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like	U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like	U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3zefa2	All alpha proteins	alpha-alpha superhelix	U5 small nuclear riboprotein particle assembly factor Aar2 C-terminal domain-like	U5 small nuclear riboprotein particle assembly factor Aar2 C-terminal domain-like	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3zefa1	All beta proteins	U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like	U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like	U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth E]	SCOP2B Superfamily	Ribonuclease H-like	8040983	3000143	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	JAB1/MPN domain-like	8053281	3001105	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8040983	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8053281	3001105	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 [auth E]	RRM_4	e3zefE1	A: a/b three-layered sandwiches	X: jelly-roll	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: RRM_4	ECOD (v294.1)
D [auth E]	U6-snRNA_bdg,U5_2-snRNA_bdg	e3zefE2	A: a/b three-layered sandwiches	X: jelly-roll	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: U6-snRNA_bdg,U5_2-snRNA_bdg	ECOD (v294.1)
D [auth E]	PROCT	e3zefE3	A: a/b three-layered sandwiches	X: jelly-roll	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: PROCT	ECOD (v294.1)
B	tRNA-synt_1b	e3zefB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: tRNA-synt_1b	ECOD (v294.1)
C [auth D]	tRNA-synt_1b	e3zefD1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: tRNA-synt_1b	ECOD (v294.1)
A	T4-gp15_tss	e3zefA1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Phage tail protein-like	T: Phage tail protein-like	F: T4-gp15_tss	ECOD (v294.1)
A		e3zefA2	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Catalytic domain of hepatitis C virus NS2-3 protease	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	3.30.43.40	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
D [auth E]	3.90.1570.40	Alpha Beta	Alpha-Beta Complex	tt1808, chain A	Pre-mRNA-processing-splicing factor 8 (Prp8), endonuclease domain	CATH (4.3.0)
D [auth E]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.30.43.40	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
B	3.90.1570.40	Alpha Beta	Alpha-Beta Complex	tt1808, chain A	Pre-mRNA-processing-splicing factor 8 (Prp8), endonuclease domain	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
C [auth D]	2.60.34.20	Mainly Beta	Sandwich	Substrate Binding Domain Of DNAk	Chain A, domain 1	CATH (4.3.0)
C [auth D]	1.25.40.550	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Aar2, C-terminal domain-like	CATH (4.3.0)
A	2.60.34.20	Mainly Beta	Sandwich	Substrate Binding Domain Of DNAk	Chain A, domain 1	CATH (4.3.0)
A	1.25.40.550	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Aar2, C-terminal domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth E]	PF10597	U5-snRNA binding site 2 of PrP8 (U5_2-snRNA_bdg)	U5-snRNA binding site 2 of PrP8	The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis [1]. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that ...	The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis [1]. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [2].	Domain
B, D [auth E]	PF10598	RNA recognition motif of the spliceosomal PrP8 (RRM_4)	RNA recognition motif of the spliceosomal PrP8	The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molec ...	The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa [1]. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RRM are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain [2].	Domain
B, D [auth E]	PF10596	U6-snRNA interacting domain of PrP8 (U6-snRNA_bdg)	U6-snRNA interacting domain of PrP8	This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 ...	This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [1].	Domain
B, D [auth E]	PF12134	PRP8 domain IV core (PRP8_domainIV)	PRP8 domain IV core	This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The dom ...	This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. This domain adopts a RNase H like fold within its core structure but with little sequence similarity. The function of PRP8 domain IV is believed to be interaction with the splicosomal core [1].	Domain
B, D [auth E]	PF08084	PROCT (NUC072) domain (PROCT)	PROCT (NUC072) domain	The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [1].	Domain
A, C [auth D]	PF05282	AAR2 C-terminal repeat region (AAR2)	AAR2 C-terminal repeat region	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth E]	PRE-MRNA-SPLICING FACTOR 8	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity RNA binding snRNA binding binding nucleic acid binding U1 snRNA binding U6 snRNA binding mRNA binding U5 snRNA binding U2 snRNA binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity RNA binding snRNA binding binding nucleic acid binding U1 snRNA binding U6 snRNA binding mRNA binding U5 snRNA binding U2 snRNA binding pre-mRNA binding pre-mRNA intronic binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process spliceosomal complex assembly mRNA splice site recognition mRNA 3'-splice site recognition mRNA 5'-splice site recognition mRNA cis splicing, via spliceosome generation of catalytic spliceosome for second transesterification step spliceosomal conformational changes to generate catalytic conformation	membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex Prp19 complex membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex Prp19 complex cytoplasm spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex U5 snRNP
A, C [auth D]	A1 CISTRON-SPLICING FACTOR AAR2	-	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process	U5 snRNP membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex U5 snRNP membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth E]	IPR012984	PROCT domain	Domain
B, D [auth E]	IPR012591	PRO8NT domain	Domain
B, D [auth E]	IPR019580	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding	Domain
B, D [auth E]	IPR027652	Pre-mRNA-processing-splicing factor 8	Family
B, D [auth E]	IPR043172	Prp8 RNase domain IV, palm region	Homologous Superfamily
B, D [auth E]	IPR012592	PROCN domain	Domain
B, D [auth E]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B, D [auth E]	IPR043173	Prp8 RNase domain IV, fingers region	Homologous Superfamily
B, D [auth E]	IPR021983	PRP8 domain IV core	Domain
B, D [auth E]	IPR019581	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding	Domain
B, D [auth E]	IPR037518	MPN domain	Domain
B, D [auth E]	IPR019582	RNA recognition motif, spliceosomal PrP8	Domain
B, D [auth E]	IPR042516	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily	Homologous Superfamily
B, D [auth E]	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
A, C [auth D]	IPR033648	AAR2, C-terminal domain	Domain
A, C [auth D]	IPR038514	AAR2, C-terminal domain superfamily	Homologous Superfamily
A, C [auth D]	IPR038516	AAR2, N-terminal domain superfamily	Homologous Superfamily
A, C [auth D]	IPR033647	AAR2, N-terminal	Domain
A, C [auth D]	IPR007946	A1 cistron-splicing factor, AAR2	Family

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.