3CJQ | pdb_00003cjq

Ribosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11 in space group P212121

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)
F [auth H]	d3cjqh1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Ribosomal protein L11, C-terminal domain	Ribosomal protein L11, C-terminal domain	Ribosomal protein L11, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
F [auth H]	d3cjqh2	Alpha and beta proteins (a+b)	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal protein L11, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth E]	d3cjqe1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Ribosomal protein L11, C-terminal domain	Ribosomal protein L11, C-terminal domain	Ribosomal protein L11, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth E]	d3cjqe2	Alpha and beta proteins (a+b)	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal protein L11, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d3cjqb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Ribosomal protein L11, C-terminal domain	Ribosomal protein L11, C-terminal domain	Ribosomal protein L11, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d3cjqb2	Alpha and beta proteins (a+b)	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal protein L11, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
E [auth G]	d3cjqg1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Ribosomal protein L11 methyltransferase PrmA	PrmA-like protein TTHA0656 (TT0836)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C [auth D]	d3cjqd1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Ribosomal protein L11 methyltransferase PrmA	PrmA-like protein TTHA0656 (TT0836)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d3cjqa1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Ribosomal protein L11 methyltransferase PrmA	PrmA-like protein TTHA0656 (TT0836)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth H]	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8040122	3000950	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8040122	3000950	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8040122	3000950	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8041051	3000118	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8041051	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8041051	3000118	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)
F [auth H]	Ribosomal_L11	e3cjqH4	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
F [auth H]	Ribosomal_L11_N	e3cjqH3	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)
D [auth E]	Ribosomal_L11	e3cjqE4	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
D [auth E]	Ribosomal_L11_N	e3cjqE3	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)
B	Ribosomal_L11	e3cjqB4	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
B	Ribosomal_L11_N	e3cjqB3	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)
E [auth G]	prmA_like	e3cjqG2	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain (From Topology)	T: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain	F: prmA_like	ECOD (1.6)
E [auth G]	Methyltransf_11_4	e3cjqG3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
C [auth D]	prmA_like	e3cjqD2	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain (From Topology)	T: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain	F: prmA_like	ECOD (1.6)
C [auth D]	Methyltransf_11_4	e3cjqD3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
A	prmA_like	e3cjqA2	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain (From Topology)	T: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain	F: prmA_like	ECOD (1.6)
A	Methyltransf_11_4	e3cjqA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth H]	3.30.1550.10	Alpha Beta	2-Layer Sandwich	Ribosomal protein L11, N-terminal domain	Ribosomal protein L11/L12, N-terminal domain	CATH (4.2.0)
F [auth H]	1.10.10.250	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ribosomal protein L11/L12, C-terminal domain	CATH (4.2.0)
D [auth E]	3.30.1550.10	Alpha Beta	2-Layer Sandwich	Ribosomal protein L11, N-terminal domain	Ribosomal protein L11/L12, N-terminal domain	CATH (4.2.0)
D [auth E]	1.10.10.250	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ribosomal protein L11/L12, C-terminal domain	CATH (4.2.0)
B	3.30.1550.10	Alpha Beta	2-Layer Sandwich	Ribosomal protein L11, N-terminal domain	Ribosomal protein L11/L12, N-terminal domain	CATH (4.2.0)
B	1.10.10.250	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ribosomal protein L11/L12, C-terminal domain	CATH (4.2.0)
E [auth G]	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	CATH (4.2.0)
E [auth G]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.2.0)
C [auth D]	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	CATH (4.2.0)
C [auth D]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.2.0)
A	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	CATH (4.2.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D], E [auth G]	PF06325	Ribosomal protein L11 methyltransferase (PrmA) (PrmA)	Ribosomal protein L11 methyltransferase (PrmA)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth E], F [auth H]	50S ribosomal protein L11	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit
A, C [auth D], E [auth G]	Ribosomal protein L11 methyltransferase	protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity	methylation metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth E], F [auth H]	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
B, D [auth E], F [auth H]	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
B, D [auth E], F [auth H]	IPR000911	Ribosomal protein uL11	Family
B, D [auth E], F [auth H]	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
B, D [auth E], F [auth H]	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
B, D [auth E], F [auth H]	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain superfamily	Homologous Superfamily
B, D [auth E], F [auth H]	IPR006519	Large ribosomal subunit protein uL11, bacteria	Family
A, C [auth D], E [auth G]	IPR050078	Ribosomal protein L11 methyltransferase PrmA	Family
A, C [auth D], E [auth G]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C [auth D], E [auth G]	IPR004498	Ribosomal protein L11 methyltransferase	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.