3EP2

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth L]	SCOP2B Superfamily	Nucleic acid-binding proteins	8106545	3000135	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8032963	3000950	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Ribosomal protein L11, C-terminal domain	8032961	3001186	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 [auth X]	GTP_EFTU_D2_1	e3ep2X1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
A [auth X]	GTP_EFTU_D3	e3ep2X2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3	ECOD (1.6)
A [auth X]	MnmE_helical_2nd	e3ep2X3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
B [auth L]	Ribosom_S12_S23	e3ep2L1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosom_S12_S23	ECOD (1.6)
C [auth I]	Ribosomal_L11	e3ep2I1	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
C [auth I]	Ribosomal_L11_N	e3ep2I2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth L]	PF00164	Ribosomal protein S12/S23 (Ribosom_S12_S23)	Ribosomal protein S12/S23	-	Family
C [auth I]	PF03946	Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)	Ribosomal protein L11, N-terminal domain	The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.	Domain
C [auth I]	PF00298	Ribosomal protein L11, RNA binding domain (Ribosomal_L11)	Ribosomal protein L11, RNA binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X]	Elongation factor Tu	-	-	-
B [auth L]	30S ribosomal protein S12	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding misfolded RNA binding tRNA binding structural molecule activity structural constituent of ribosome	regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process RNA splicing regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of RNA splicing regulation of metabolic process positive regulation of cellular biosynthetic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process translation cytoplasmic translation protein metabolic process RNA folding Group I intron splicing RNA splicing, via transesterification reactions with guanosine as nucleophile RNA splicing, via transesterification reactions response to stimulus response to chemical response to antibiotic maintenance of translational fidelity	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle
C [auth I]	50S ribosomal protein L11	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding structural molecule activity structural constituent of ribosome	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response cellular process response to starvation cellular response to starvation organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response cellular process response to starvation cellular response to starvation organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process protein metabolic process macromolecule metabolic process cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization translational termination cellular component organization or biogenesis ribonucleoprotein complex biogenesis organelle assembly non-membrane-bounded organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly ribosome assembly	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome large ribosomal subunit intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome large ribosomal subunit non-membrane-bounded organelle
D [auth Y]	tRNA	-	-	-
E [auth A]	Fragment h18 of the 16S rRNA	-	-	-
F [auth C]	Fragment h44 of the 16S rRNA	-	-	-
G [auth B]	Fragment H43-44 of the 23S rRNA	-	-	-
H [auth D]	Fragment H95 of the 23S rRNA	-	-	-
I [auth E]	Fragment H69 of the 23S rRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth L]	IPR005679	Ribosomal protein uS12, bacterial-type	Family
B [auth L]	IPR006032	Small ribosomal subunit protein uS12	Family
B [auth L]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C [auth I]	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
C [auth I]	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
C [auth I]	IPR000911	Ribosomal protein uL11	Family
C [auth I]	IPR006519	Large ribosomal subunit protein uL11, bacterial-type	Family
C [auth I]	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
C [auth I]	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
C [auth I]	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain superfamily	Homologous Superfamily

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.