3EQ3 | pdb_00003eq3

Model of tRNA(Trp)-EF-Tu 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)
C [auth I]	SCOP2B Superfamily	Ribosomal protein L11, C-terminal domain	8032961	3001186	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8032963	3000950	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	Nucleic acid-binding proteins	8106545	3000135	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)
C [auth I]	IL7	e3eq3I1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
B [auth L]	IL7	e3eq3L1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
A [auth X]	IL7	e3eq3X1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B [auth L]	PF00164	Ribosomal protein S12/S23 (Ribosom_S12_S23)	Ribosomal protein S12/S23	This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth E]	Fragment H69 of the 23S rRNA	-	-	-
H [auth D]	Fragment H95 of the 23S rRNA	-	-	-
G [auth B]	Fragment H43-44 of the 23S rRNA	-	-	-
F [auth C]	Fragment h44 of the 16S rRNA	-	-	-
E [auth A]	Fragment h18 of the 16S rRNA	-	-	-
D [auth Y]	tRNA	-	-	-
C [auth I]	50S ribosomal protein L11	RNA binding 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 primary metabolic process translation gene expression protein 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 primary metabolic process translation gene expression protein biosynthetic process 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 membraneless 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome large ribosomal subunit
B [auth L]	30S ribosomal protein S12	RNA binding binding rRNA binding nucleic acid binding misfolded RNA binding tRNA binding structural molecule activity structural constituent of ribosome	regulation of cellular process positive regulation of biological process RNA 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 regulation of cellular process positive regulation of biological process RNA 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 biological regulation primary 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 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 translation protein biosynthetic process 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome
A [auth X]	Elongation factor Tu	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	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
C [auth I]	IPR006519	Large ribosomal subunit protein uL11, bacteria	Family
B [auth L]	IPR005679	Ribosomal protein uS12, bacteria	Family
B [auth L]	IPR006032	Small ribosomal subunit protein uS12	Family
B [auth L]	IPR012340	Nucleic acid-binding, OB-fold	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.