Structure of PDB 8fiz Chain BG

Receptor sequence

>8fizBG (length=177) Species: 562 (Escherichia coli)

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFR

3D structure

• PDB: 8fiz A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery.
• Chain: BG
• Resolution: 3.8 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	BG	T35 N37 G39 G41 T68 R71 G76 F77 I85 K88 S121 F122 D123 R125 S129 M130 G131 R133 D153	T34 N36 G38 G40 T67 R70 G75 F76 I84 K87 S120 F121 D122 R124 S128 M129 G130 R132 D152
BS02	rna	BG	S73 V74 A75 K78 R80	S72 V73 A74 K77 R79
BS03	rna	BG	S24 M26 Q27 Q63 K64 L66 K69 T90 R92	S23 M25 Q26 Q62 K63 L65 K68 T89 R91

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fiz, PDBe:8fiz, PDBj:8fiz
• PDBsum: 8fiz
• PubMed: 36931247
• UniProt: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)