Structure of PDB 8fiz Chain AP

Receptor sequence

>8fizAP (length=155) Species: 562 (Escherichia coli)

ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK
SVEEI

3D structure

• PDB: 8fiz A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery.
• Chain: AP
• 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	AP	V21 S22 K23 T24 K26 R29 K52 R54 K62 T90 F95 A99 S100 T103 I106 A107 G108 R112 A125 K126 A127 Y128 S130 T131 N132 R138	V12 S13 K14 T15 K17 R20 K43 R45 K53 T81 F86 A90 S91 T94 I97 A98 G99 R103 A116 K117 A118 Y119 S121 T122 N123 R129
BS02	rna	AP	R20 V56 I60	R11 V47 I51

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fiz, PDBe:8fiz, PDBj:8fiz
• PDBsum: 8fiz
• PubMed: 36931247
• UniProt: P0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)