Structure of PDB 5new Chain B

Receptor sequence

>5newB (length=64) Species: 585035 (Escherichia coli S88)

QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMV
YKHAISTVVPSRPV

3D structure

• PDB: 5new Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.
• Chain: B
• Resolution: 2.511 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	B	Y25 G29 I30 K31 L32 Q33 N48 Q52 T61	Y21 G25 I26 K27 L28 Q29 N44 Q48 T57
BS02	rna	B	F42 Y55 H57	F38 Y51 H53

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003677 DNA binding
• GO:0003681 bent DNA binding
• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0140691 RNA folding chaperone

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0008033 tRNA processing
• GO:0034337 RNA folding
• GO:0040033 sRNA-mediated post-transcriptional gene silencing
• GO:0043487 regulation of RNA stability
• GO:0045974 regulation of translation, ncRNA-mediated
• GO:0045975 positive regulation of translation, ncRNA-mediated

Cellular Component

• GO:0005829 cytosol
• GO:0043590 bacterial nucleoid

External links

• PDB: RCSB:5new, PDBe:5new, PDBj:5new
• PDBsum: 5new
• PubMed: 28852099
• UniProt: P0A6X3|HFQ_ECOLI RNA-binding protein Hfq (Gene Name=hfq)