Structure of PDB 6zme Chain CI

Receptor sequence

>6zmeCI (length=582) Species: 9606 (Homo sapiens)

KLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISET
LCIGCGICIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPG
EVLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQ
NYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQ
LDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRL
KAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPF
SVREGINIFLDGYVPTENLRFRDASLVFKMCMYKYPGMKKKMGEFELAIV
AGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQK
ISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGG
ELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTA
FVVEHDFIMATYLADRVIVFDGVPSKNTVANSPQTLLAGMNKFLSQLEIT
FRRDPNNYRPRINKLNSIKDVEQKKSGNYFFL

3D structure

• PDB: 6zme Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
• Chain: CI
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

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	CI	T443 R502 R506	T428 R487 R491
BS02	rna	CI	R148 G149 S150 E151 S304 R306 E307 R567 R576 K579 S582 I583 K584	R145 G146 S147 E148 S301 R303 E304 R552 R561 K564 S567 I568 K569
BS03	SF4	CI	C29 P30 C38 C55 I56 G57 C58 C61	C26 P27 C35 C52 I53 G54 C55 C58
BS04	SF4	CI	C16 K17 P18 R22 Q23 C25 V41 C65	C13 K14 P15 R19 Q20 C22 V38 C62
BS05	ADP	CI	Y87 G113 I114 G115 K116 S117	Y84 G110 I111 G112 K113 S114

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005506 iron ion binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0017111 ribonucleoside triphosphate phosphatase activity
• GO:0043024 ribosomal small subunit binding
• GO:0043273 CTPase activity
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0060698 endoribonuclease inhibitor activity

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0006413 translational initiation
• GO:0006415 translational termination
• GO:0006417 regulation of translation
• GO:0032790 ribosome disassembly
• GO:0060702 negative regulation of endoribonuclease activity
• GO:0072344 rescue of stalled ribosome

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome

External links

• PDB: RCSB:6zme, PDBe:6zme, PDBj:6zme
• PDBsum: 6zme
• PubMed: 32680882
• UniProt: P61221|ABCE1_HUMAN ATP-binding cassette sub-family E member 1 (Gene Name=ABCE1)