Structure of PDB 8d6j Chain A Binding Site BS01

Receptor Information

>8d6j Chain A (length=810) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

FKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNR
EIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPDR
IFKVSIKWVSCVSLQALHDALSGRLSVPFETIQALDVVMRHLPSMRYTPV
GRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKA
QPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITKRKYRVC
NVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQ
EQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKL
MRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQ
GVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAG
MPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEV
KRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQG
RPPVFQQPVIFLGADVTHPENGEESSPSIAAVVGSMDAHPNRYCATVRVQ
QHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSGQFQQVLHHE
LLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAG
TTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILT
YQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKRDHQALAKAVQVH
QDTLRTMYFA

Ligand information

>8d6j Chain B (length=11) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

uggaguguguu

...........

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8d6j A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength.
Resolution	2.5 Å
Binding residue (original residue number in PDB)	S220 A221 R277 Y279 F294 Y311 H316 H336 T337 Y338 I365 T368 A369 L522 G524 T526 Y529 K533 Q545 C546 Q548 N551 T559 N562 L563 K566 K570 R710 H753 I756 Q757 T759 S760 R761 Y790 R792 C793 S798 Y804
Binding residue (residue number reindexed from 1)	S193 A194 R245 Y247 F262 Y279 H284 H304 T305 Y306 I333 T336 A337 L490 G492 T494 Y497 K501 Q513 C514 Q516 N519 T527 N530 L531 K534 K538 R677 H720 I723 Q724 T726 S727 R728 Y757 R759 C760 S765 Y771

Enzymatic activity

Enzyme Commision number

3.1.26.n2: argonaute-2.

Gene Ontology

	Molecular Function
GO:0000340	RNA 7-methylguanosine cap binding
GO:0000993	RNA polymerase II complex binding
GO:0001046	core promoter sequence-specific DNA binding
GO:0003676	nucleic acid binding
GO:0003723	RNA binding
GO:0003725	double-stranded RNA binding
GO:0003727	single-stranded RNA binding
GO:0003729	mRNA binding
GO:0003743	translation initiation factor activity
GO:0004519	endonuclease activity
GO:0004521	RNA endonuclease activity
GO:0005515	protein binding
GO:0016891	RNA endonuclease activity, producing 5'-phosphomonoesters
GO:0035197	siRNA binding
GO:0035198	miRNA binding
GO:0035925	mRNA 3'-UTR AU-rich region binding
GO:0046872	metal ion binding
GO:0061980	regulatory RNA binding
GO:0070551	endoribonuclease activity, cleaving siRNA-paired mRNA
GO:0090624	endoribonuclease activity, cleaving miRNA-paired mRNA
GO:0098808	mRNA cap binding

	Biological Process
GO:0006355	regulation of DNA-templated transcription
GO:0006412	translation
GO:0006413	translational initiation
GO:0006417	regulation of translation
GO:0009791	post-embryonic development
GO:0010501	RNA secondary structure unwinding
GO:0010586	miRNA metabolic process
GO:0010628	positive regulation of gene expression
GO:0030422	siRNA processing
GO:0031047	regulatory ncRNA-mediated gene silencing
GO:0031054	pre-miRNA processing
GO:0033962	P-body assembly
GO:0035194	regulatory ncRNA-mediated post-transcriptional gene silencing
GO:0035196	miRNA processing
GO:0035278	miRNA-mediated gene silencing by inhibition of translation
GO:0035279	miRNA-mediated gene silencing by mRNA destabilization
GO:0042985	negative regulation of amyloid precursor protein biosynthetic process
GO:0045727	positive regulation of translation
GO:0045766	positive regulation of angiogenesis
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0045947	negative regulation of translational initiation
GO:0060213	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
GO:0070922	RISC complex assembly
GO:0090128	regulation of synapse maturation
GO:0090625	siRNA-mediated gene silencing by mRNA destabilization
GO:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:1901165	positive regulation of trophoblast cell migration

	Cellular Component
GO:0000932	P-body
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0016020	membrane
GO:0016442	RISC complex
GO:0030425	dendrite
GO:0036464	cytoplasmic ribonucleoprotein granule
GO:0043232	intracellular non-membrane-bounded organelle
GO:0070062	extracellular exosome
GO:0070578	RISC-loading complex
GO:0098794	postsynapse
GO:0098978	glutamatergic synapse
GO:1990904	ribonucleoprotein complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8d6j, PDBe:8d6j, PDBj:8d6j
PDBsum	8d6j
PubMed	37082939
UniProt	Q9UKV8\|AGO2_HUMAN Protein argonaute-2 (Gene Name=AGO2)

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