Structure of PDB 5nfv Chain A

Receptor sequence

>5nfvA (length=1258) Species: 401614 (Francisella tularensis subsp. novicida U112)

NASIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKK
AKQIIDKYHQFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFK
SAKDTIKKQISEYIKDSEKFKNLFNQNLIDAKKSDLILWLKQSKDNGIEL
FKANSDITDIDEALEIIKSFKGWTTYFKGFHENRKNVYSSNDIPTSIIYR
IVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAEELTFDIDYKTSE
VNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKGINE
YINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTM
QSFYEQIAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDL
SQQVFDDYSVIGTAVLEYITQKTEKAKYLSLETIKLALEEFNKHRDIDKQ
CRFEEILANFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDD
VKAIKDLLDQTNNLLHKLKIFHISQSEDKANILDKDEHFYLVFEECYFEL
ANIVPLYNKIRNYITQKPYSDEKFKLNFENSTLANGWDKNKEPDNTAILF
IKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIVYKLLPGANKMLPKV
FFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCRKFID
FYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENISES
YIDSVVNQGKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVY
KLNGEAELFYRKQSIPKKITHPAKEAIANKNKDNPKKESVFEYDLIKDKR
FTEDKFFFHCPITINFKSSGANKFNDEINLLLKEKANDVHILSIDRGERH
LAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLAAIEKDRDSARKDWK
KINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFQDLKVEKQVYQKLEKML
IEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIYYVPAGF
TSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEFSFDYK
NFGDKAAKGKWTIASFGSRLINFRNDTREVYPTKELEKLLKDYSIEYGHG
ECIKAAICGESDKKFFAKLTSVLNTILQMANSKTDYLISPVADVNGNFFD
SRQAPKNMPQDADANGAYHIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYF
EFVQNRNN

3D structure

• PDB: 5nfv Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.
• Chain: A
• Resolution: 2.501 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.1: deoxyribonuclease I.
  4.6.1.22: Bacillus subtilis ribonuclease.

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	A	S14 K15 T16 R18 F19 E20 K51 N185 R186 R202 F289 N294 T295 Q309 F325 K326 L329 Y410 H538 K541 N580 R583 N790 K791 S794 Y796 S797 G799 R800 N802 L803 H804 E829 T842 I849 A850 N851 K852 N853 N856 K858 S861 V862 F863 Y865 L867 I868 K869 K871 R872 F879 H881 R948 K956 R968 E979 S986 Q987 H990 K1034 K1041	S15 K16 T17 R19 F20 E21 K52 N183 R184 R200 F287 N292 T293 Q307 F323 K324 L327 Y408 H516 K519 N558 R561 N768 K769 S772 Y774 S775 G777 R778 N780 L781 H782 E807 T820 I827 A828 N829 K830 N831 N834 K836 S839 V840 F841 Y843 L845 I846 K847 K849 R850 F857 H859 R926 K934 R946 E957 S964 Q965 H968 K1003 K1010
BS02	dna	A	K131 N188 P196 G286 K296 N301 E302 N305 S334 S336 K397 T400 Y410 N584 T587 Q588 K589 G608 D610 N612 K613 L661 P663 M668 K671 S675 A676 K677 N825 G826 E827 K978 K1026 T1063 F1064 R1155	K132 N186 P194 G284 K294 N299 E300 N303 S332 S334 K395 T398 Y408 N562 T565 Q566 K567 G586 D588 N590 K591 L639 P641 M646 K649 S653 A654 K655 N803 G804 E805 K956 K995 T1032 F1033 R1124
BS03	dna	A	N124 Q125 G174 T176 T177 K471 K639 N666 K667 K671 T698 K699 N700 G701 S702 D751 Y754 R755	N125 Q126 G172 T174 T175 K449 K617 N644 K645 K649 T676 K677 N678 G679 S680 D729 Y732 R733
BS04	MG	A	S67 V69 Y248 N270	S68 V70 Y246 N268

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004530 deoxyribonuclease I activity
• GO:0016829 lyase activity

Biological Process

• GO:0006259 DNA metabolic process
• GO:0051607 defense response to virus

External links

• PDB: RCSB:5nfv, PDBe:5nfv, PDBj:5nfv
• PDBsum: 5nfv
• PubMed: 28431230
• UniProt: A0Q7Q2|CS12A_FRATN CRISPR-associated endonuclease Cas12a (Gene Name=cas12a)