Structure of PDB 8sfo Chain A

Receptor sequence

>8sfoA (length=1240) Species: 1111120 (Acidaminococcus sp. BV3L6)

MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKEL
KPIIDRIYKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQA
TYRNAIHDYFIGRTDNLTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVT
TTEHENALLRSFDKFTTYFSGFYENRKNVFSAEDISTAIPHRIVQDNFPK
FKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEVFSFPFYNQLL
TQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPH
RFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAE
ALFNELNSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELKSA
KEKVQRSLKHEDINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLP
TTLKKQEEKEILKSQLDSLLGLYHLLDWFAVDESNEVDPEFSARLTGIKL
EMEPSLSFYNKARNYATKKPYSVEKFKLNFQMPTLASGWDVNKEKNNGAI
LFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPDAAKMI
PKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKF
QTAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYK
DLGEYYAELNPLLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHH
GKPNLHTLYWTGLFSPENLAKTSIKLNGQAELFYRPKSHEIIKDRRFTSD
KFFFHVPITLNYQAANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYI
TVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSVVGTIKDL
KQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEK
MLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPA
PYTSKIDPLTGFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHF
KMNRNLSFQRGLPGFMPAWDIVFEKNETQFDAKGTPFIAGKRIVPVIENH
RFTGRYRDLYPANELIALLEEKGIVFRDGSNILPKLLENDDSHAIDTMVA
LIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPMDADANGA
YHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

3D structure

• PDB: 8sfo WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site.
• Chain: A
• Resolution: 3.3 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	A	S14 K15 T16 R18 K51 N175 R176 R192 K273 L283 Q286 F306 K307 I309 K369 E372 W382 H479 L511 Y514 N515 R518 K530 N747 K748 A751 G753 H754 H755 G756 K757 N759 F788 H856 I858 K860 R863 H872 F938 Y940 R955 D966 G970 S973 K1022 K1029 R1168	S14 K15 T16 R18 K51 N175 R176 R192 K273 L283 Q286 F306 K307 I309 K369 E372 W382 H474 L506 Y509 N510 R513 K525 N742 K743 A746 G748 H749 H750 G751 K752 N754 F783 H789 I791 K793 R796 H805 F871 Y873 R888 D899 G903 S906 K955 K962 R1101
BS02	dna	A	N178 I185 S186 N278 E279 N282 Q286 R301 I319 E372 S376 W382 N519 K523 K524 D545 N547 K548 P599 M604 K607 L612 K613 Y687 K689 N782 G783 Q784 T963 I964 K965 Q1013 Q1014 F1052 A1053	N178 I185 S186 N278 E279 N282 Q286 R301 I319 E372 S376 W382 N514 K518 K519 D540 N542 K543 P594 M599 K602 L607 K608 Y682 K684 N777 G778 Q779 T896 I897 K898 Q946 Q947 F985 A986
BS03	dna	A	R92 K134 A135 K164 F165 T166 T167 P538 R574 Y575 A602 K603 K607 Q611 K653 Q656 T657 Y711 S884 S886 K887 E911 R912 L995 F999 K1054 A1067 P1068 T1070 S1071 K1072 R1127 R1172 Y1173 N1291 N1295	R92 K134 A135 K164 F165 T166 T167 P533 R569 Y570 A597 K598 K602 Q606 K648 Q651 T652 Y706 S817 S819 K820 E844 R845 L928 F932 K987 A1000 P1001 T1003 S1004 K1005 R1060 R1105 Y1106 N1224 N1228
BS04	MG	A	D908 E993	D841 E926
BS05	MG	A	D908 D1263	D841 D1196

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:8sfo, PDBe:8sfo, PDBj:8sfo
• PDBsum: 8sfo
• UniProt: U2UMQ6|CS12A_ACISB CRISPR-associated endonuclease Cas12a (Gene Name=cas12a)