Structure of PDB 8ygj Chain A

Receptor sequence

>8ygjA (length=1326) Species: 301447 (Streptococcus pyogenes serotype M1)

DKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGAL
LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRL
EESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADL
RLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPI
NASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPN
FKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAIL
LSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIF
FDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRK
QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY
VGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKN
LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDL
LFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKII
KDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQL
KRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDS
LTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVM
GRHKPENIVIEMARENSRERMKRIEEGIKELGSQILKEHPVENTQLQNEK
LYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRS
DKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSE
LDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS
KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVY
GKATAKYFFYSNIMNFFKTEIIRKRPLIETNGETGEIVWDKGRDFATVRK
VLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFD
SPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAK
GYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNF
LYLASHYEKPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDK
VLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTST
KEVLDATLIHQSITGLYETRIDLSQL

3D structure

• PDB: 8ygj Structural basis for pegRNA-guided reverse transcription by a prime editor.
• Chain: A
• Resolution: 3.2 Å

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

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	K3 K30 I43 K44 N46 E57 T58 A59 T62 R63 R66 R69 R70 R71 Y72 R74 R75 K76 N77 L101 S104 F105 K111 R115 H116 I122 V126 H129 T134 I135 H160 K163 F164 R165 G166 Y325 H328 H329 L332 K336 R340 K348 F351 F352 Y359 I363 Q402 R403 T404 F405 N407 G408 F446 R447 I448 Y450 G453 P454 L455 A456 R457 N459 S460 F462 W464 I473 E584 N588 H721 M1089 P1090 Q1091 K1097 E1099 V1100 G1103 G1104 F1105 I1110 P1112 K1113 R1122 K1123 K1124 Y1131 M1169 A1227 Q1272 H1349 Q1350 S1351 T1358	K2 K29 I42 K43 N45 E56 T57 A58 T61 R62 R65 R68 R69 R70 Y71 R73 R74 K75 N76 L100 S103 F104 K110 R114 H115 I121 V125 H128 T133 I134 H159 K162 F163 R164 G165 Y324 H327 H328 L331 K335 R339 K347 F350 F351 Y358 I362 Q401 R402 T403 F404 N406 G407 F445 R446 I447 Y449 G452 P453 L454 A455 R456 N458 S459 F461 W463 I472 E583 N587 H720 M1054 P1055 Q1056 K1062 E1064 V1065 G1068 G1069 F1070 I1075 P1077 K1078 R1087 K1088 K1089 Y1096 M1134 A1192 Q1233 H1310 Q1311 S1312 T1319
BS02	dna	A	Y450 M495 N497 K562 E584 D585 R586 R778 R905 R925 Q926 K1107 E1108 S1109 K1151	Y449 M494 N496 K561 E583 D584 R585 R768 R895 R915 Q916 K1072 E1073 S1074 K1116
BS03	dna	A	N776 S777 R1114 K1118 D1135 S1136 K1200 S1216 E1219 R1333 R1335	N766 S767 R1079 K1083 D1100 S1101 K1165 S1181 E1184 R1294 R1296

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004520 DNA endonuclease activity
• GO:0004527 exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0043571 maintenance of CRISPR repeat elements
• GO:0051607 defense response to virus

External links

• PDB: RCSB:8ygj, PDBe:8ygj, PDBj:8ygj
• PDBsum: 8ygj
• PubMed: 38811740
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)