5F9R: CRISPR-associated endonuclease Cas9/Csn1

Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage. Determined by X-ray diffraction at 3.4 Å resolution. Released 27 Jan 2016.

Method
X-ray diffraction
Resolution
3.4 Å
Organisms
Streptococcus pyogenes serotype M1, Streptococcus pyogenes MGAS8232, Lambdapapillomavirus 1
Chains
4
Atoms
13,652
Mol. weight
215.73 kDa
Released
27 Jan 2016

Explore 5F9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F9R contains 70 α-helices and 50 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 70 helices, 50 β-strands

ElementResiduesLengthSheet
β-strand6-1271
β-strand15-2171
β-strand29-3352
β-strand35-3623
β-strand42-4652
β-strand48-5251
α-helix54-574
α-helix60-8526
α-helix87-937
α-helix97-1026
β-strand11614
β-strand12014
α-helix123-1319
α-helix135-14410
α-helix151-16313
β-strand16715
α-helix181-19515
α-helix218-22710
α-helix237-2459
α-helix271-28212
α-helix288-30114
α-helix316-34227
α-helix347-3504
α-helix359-3635
α-helix369-38113
α-helix388-3947
α-helix405-4095
β-strand41115
α-helix412-42615
α-helix432-4354
α-helix437-4459
β-strand46716
α-helix478-4814
β-strand48216
α-helix484-49310
β-strand50917
α-helix513-52412
β-strand528-52928
β-strand538-53928
α-helix540-5412
α-helix542-5487
α-helix549-5535
β-strand56019
α-helix561-5633
α-helix564-57310
β-strand580-58128
β-strand58619
α-helix592-6009
α-helix604-6085
α-helix610-6123
α-helix613-62513
α-helix629-6357
α-helix637-6393
α-helix645-6539
β-strand65917
α-helix664-6685
α-helix679-6846
α-helix693-6975
α-helix704-7085
α-helix724-7263
α-helix731-75020
β-strand758-76361
α-helix770-7767
α-helix780-79112
α-helix795-7984
α-helix803-8064
α-helix809-8168
β-strand820110
β-strand827110
β-strand837-840411
β-strand855-858411
α-helix861-8644
α-helix873-88816
α-helix894-9007
α-helix902-9054
α-helix918-93821
β-strand943112
β-strand949112
β-strand954-95961
α-helix960-9689
α-helix981-100020
α-helix1005-10073
β-strand100911
α-helix1032-104312
α-helix1044-10463
β-strand1049-1051313
β-strand1057-1059313
β-strand1066114
β-strand1071114
α-helix1079-10879
β-strand1093-109641
β-strand1106-1107215
β-strand1120116
β-strand1134116
β-strand1135-1137315
α-helix11381
β-strand1139-11491117
β-strand1158-11671017
α-helix1168-11769
α-helix1178-11858
β-strand1188117
α-helix1192-11943
β-strand1196-1198317
β-strand1202-120543
β-strand1211-121443
β-strand1220-122233
α-helix1230-124011
α-helix1249-126113
α-helix1264-127613
α-helix1277-12815
α-helix1285-129612
α-helix1302-131211
α-helix1313-13164
β-strand131913
β-strand1324-1325218
β-strand1330-1331218
β-strand133613
α-helix1341-13444
β-strand1346-134943
β-strand1358-136143

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CRISPR-associated endonuclease Cas9/Csn1Bprotein1368Streptococcus pyogenes serotype M1Q99ZW2 (AlphaFold model)
RNA (116-mer)ARNA118Streptococcus pyogenes MGAS8232
DNA (30-mer)CDNA30Lambdapapillomavirus 1
DNA (5'-d(p*ap*tp*gp*ap*gp*ap*cp*gp*cp*tp*gp*gp*ap*gp*tp*ap*cp*ap*c)-3')DDNA30Lambdapapillomavirus 1
Sequence of entity 1 (B), FASTA
>5F9R_1 CRISPR-associated endonuclease Cas9/Csn1 (chains B)
MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE
ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG
NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD
VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN
LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI
LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA
GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELH
AILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE
VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL
SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI
IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWG
RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL
HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRER
MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDH
IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL
TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS
KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK
MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF
ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVA
YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK
YSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE
QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA
PAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD
Sequence of entity 2 (A), FASTA
>5F9R_2 RNA (116-MER) (chains A)
GGCGCAUAAAGAUGAGACGCGUUUUAGAGCUAUGCUGUUUUGAAAAAAACAGCAUAGCAA
GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUCG
Sequence of entity 3 (C), FASTA
>5F9R_3 DNA (30-MER) (chains C)
CTAATCGCCAGCGTCTCATCTTTATGCGCC
Sequence of entity 4 (D), FASTA
>5F9R_4 DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') (chains D)
GGCGCATAAAGATGAGACGCTGGCGATTAG

Primary citation

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Jiang, F., Taylor, D.W., Chen, J.S. et al. Science (2016) 351:867-871. DOI 10.1126/science.aad8282 · PubMed

Other PDB entries of the same protein (UniProt Q99ZW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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5F9R is part of these collections:

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