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FASTA Sequence PDB Format mmCIF Format
FASTA Sequence PDB Format PDB Format(gz) PDBx/mmCIF Format PDBx/mmCIF Format(gz) PDBML/XML Format Validation Full PDF Validation CIF

9VTR

Target dna-bound type i-f3 tniq-cascade of vibrio parahaemolyticus in full r-loop state 2

PDB DOI: 10.2210/pdb9vtr/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct

Deposited: 2025-07-11
Deposition Author(s): Ishihara, K. , Numata, T.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å

Literature

Target dna-bound type i-f3 tniq-cascade of vibrio parahaemolyticus in full r-loop state 2

Ishihara, K. , Numata, T.

Primary Citation of Related Structures: 9VTR


Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
crRNA from Vibrio parahaemolyticus 1 60 NA CUGAUAAUGAGAUACCACAAGCUCAAGCAGAUGCUAACAGGUGAACUGCCGAAUAGGUAG
Target strand DNA 2 75 NA GCTGAAGCACGTTGACGGAGCTGTTAGCATCTGCTTGAGCTTGTGGTATCTCGGACCTGACTGGGCTAATGGAAG
Non-target strand DNA 3 75 NA CTTCCATTAGCCCAGTCAGGTCCGAGATACCACAAGCTCAAGCAGATGCTAACAGCTCCGTCAACGTGCTTCAGC

Proteins
Molecule Chains Sequence Length Organism Sequence
Type I-F CRISPR-associated protein Csy3 A 347 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT
Type I-F CRISPR-associated protein Csy3 B 347 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT
Type I-F CRISPR-associated protein Csy3 C 347 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT
Type I-F CRISPR-associated protein Csy3 D 347 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT
Type I-F CRISPR-associated protein Csy3 E 347 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT
Type I-F CRISPR-associated protein Csy3 F 347 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT
CRISPR-associated protein Csy2 G 640 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MATLAEILDNKTDDLNKDLRRAFRPLSAPVDISDTPIEALTILVNLTDRVIEQKNLLDRQKCKDKLRDEKWWANCFRTVKYRQSHNPKFPDIRANGVIRAAPVGHLPACMLSSSKLPQNSWAYANDSSQMNKSCFLTSEFIWNGDVHCLGQLLTELEHPLWNVLRKLGCYVKTAKYISKELALIPPLEINTSLVRNYLAQISLPNNEDSYISLSPVVSQSMQEDCYQVLSEHYRFSAITRFSRATNMGTLAMSCGGKFKMIRSLPPIEKYQHHHLDSVNWLTKRSVRAIRDYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKYLLLPNLRISGASAMNTSVSIGIPSMMAFYGFVHAFQRNVQTANPNFKIESFAVCIHNIHVENRGLTREWVPNTKGQITAPATRDDWQCDVAVSLILRCSHYSQLIPRDFIRLLPGRIARGKVTVSISDIKHLGRCLSLADAIKAIPVETGRWLSLNNEVTLNSIQDVIDELKNNKLQTVNCIGYHRLETPCEKRGSLHGYKHAFVETILGIIKFLTISENTNPSQYFWQYHYSKQGPILLPRSVSDETS
CRISPR-associated protein, Csy4 family H 198 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct MDWHYRTITFLPEYRNNEAIAAKCIKELHRFNYKYETRSIGVSFPLWGQETVGRKITFVSTNKMELDFLISRRYFVQMTKLGYFSISTTQTVPDDCSYVLFKRAHSIDKGTFAGRARELKRLERRALERGEIFDPIAYSKTTSHAFQSYHSLEEDSSSGNKFRLNIQMKERSGTVGTGKFSSYGLGNTDNSLQVVPLI
TniQ I 406 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct GPRISEFMVQMMLLQRPKSYPDESLESFFIRVANKNGYNDVHWFLVAVKRYLLDIDPRKFQTFPTDICCINPYSSKKHSISRTHALHHLSQLTFNEPVDLLGIALNRNQMQFSPSTTALIRGAEVIPRSLLRKGAIPCCPCCLGEHGYASYRWHFSGYEYCHEHDVKLIERCSCGAIYDYRYAGLSGVCTECGENISASQENHEPKATRIASWLAGDDVKPLPDVPLSYRWGFMHWWSQISSSCKTRNNGEFLAFWEHWPNSFHKLIGKEIDFNFEYCVLSKNDLRVKDILGKILFSSIQLPDRNFRSNIILKEMFQYIETHLWDDNGKLANLRMNMLEICVLLNCSREQVTSMIEQGLLPPNRQLGKREILIVTEYAFYLGDVYCLWLSEFQSDEFNRSFYLSRW
TniQ J 406 Vibrio Parahaemolyticus Rimd 2210633 , Synthetic Construct GPRISEFMVQMMLLQRPKSYPDESLESFFIRVANKNGYNDVHWFLVAVKRYLLDIDPRKFQTFPTDICCINPYSSKKHSISRTHALHHLSQLTFNEPVDLLGIALNRNQMQFSPSTTALIRGAEVIPRSLLRKGAIPCCPCCLGEHGYASYRWHFSGYEYCHEHDVKLIERCSCGAIYDYRYAGLSGVCTECGENISASQENHEPKATRIASWLAGDDVKPLPDVPLSYRWGFMHWWSQISSSCKTRNNGEFLAFWEHWPNSFHKLIGKEIDFNFEYCVLSKNDLRVKDILGKILFSSIQLPDRNFRSNIILKEMFQYIETHLWDDNGKLANLRMNMLEICVLLNCSREQVTSMIEQGLLPPNRQLGKREILIVTEYAFYLGDVYCLWLSEFQSDEFNRSFYLSRW
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2025-07-11
Deposition Author(s): Ishihara, K. , Numata, T.