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FASTA Sequence PDB Format mmCIF Format
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9OM4

Cryo-em structure of filament form acidithiobacillus caldus (aca) short prokaryotic argonautes, hnh-associated (sparha) with grna and tdna

PDB DOI: 10.2210/pdb9om4/pdb

Classification: IMMUNE SYSTEM/DNA/RNA
Organism(s): Acidithiobacillus Caldus , Synthetic Construct

Deposited: 2025-05-13
Deposition Author(s): Murakami, K.S. , Narwal, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.38 Å

9om4
Literature

Cryo-em structure of filament form acidithiobacillus caldus (aca) short prokaryotic argonautes, hnh-associated (sparha) with grna and tdna

Murakami, K.S. , Narwal, M.

Primary Citation of Related Structures: 9OM4


Proteins
Molecule Chains Sequence Length Organism Sequence
HNH endonuclease A 435 Acidithiobacillus Caldus , Synthetic Construct MAIEPRTKQILWGRAGATCSFPGCGRNLVRDATPEDREVLVGEIAHIVGQSKGGPRAEMSVPGGNVDGYDNLILLCHEHHELVDQQPNTYPVEKLRQYKTDHEEWVRARLSREQEFEGLTRPEAMVTETVYSNVLPITQLPHYVYSGPCTVPEAEVKTLIKWPSDKRILTPYIIRGGRLYAFNDLKDYESPFATIVDPYSAQRHTLNEWLDKPDEMRWYVELLNRTVNKITGHLRLKLDKEHHRYFFEPDEPGKDKSVTYQSVGGVRSERKVAWNPHFKHNDMPKRYWEHLAVGLRFHRLGDMAWGFAIRPERRFTKDGFESLEGKATGKKSTKKKSRMYNFDVLKEVQFWRDFLSQGNPRITCLFGKQALVIDNSLMSAAITWPEISGDQANRMSASYEDDLFSLADLQEVSEFDEFDSDTDDLETEDEVQGED
HNH endonuclease E 435 Acidithiobacillus Caldus , Synthetic Construct MAIEPRTKQILWGRAGATCSFPGCGRNLVRDATPEDREVLVGEIAHIVGQSKGGPRAEMSVPGGNVDGYDNLILLCHEHHELVDQQPNTYPVEKLRQYKTDHEEWVRARLSREQEFEGLTRPEAMVTETVYSNVLPITQLPHYVYSGPCTVPEAEVKTLIKWPSDKRILTPYIIRGGRLYAFNDLKDYESPFATIVDPYSAQRHTLNEWLDKPDEMRWYVELLNRTVNKITGHLRLKLDKEHHRYFFEPDEPGKDKSVTYQSVGGVRSERKVAWNPHFKHNDMPKRYWEHLAVGLRFHRLGDMAWGFAIRPERRFTKDGFESLEGKATGKKSTKKKSRMYNFDVLKEVQFWRDFLSQGNPRITCLFGKQALVIDNSLMSAAITWPEISGDQANRMSASYEDDLFSLADLQEVSEFDEFDSDTDDLETEDEVQGED
HNH endonuclease I 435 Acidithiobacillus Caldus , Synthetic Construct MAIEPRTKQILWGRAGATCSFPGCGRNLVRDATPEDREVLVGEIAHIVGQSKGGPRAEMSVPGGNVDGYDNLILLCHEHHELVDQQPNTYPVEKLRQYKTDHEEWVRARLSREQEFEGLTRPEAMVTETVYSNVLPITQLPHYVYSGPCTVPEAEVKTLIKWPSDKRILTPYIIRGGRLYAFNDLKDYESPFATIVDPYSAQRHTLNEWLDKPDEMRWYVELLNRTVNKITGHLRLKLDKEHHRYFFEPDEPGKDKSVTYQSVGGVRSERKVAWNPHFKHNDMPKRYWEHLAVGLRFHRLGDMAWGFAIRPERRFTKDGFESLEGKATGKKSTKKKSRMYNFDVLKEVQFWRDFLSQGNPRITCLFGKQALVIDNSLMSAAITWPEISGDQANRMSASYEDDLFSLADLQEVSEFDEFDSDTDDLETEDEVQGED
HNH endonuclease M 435 Acidithiobacillus Caldus , Synthetic Construct MAIEPRTKQILWGRAGATCSFPGCGRNLVRDATPEDREVLVGEIAHIVGQSKGGPRAEMSVPGGNVDGYDNLILLCHEHHELVDQQPNTYPVEKLRQYKTDHEEWVRARLSREQEFEGLTRPEAMVTETVYSNVLPITQLPHYVYSGPCTVPEAEVKTLIKWPSDKRILTPYIIRGGRLYAFNDLKDYESPFATIVDPYSAQRHTLNEWLDKPDEMRWYVELLNRTVNKITGHLRLKLDKEHHRYFFEPDEPGKDKSVTYQSVGGVRSERKVAWNPHFKHNDMPKRYWEHLAVGLRFHRLGDMAWGFAIRPERRFTKDGFESLEGKATGKKSTKKKSRMYNFDVLKEVQFWRDFLSQGNPRITCLFGKQALVIDNSLMSAAITWPEISGDQANRMSASYEDDLFSLADLQEVSEFDEFDSDTDDLETEDEVQGED
Prokaryotic argonaute MID-PIWI family protein B 471 Acidithiobacillus Caldus , Synthetic Construct MKTNTATVRCELFEEPSLEFASSRLHLCPKRGITIFGPRSLDMGKRHPDIVRVGFIGTGETIDSATRWLESCADGVEGDVANYRFPGFRADRGFFSDLSFDAETVERLTLRELEALARPRTKRERFEQAVALLDDKLRLLSQKDRPPDYVVLALPTELVKAQGRVDYYDKQDGEVHRDLRRAIKASAMKYRLPTQILLQRTTEATPGSKDVDHLSKCAWNFFTGLYYKTGGVPWIPAGLSNGTCYVGISFHQLLGSKNSGYFTGLAQAFDEQGNGLVLRGQDFVWDVGKHGNSAHMPAPIAEELVSRVLKRYRDELKQSPRRVVIHKTTEFWPEERAGLQSALSGVDQFDLVAVRPTEDIRLFRDARYPILRGSHISLGDMHLLYTTGYISALQAFPHGHVPLPLKLTDHLGDSSISTVLRELMVLTKMNWNSANFGGLLPITLRFSKLVGEIMKEIPNSVDPLPQFKYYM
Prokaryotic argonaute MID-PIWI family protein F 471 Acidithiobacillus Caldus , Synthetic Construct MKTNTATVRCELFEEPSLEFASSRLHLCPKRGITIFGPRSLDMGKRHPDIVRVGFIGTGETIDSATRWLESCADGVEGDVANYRFPGFRADRGFFSDLSFDAETVERLTLRELEALARPRTKRERFEQAVALLDDKLRLLSQKDRPPDYVVLALPTELVKAQGRVDYYDKQDGEVHRDLRRAIKASAMKYRLPTQILLQRTTEATPGSKDVDHLSKCAWNFFTGLYYKTGGVPWIPAGLSNGTCYVGISFHQLLGSKNSGYFTGLAQAFDEQGNGLVLRGQDFVWDVGKHGNSAHMPAPIAEELVSRVLKRYRDELKQSPRRVVIHKTTEFWPEERAGLQSALSGVDQFDLVAVRPTEDIRLFRDARYPILRGSHISLGDMHLLYTTGYISALQAFPHGHVPLPLKLTDHLGDSSISTVLRELMVLTKMNWNSANFGGLLPITLRFSKLVGEIMKEIPNSVDPLPQFKYYM
Prokaryotic argonaute MID-PIWI family protein J 471 Acidithiobacillus Caldus , Synthetic Construct MKTNTATVRCELFEEPSLEFASSRLHLCPKRGITIFGPRSLDMGKRHPDIVRVGFIGTGETIDSATRWLESCADGVEGDVANYRFPGFRADRGFFSDLSFDAETVERLTLRELEALARPRTKRERFEQAVALLDDKLRLLSQKDRPPDYVVLALPTELVKAQGRVDYYDKQDGEVHRDLRRAIKASAMKYRLPTQILLQRTTEATPGSKDVDHLSKCAWNFFTGLYYKTGGVPWIPAGLSNGTCYVGISFHQLLGSKNSGYFTGLAQAFDEQGNGLVLRGQDFVWDVGKHGNSAHMPAPIAEELVSRVLKRYRDELKQSPRRVVIHKTTEFWPEERAGLQSALSGVDQFDLVAVRPTEDIRLFRDARYPILRGSHISLGDMHLLYTTGYISALQAFPHGHVPLPLKLTDHLGDSSISTVLRELMVLTKMNWNSANFGGLLPITLRFSKLVGEIMKEIPNSVDPLPQFKYYM
Prokaryotic argonaute MID-PIWI family protein N 471 Acidithiobacillus Caldus , Synthetic Construct MKTNTATVRCELFEEPSLEFASSRLHLCPKRGITIFGPRSLDMGKRHPDIVRVGFIGTGETIDSATRWLESCADGVEGDVANYRFPGFRADRGFFSDLSFDAETVERLTLRELEALARPRTKRERFEQAVALLDDKLRLLSQKDRPPDYVVLALPTELVKAQGRVDYYDKQDGEVHRDLRRAIKASAMKYRLPTQILLQRTTEATPGSKDVDHLSKCAWNFFTGLYYKTGGVPWIPAGLSNGTCYVGISFHQLLGSKNSGYFTGLAQAFDEQGNGLVLRGQDFVWDVGKHGNSAHMPAPIAEELVSRVLKRYRDELKQSPRRVVIHKTTEFWPEERAGLQSALSGVDQFDLVAVRPTEDIRLFRDARYPILRGSHISLGDMHLLYTTGYISALQAFPHGHVPLPLKLTDHLGDSSISTVLRELMVLTKMNWNSANFGGLLPITLRFSKLVGEIMKEIPNSVDPLPQFKYYM

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
RNA (5'-R(P*AP*UP*UP*UP*GP*GP*UP*UP*GP*CP*GP*GP*UP*GP*CP*UP*CP*U)-3') c 18 NA AUUUGGUUGCGGUGCUCU
RNA (5'-R(P*AP*UP*UP*UP*GP*GP*UP*UP*GP*CP*GP*GP*UP*GP*CP*UP*CP*U)-3') g 18 NA AUUUGGUUGCGGUGCUCU
RNA (5'-R(P*AP*UP*UP*UP*GP*GP*UP*UP*GP*CP*GP*GP*UP*GP*CP*UP*CP*U)-3') k 18 NA AUUUGGUUGCGGUGCUCU
RNA (5'-R(P*AP*UP*UP*UP*GP*GP*UP*UP*GP*CP*GP*GP*UP*GP*CP*UP*CP*U)-3') o 18 NA AUUUGGUUGCGGUGCUCU
DNA (5'-D(*AP*GP*AP*GP*CP*AP*CP*CP*GP*CP*AP*AP*CP*CP*AP*AP*AP*T)-3') d 18 NA AGAGCACCGCAACCAAAT
DNA (5'-D(*AP*GP*AP*GP*CP*AP*CP*CP*GP*CP*AP*AP*CP*CP*AP*AP*AP*T)-3') h 18 NA AGAGCACCGCAACCAAAT
DNA (5'-D(*AP*GP*AP*GP*CP*AP*CP*CP*GP*CP*AP*AP*CP*CP*AP*AP*AP*T)-3') l 18 NA AGAGCACCGCAACCAAAT
DNA (5'-D(*AP*GP*AP*GP*CP*AP*CP*CP*GP*CP*AP*AP*CP*CP*AP*AP*AP*T)-3') p 18 NA AGAGCACCGCAACCAAAT
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2025-05-13
Deposition Author(s): Murakami, K.S. , Narwal, M.