HEADER RNA BINDING PROTEIN/RNA 12-JAN-23 8FTI TITLE CRYO-EM STRUCTURE OF THE CAS13BT3-CRRNA-TARGET RNA TERNARY COMPLEX IN TITLE 2 ACTIVATED STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CRRNA-LINKER-TARGET HAIRPIN RNA; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: HPRNA; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLANCTOMYCETOTA BACTERIUM; SOURCE 3 ORGANISM_TAXID: 2026780; SOURCE 4 GENE: DRP66_05270; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS CAS13BT3-CRRNA-TARGET RNA TERNARY COMPLEX, ACTIVATED STATE, RNA KEYWDS 2 BINDING PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Y.GAO,X.DENG REVDAT 2 01-MAY-24 8FTI 1 JRNL REVDAT 1 27-SEP-23 8FTI 0 JRNL AUTH X.DENG,E.OSIKPA,J.YANG,S.J.OLADEJI,J.SMITH,X.GAO,Y.GAO JRNL TITL STRUCTURAL BASIS FOR THE ACTIVATION OF A COMPACT JRNL TITL 2 CRISPR-CAS13 NUCLEASE. JRNL REF NAT COMMUN V. 14 5845 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37730702 JRNL DOI 10.1038/S41467-023-41501-5 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.500 REMARK 3 NUMBER OF PARTICLES : 37228 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8FTI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271308. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : TERNARY COMPLEX OF CAS13BT3 IN REMARK 245 COMPLEX WITH CRRNA AND 30 NT REMARK 245 TARGET RNA; INTEGRASE; CRRNA- REMARK 245 LINKER-TARGET HAIRPIN RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.80 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4900.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 VAL A 4 REMARK 465 SER A 5 REMARK 465 LYS A 6 REMARK 465 GLN A 7 REMARK 465 THR A 8 REMARK 465 SER A 9 REMARK 465 LYS A 10 REMARK 465 LYS A 11 REMARK 465 ARG A 12 REMARK 465 GLU A 13 REMARK 465 LYS A 228 REMARK 465 LYS A 229 REMARK 465 ARG A 230 REMARK 465 ALA A 231 REMARK 465 ASN A 232 REMARK 465 GLU A 271 REMARK 465 GLU A 272 REMARK 465 ALA A 273 REMARK 465 GLY A 274 REMARK 465 ALA A 275 REMARK 465 GLY A 276 REMARK 465 ASP A 277 REMARK 465 GLU A 278 REMARK 465 HIS A 279 REMARK 465 LYS A 280 REMARK 465 MET A 707 REMARK 465 SER A 708 REMARK 465 GLU A 709 REMARK 465 LYS A 710 REMARK 465 GLU A 711 REMARK 465 GLY A 712 REMARK 465 ALA A 713 REMARK 465 HIS A 714 REMARK 465 TYR A 715 REMARK 465 ILE A 716 REMARK 465 U B -36 REMARK 465 U B -35 REMARK 465 C B -34 REMARK 465 U B -33 REMARK 465 U B -32 REMARK 465 C B -31 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 775 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 74 -6.73 71.29 REMARK 500 ASN A 234 -119.18 63.87 REMARK 500 THR A 237 -60.39 -96.96 REMARK 500 ASN A 315 -119.20 57.77 REMARK 500 LYS A 645 89.24 -69.29 REMARK 500 ASP A 650 -159.93 -148.34 REMARK 500 ALA A 652 -63.00 -96.53 REMARK 500 LYS A 771 59.75 39.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29433 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE CAS13BT3-CRRNA-TARGET RNA TERNARY COMPLEX REMARK 900 IN ACTIVATED STATE DBREF1 8FTI A 1 775 UNP A0A660UUL5_9BACT DBREF2 8FTI A A0A660UUL5 1 775 DBREF 8FTI B -67 35 PDB 8FTI 8FTI -67 35 SEQADV 8FTI ALA A 84 UNP A0A660UUL ARG 84 ENGINEERED MUTATION SEQADV 8FTI ALA A 89 UNP A0A660UUL HIS 89 ENGINEERED MUTATION SEQADV 8FTI ALA A 739 UNP A0A660UUL ARG 739 ENGINEERED MUTATION SEQADV 8FTI ALA A 744 UNP A0A660UUL HIS 744 ENGINEERED MUTATION SEQRES 1 A 775 MET ALA GLN VAL SER LYS GLN THR SER LYS LYS ARG GLU SEQRES 2 A 775 LEU SER ILE ASP GLU TYR GLN GLY ALA ARG LYS TRP CYS SEQRES 3 A 775 PHE THR ILE ALA PHE ASN LYS ALA LEU VAL ASN ARG ASP SEQRES 4 A 775 LYS ASN ASP GLY LEU PHE VAL GLU SER LEU LEU ARG HIS SEQRES 5 A 775 GLU LYS TYR SER LYS HIS ASP TRP TYR ASP GLU ASP THR SEQRES 6 A 775 ARG ALA LEU ILE LYS CYS SER THR GLN ALA ALA ASN ALA SEQRES 7 A 775 LYS ALA GLU ALA LEU ALA ASN TYR PHE SER ALA TYR ARG SEQRES 8 A 775 HIS SER PRO GLY CYS LEU THR PHE THR ALA GLU ASP GLU SEQRES 9 A 775 LEU ARG THR ILE MET GLU ARG ALA TYR GLU ARG ALA ILE SEQRES 10 A 775 PHE GLU CYS ARG ARG ARG GLU THR GLU VAL ILE ILE GLU SEQRES 11 A 775 PHE PRO SER LEU PHE GLU GLY ASP ARG ILE THR THR ALA SEQRES 12 A 775 GLY VAL VAL PHE PHE VAL SER PHE PHE VAL GLU ARG ARG SEQRES 13 A 775 VAL LEU ASP ARG LEU TYR GLY ALA VAL SER GLY LEU LYS SEQRES 14 A 775 LYS ASN GLU GLY GLN TYR LYS LEU THR ARG LYS ALA LEU SEQRES 15 A 775 SER MET TYR CYS LEU LYS ASP SER ARG PHE THR LYS ALA SEQRES 16 A 775 TRP ASP LYS ARG VAL LEU LEU PHE ARG ASP ILE LEU ALA SEQRES 17 A 775 GLN LEU GLY ARG ILE PRO ALA GLU ALA TYR GLU TYR TYR SEQRES 18 A 775 HIS GLY GLU GLN GLY ASP LYS LYS ARG ALA ASN ASP ASN SEQRES 19 A 775 GLU GLY THR ASN PRO LYS ARG HIS LYS ASP LYS PHE ILE SEQRES 20 A 775 GLU PHE ALA LEU HIS TYR LEU GLU ALA GLN HIS SER GLU SEQRES 21 A 775 ILE CYS PHE GLY ARG ARG HIS ILE VAL ARG GLU GLU ALA SEQRES 22 A 775 GLY ALA GLY ASP GLU HIS LYS LYS HIS ARG THR LYS GLY SEQRES 23 A 775 LYS VAL VAL VAL ASP PHE SER LYS LYS ASP GLU ASP GLN SEQRES 24 A 775 SER TYR TYR ILE SER LYS ASN ASN VAL ILE VAL ARG ILE SEQRES 25 A 775 ASP LYS ASN ALA GLY PRO ARG SER TYR ARG MET GLY LEU SEQRES 26 A 775 ASN GLU LEU LYS TYR LEU VAL LEU LEU SER LEU GLN GLY SEQRES 27 A 775 LYS GLY ASP ASP ALA ILE ALA LYS LEU TYR ARG TYR ARG SEQRES 28 A 775 GLN HIS VAL GLU ASN ILE LEU ASP VAL VAL LYS VAL THR SEQRES 29 A 775 ASP LYS ASP ASN HIS VAL PHE LEU PRO ARG PHE VAL LEU SEQRES 30 A 775 GLU GLN HIS GLY ILE GLY ARG LYS ALA PHE LYS GLN ARG SEQRES 31 A 775 ILE ASP GLY ARG VAL LYS HIS VAL ARG GLY VAL TRP GLU SEQRES 32 A 775 LYS LYS LYS ALA ALA THR ASN GLU MET THR LEU HIS GLU SEQRES 33 A 775 LYS ALA ARG ASP ILE LEU GLN TYR VAL ASN GLU ASN CYS SEQRES 34 A 775 THR ARG SER PHE ASN PRO GLY GLU TYR ASN ARG LEU LEU SEQRES 35 A 775 VAL CYS LEU VAL GLY LYS ASP VAL GLU ASN PHE GLN ALA SEQRES 36 A 775 GLY LEU LYS ARG LEU GLN LEU ALA GLU ARG ILE ASP GLY SEQRES 37 A 775 ARG VAL TYR SER ILE PHE ALA GLN THR SER THR ILE ASN SEQRES 38 A 775 GLU MET HIS GLN VAL VAL CYS ASP GLN ILE LEU ASN ARG SEQRES 39 A 775 LEU CYS ARG ILE GLY ASP GLN LYS LEU TYR ASP TYR VAL SEQRES 40 A 775 GLY LEU GLY LYS LYS ASP GLU ILE ASP TYR LYS GLN LYS SEQRES 41 A 775 VAL ALA TRP PHE LYS GLU HIS ILE SER ILE ARG ARG GLY SEQRES 42 A 775 PHE LEU ARG LYS LYS PHE TRP TYR ASP SER LYS LYS GLY SEQRES 43 A 775 PHE ALA LYS LEU VAL GLU GLU HIS LEU GLU SER GLY GLY SEQRES 44 A 775 GLY GLN ARG ASP VAL GLY LEU ASP LYS LYS TYR TYR HIS SEQRES 45 A 775 ILE ASP ALA ILE GLY ARG PHE GLU GLY ALA ASN PRO ALA SEQRES 46 A 775 LEU TYR GLU THR LEU ALA ARG ASP ARG LEU CYS LEU MET SEQRES 47 A 775 MET ALA GLN TYR PHE LEU GLY SER VAL ARG LYS GLU LEU SEQRES 48 A 775 GLY ASN LYS ILE VAL TRP SER ASN ASP SER ILE GLU LEU SEQRES 49 A 775 PRO VAL GLU GLY SER VAL GLY ASN GLU LYS SER ILE VAL SEQRES 50 A 775 PHE SER VAL SER ASP TYR GLY LYS LEU TYR VAL LEU ASP SEQRES 51 A 775 ASP ALA GLU PHE LEU GLY ARG ILE CYS GLU TYR PHE MET SEQRES 52 A 775 PRO HIS GLU LYS GLY LYS ILE ARG TYR HIS THR VAL TYR SEQRES 53 A 775 GLU LYS GLY PHE ARG ALA TYR ASN ASP LEU GLN LYS LYS SEQRES 54 A 775 CYS VAL GLU ALA VAL LEU ALA PHE GLU GLU LYS VAL VAL SEQRES 55 A 775 LYS ALA LYS LYS MET SER GLU LYS GLU GLY ALA HIS TYR SEQRES 56 A 775 ILE ASP PHE ARG GLU ILE LEU ALA GLN THR MET CYS LYS SEQRES 57 A 775 GLU ALA GLU LYS THR ALA VAL ASN LYS VAL ALA ARG ALA SEQRES 58 A 775 PHE PHE ALA HIS HIS LEU LYS PHE VAL ILE ASP GLU PHE SEQRES 59 A 775 GLY LEU PHE SER ASP VAL MET LYS LYS TYR GLY ILE GLU SEQRES 60 A 775 LYS GLU TRP LYS PHE PRO VAL LYS SEQRES 1 B 103 G G A A G A A G A G U U U SEQRES 2 B 103 A U U C A G A U A G A U U SEQRES 3 B 103 U G U C C U U C U U C G G SEQRES 4 B 103 A C A A A U C U A U C U G SEQRES 5 B 103 A A U A A A C U C U U C U SEQRES 6 B 103 U C G C U G G A G C A G C SEQRES 7 B 103 C C C C G A U U U G U G G SEQRES 8 B 103 G G U G A U U A C A G C HELIX 1 AA1 GLN A 20 LYS A 24 5 5 HELIX 2 AA2 TRP A 25 ASN A 41 1 17 HELIX 3 AA3 GLY A 43 LEU A 50 1 8 HELIX 4 AA4 ASP A 62 SER A 72 1 11 HELIX 5 AA5 ALA A 75 ALA A 89 1 15 HELIX 6 AA6 ASP A 103 ARG A 123 1 21 HELIX 7 AA7 THR A 141 PHE A 151 1 11 HELIX 8 AA8 GLU A 154 TYR A 162 1 9 HELIX 9 AA9 SER A 166 LYS A 170 5 5 HELIX 10 AB1 GLN A 174 MET A 184 1 11 HELIX 11 AB2 ASP A 197 GLY A 211 1 15 HELIX 12 AB3 PRO A 214 TYR A 221 1 8 HELIX 13 AB4 LYS A 245 HIS A 258 1 14 HELIX 14 AB5 LEU A 325 GLY A 338 1 14 HELIX 15 AB6 LYS A 339 VAL A 360 1 22 HELIX 16 AB7 ASP A 365 VAL A 370 1 6 HELIX 17 AB8 PRO A 373 HIS A 380 1 8 HELIX 18 AB9 ALA A 386 ALA A 408 1 23 HELIX 19 AC1 THR A 413 CYS A 429 1 17 HELIX 20 AC2 ASN A 434 GLY A 447 1 14 HELIX 21 AC3 ASP A 449 ALA A 463 1 15 HELIX 22 AC4 ASP A 467 GLN A 476 1 10 HELIX 23 AC5 THR A 479 ARG A 497 1 19 HELIX 24 AC6 ASP A 500 GLY A 508 1 9 HELIX 25 AC7 ASP A 516 HIS A 527 1 12 HELIX 26 AC8 GLY A 533 TRP A 540 1 8 HELIX 27 AC9 GLY A 546 GLY A 558 1 13 HELIX 28 AD1 ALA A 582 SER A 606 1 25 HELIX 29 AD2 SER A 639 GLY A 644 1 6 HELIX 30 AD3 ALA A 652 PHE A 662 1 11 HELIX 31 AD4 TYR A 672 LYS A 706 1 35 HELIX 32 AD5 ARG A 719 THR A 725 1 7 HELIX 33 AD6 LYS A 728 ALA A 744 1 17 HELIX 34 AD7 VAL A 750 TYR A 764 1 15 SHEET 1 AA1 3 VAL A 289 ASP A 291 0 SHEET 2 AA1 3 ARG A 265 HIS A 267 -1 N ARG A 265 O ASP A 291 SHEET 3 AA1 3 SER A 300 TYR A 301 -1 O SER A 300 N ARG A 266 SHEET 1 AA2 2 ASN A 307 LYS A 314 0 SHEET 2 AA2 2 GLY A 317 GLY A 324 -1 O ARG A 319 N ILE A 312 SHEET 1 AA3 4 VAL A 616 SER A 618 0 SHEET 2 AA3 4 SER A 621 LEU A 624 -1 O GLU A 623 N VAL A 616 SHEET 3 AA3 4 ILE A 636 PHE A 638 -1 O PHE A 638 N ILE A 622 SHEET 4 AA3 4 ILE A 670 ARG A 671 1 O ILE A 670 N VAL A 637 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000