HEADER RNA 03-OCT-25 9X21 TITLE TETRAHYMENA RIBOZYME SCAFFOLDED SICX SRNA IN COMPLEX WITH C-DI-GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (381-MER); COMPND 3 CHAIN: N; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 4 ORGANISM_TAXID: 287 KEYWDS RNA, SRNA, C-DI-GMP EXPDTA ELECTRON MICROSCOPY AUTHOR C.C.WANG REVDAT 1 07-OCT-26 9X21 0 JRNL AUTH C.C.WANG JRNL TITL TETRAHYMENA RIBOZYME SCAFFOLDED SICX SRNA IN COMPLEX WITH JRNL TITL 2 C-DI-GMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC, CRYOSPARC 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) : 3.280 REMARK 3 NUMBER OF PARTICLES : 173332 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 9X21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 07-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300064354. 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 : TETRAHYMENA RIBOZYME SCAFFOLDED REMARK 245 SICX SRNA IN COMPLEX WITH C-DI- REMARK 245 GMP REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 156.25 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: N 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 G N 1 REMARK 465 G N 2 REMARK 465 G N 3 REMARK 465 U N 4 REMARK 465 C N 5 REMARK 465 U N 6 REMARK 465 G N 7 REMARK 465 U N 8 REMARK 465 U N 162A REMARK 465 U N 162B REMARK 465 G N 162C REMARK 465 G N 162D REMARK 465 A N 162E REMARK 465 G N 162F REMARK 465 G N 162G REMARK 465 G N 162H REMARK 465 A N 373 REMARK 465 C N 374 REMARK 465 A N 375 REMARK 465 G N 376 REMARK 465 A N 377 REMARK 465 C N 378 REMARK 465 C N 379 REMARK 465 C N 380 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C N 127 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 G N 133 O3' - P - OP2 ANGL. DEV. = 7.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 409 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 21 OP1 REMARK 620 2 U N 38 OP1 108.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 412 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 22 OP1 REMARK 620 2 U N 23 OP2 100.7 REMARK 620 3 U N 70 OP2 93.4 108.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 416 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 66 OP1 REMARK 620 2 A N 67 OP2 109.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 422 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 69 OP1 REMARK 620 2 A N 71 OP1 77.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 423 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U N 72 OP2 REMARK 620 2 A N 73 OP2 65.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 305 N7 REMARK 620 2 G N 305 O6 67.6 REMARK 620 3 G N 305 N1 87.6 48.9 REMARK 620 4 G N 306 O6 84.8 95.2 143.2 REMARK 620 5 G N 306 N1 132.9 97.9 117.2 50.8 REMARK 620 6 G N 306 N3 155.9 136.5 109.3 90.8 54.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 419 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 314 OP2 REMARK 620 2 A N 315 OP2 97.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 325 OP1 REMARK 620 2 A N 326 OP2 92.0 REMARK 620 3 A N 328 OP2 101.4 78.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 326 OP1 REMARK 620 2 A N 328 OP1 86.3 REMARK 620 3 A N 329 OP2 169.7 83.8 REMARK 620 4 G N 330 OP2 85.1 155.1 105.2 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66469 RELATED DB: EMDB REMARK 900 TETRAHYMENA RIBOZYME SCAFFOLDED SICX SRNA IN COMPLEX WITH C-DI-GMP DBREF 9X21 N 1 380 PDB 9X21 9X21 1 380 SEQRES 1 N 381 G G G U C U G U U G A U A SEQRES 2 N 381 U G G A U G C A G U U C A SEQRES 3 N 381 C A G A C U A A A U G U C SEQRES 4 N 381 G G U C G G G G A A G A U SEQRES 5 N 381 G U A U U C U U C U C A U SEQRES 6 N 381 A A G A U A U A G U C G G SEQRES 7 N 381 A C C U C U C C U U A A U SEQRES 8 N 381 G G G A G C U A G C G G A SEQRES 9 N 381 U G A A G U G A U G C A A SEQRES 10 N 381 C A C U G G A G C C G C U SEQRES 11 N 381 G G G G C G G A G A G U G SEQRES 12 N 381 G G A C G C C U U G G A G SEQRES 13 N 381 U A C U C G U U G G A G G SEQRES 14 N 381 G A A A A G U U A U C A G SEQRES 15 N 381 G C A U G C A C C U G G U SEQRES 16 N 381 A G C U A G U C U U U A A SEQRES 17 N 381 A C C A A U A G A U U G C SEQRES 18 N 381 A U C G G U U U A A A A G SEQRES 19 N 381 G C A A G A C C G U C A A SEQRES 20 N 381 A U U G C G G G A A A G G SEQRES 21 N 381 G G U C A A C A G C C G U SEQRES 22 N 381 U C A G U A C C A A G U C SEQRES 23 N 381 U C A G G G G A A A C U U SEQRES 24 N 381 U G A G A U G G C C U U G SEQRES 25 N 381 C A A A G G G U A U G G U SEQRES 26 N 381 A A U A A G C U G A C G G SEQRES 27 N 381 A C A U G G U C C U A A C SEQRES 28 N 381 C A C G C A G C C A A G U SEQRES 29 N 381 C C U A A G U C A A C A G SEQRES 30 N 381 A C C C HET C2E N 401 46 HET MG N 402 1 HET MG N 403 1 HET MG N 404 1 HET MG N 405 1 HET MG N 406 1 HET MG N 407 1 HET MG N 408 1 HET MG N 409 1 HET MG N 410 1 HET MG N 411 1 HET MG N 412 1 HET MG N 413 1 HET MG N 414 1 HET MG N 415 1 HET MG N 416 1 HET MG N 417 1 HET MG N 418 1 HET MG N 419 1 HET MG N 420 1 HET MG N 421 1 HET MG N 422 1 HET MG N 423 1 HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETNAM MG MAGNESIUM ION HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 C2E C20 H24 N10 O14 P2 FORMUL 3 MG 22(MG 2+) LINK OP1 A N 21 MG MG N 409 1555 1555 1.86 LINK OP1 G N 22 MG MG N 412 1555 1555 1.92 LINK OP2 U N 23 MG MG N 412 1555 1555 1.87 LINK OP1 U N 23 MG MG N 413 1555 1555 1.91 LINK OP1 U N 24 MG MG N 414 1555 1555 2.29 LINK OP2 A N 28 MG MG N 403 1555 1555 2.66 LINK OP1 U N 38 MG MG N 409 1555 1555 2.16 LINK OP1 A N 66 MG MG N 416 1555 1555 1.92 LINK OP2 A N 67 MG MG N 416 1555 1555 1.90 LINK OP1 A N 69 MG MG N 422 1555 1555 2.09 LINK OP2 U N 70 MG MG N 412 1555 1555 1.86 LINK OP1 U N 70 MG MG N 415 1555 1555 2.14 LINK OP1 A N 71 MG MG N 422 1555 1555 2.33 LINK OP2 U N 72 MG MG N 423 1555 1555 2.61 LINK OP2 A N 73 MG MG N 423 1555 1555 2.46 LINK N7 G N 305 MG MG N 408 1555 1555 2.60 LINK O6 G N 305 MG MG N 408 1555 1555 2.83 LINK N1 G N 305 MG MG N 408 1555 1555 2.65 LINK O6 G N 306 MG MG N 408 1555 1555 2.93 LINK N1 G N 306 MG MG N 408 1555 1555 1.94 LINK N3 G N 306 MG MG N 408 1555 1555 2.89 LINK OP2 A N 313 MG MG N 418 1555 1555 1.90 LINK OP2 A N 314 MG MG N 419 1555 1555 1.82 LINK OP2 A N 315 MG MG N 419 1555 1555 2.00 LINK OP1 A N 325 MG MG N 406 1555 1555 2.07 LINK OP1 A N 326 MG MG N 405 1555 1555 1.82 LINK OP2 A N 326 MG MG N 406 1555 1555 2.36 LINK OP1 A N 328 MG MG N 405 1555 1555 2.05 LINK OP2 A N 328 MG MG N 406 1555 1555 1.90 LINK OP2 A N 329 MG MG N 405 1555 1555 1.85 LINK OP2 G N 330 MG MG N 405 1555 1555 2.10 LINK O6 G N 330 MG MG N 407 1555 1555 1.90 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 CONECT 260 7705 CONECT 282 7708 CONECT 305 7709 CONECT 306 7708 CONECT 325 7710 CONECT 408 7699 CONECT 623 7705 CONECT 1217 7712 CONECT 1240 7712 CONECT 1284 7718 CONECT 1306 7711 CONECT 1307 7708 CONECT 1326 7718 CONECT 1349 7719 CONECT 1369 7719 CONECT 6211 7704 CONECT 6214 7704 CONECT 6215 7704 CONECT 6237 7704 CONECT 6238 7704 CONECT 6241 7704 CONECT 6368 7714 CONECT 6390 7715 CONECT 6412 7715 CONECT 6630 7702 CONECT 6652 7701 CONECT 6653 7702 CONECT 6694 7701 CONECT 6695 7702 CONECT 6717 7701 CONECT 6739 7701 CONECT 6754 7703 CONECT 7652 7653 7654 7655 7683 CONECT 7653 7652 CONECT 7654 7652 CONECT 7655 7652 7656 CONECT 7656 7655 7657 CONECT 7657 7656 7658 7659 CONECT 7658 7657 7663 CONECT 7659 7657 7660 7661 CONECT 7660 7659 7675 CONECT 7661 7659 7662 7663 CONECT 7662 7661 CONECT 7663 7658 7661 7664 CONECT 7664 7663 7665 7674 CONECT 7665 7664 7666 CONECT 7666 7665 7667 CONECT 7667 7666 7668 7674 CONECT 7668 7667 7669 7670 CONECT 7669 7668 CONECT 7670 7668 7671 CONECT 7671 7670 7672 7673 CONECT 7672 7671 CONECT 7673 7671 7674 CONECT 7674 7664 7667 7673 CONECT 7675 7660 7676 7677 7678 CONECT 7676 7675 CONECT 7677 7675 CONECT 7678 7675 7679 CONECT 7679 7678 7680 CONECT 7680 7679 7681 7682 CONECT 7681 7680 7686 CONECT 7682 7680 7683 7684 CONECT 7683 7652 7682 CONECT 7684 7682 7685 7686 CONECT 7685 7684 CONECT 7686 7681 7684 7687 CONECT 7687 7686 7688 7697 CONECT 7688 7687 7689 CONECT 7689 7688 7690 CONECT 7690 7689 7691 7697 CONECT 7691 7690 7692 7693 CONECT 7692 7691 CONECT 7693 7691 7694 CONECT 7694 7693 7695 7696 CONECT 7695 7694 CONECT 7696 7694 7697 CONECT 7697 7687 7690 7696 CONECT 7699 408 CONECT 7701 6652 6694 6717 6739 CONECT 7702 6630 6653 6695 CONECT 7703 6754 CONECT 7704 6211 6214 6215 6237 CONECT 7704 6238 6241 CONECT 7705 260 623 CONECT 7708 282 306 1307 CONECT 7709 305 CONECT 7710 325 CONECT 7711 1306 CONECT 7712 1217 1240 CONECT 7714 6368 CONECT 7715 6390 6412 CONECT 7718 1284 1326 CONECT 7719 1349 1369 MASTER 226 0 23 0 0 0 0 6 7718 1 94 30 END