HEADER RNA 14-JUN-23 8T5O TITLE CRYO-EM STRUCTURE OF RNA DEVICE 43, HOLO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEVICE 43; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA DEVICE, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR J.R.STAGNO,J.C.DEME,Y.-T.LEE,Y.-X.WANG,S.M.LEA REVDAT 1 19-FEB-25 8T5O 0 JRNL AUTH J.R.STAGNO,J.C.DEME,Y.-T.LEE,Y.-X.WANG,S.M.LEA JRNL TITL CRYO-EM STRUCTURE OF RNA DEVICE 43 FULL-LENGTH, HOLO STATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 2.980 REMARK 3 NUMBER OF PARTICLES : 369486 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 8T5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000274794. 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 : SYNTHETIC RNA DEVICE CONTAINING REMARK 245 HAMMERHEAD RIBOZYME AND REMARK 245 TETRACYCLINE-BINDING APTAMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.50 REMARK 245 SAMPLE SUPPORT DETAILS : 30 S, 30 MA ON BOTH SIDES REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.80 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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) : 5090.00 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: A 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 A 1 REMARK 465 U A 2 REMARK 465 G A 3 REMARK 465 A A 4 REMARK 465 A A 113 REMARK 465 C A 114 REMARK 465 U A 118 REMARK 465 A A 119 REMARK 465 U A 120 REMARK 465 C A 121 REMARK 465 C A 122 REMARK 465 A A 123 REMARK 465 C A 124 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4 U A 78 H61 A A 85 1.60 REMARK 500 O2' U A 63 OP2 C A 65 2.03 REMARK 500 N4 C A 79 O6 G A 84 2.15 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 A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 53 OP1 REMARK 620 2 A A 53 OP2 78.1 REMARK 620 3 A A 53 O5' 62.7 60.9 REMARK 620 4 G A 54 OP2 77.1 134.3 73.6 REMARK 620 5 HOH A 402 O 121.6 160.2 127.9 59.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 53 OP1 REMARK 620 2 G A 54 OP2 80.5 REMARK 620 3 HOH A 401 O 63.9 107.3 REMARK 620 4 HOH A 402 O 94.7 76.7 156.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 66 OP2 REMARK 620 2 TAC A 301 O11 100.6 REMARK 620 3 TAC A 301 O12 172.3 72.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 310 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 91 OP1 REMARK 620 2 A A 91 OP2 76.0 REMARK 620 3 A A 91 O5' 54.5 56.4 REMARK 620 4 HOH A 402 O 90.2 148.9 134.8 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8SYK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DEVICE REMARK 900 RELATED ID: EMD-41059 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNA DEVICE 43 FULL-LENGTH, HOLO STATE DBREF 8T5O A 1 124 PDB 8T5O 8T5O 1 124 SEQRES 1 A 124 G U G A G G U G C A G G U SEQRES 2 A 124 A C A U C C A G C U G A U SEQRES 3 A 124 G A G U C C C A A A U A G SEQRES 4 A 124 G A C A A A A A G G G A G SEQRES 5 A 124 A G G U G A A G A A U A C SEQRES 6 A 124 G A C C A C C U A G G C U SEQRES 7 A 124 C G A A A G A G C C U A A SEQRES 8 A 124 A A C A U A C C U U U C C SEQRES 9 A 124 U G G A U U C C A C U G C SEQRES 10 A 124 U A U C C A C HET TAC A 301 53 HET MG A 302 1 HET MG A 303 1 HET MG A 304 1 HET MG A 305 1 HET MG A 306 1 HET MG A 307 1 HET MG A 308 1 HET MG A 309 1 HET MG A 310 1 HET MG A 311 1 HET MG A 312 1 HET MG A 313 1 HET MG A 314 1 HET MG A 315 1 HET MG A 316 1 HETNAM TAC TETRACYCLINE HETNAM MG MAGNESIUM ION FORMUL 2 TAC C22 H24 N2 O8 FORMUL 3 MG 15(MG 2+) FORMUL 18 HOH *2(H2 O) LINK O2' A A 35 MG MG A 305 1555 1555 2.93 LINK O6 G A 52 MG MG A 311 1555 1555 1.96 LINK OP1 A A 53 MG MG A 303 1555 1555 1.95 LINK OP2 A A 53 MG MG A 303 1555 1555 2.10 LINK O5' A A 53 MG MG A 303 1555 1555 2.68 LINK OP1 A A 53 MG MG A 312 1555 1555 2.59 LINK OP2 G A 54 MG MG A 303 1555 1555 2.96 LINK OP2 G A 54 MG MG A 312 1555 1555 2.29 LINK OP2 G A 60 MG MG A 316 1555 1555 2.54 LINK OP2 G A 66 MG MG A 302 1555 1555 1.96 LINK OP1 A A 91 MG MG A 310 1555 1555 2.27 LINK OP2 A A 91 MG MG A 310 1555 1555 1.87 LINK O5' A A 91 MG MG A 310 1555 1555 2.98 LINK O11 TAC A 301 MG MG A 302 1555 1555 1.90 LINK O12 TAC A 301 MG MG A 302 1555 1555 1.82 LINK MG MG A 303 O HOH A 402 1555 1555 1.82 LINK MG MG A 310 O HOH A 402 1555 1555 2.44 LINK MG MG A 312 O HOH A 401 1555 1555 1.89 LINK MG MG A 312 O HOH A 402 1555 1555 1.83 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 TER 3572 C A 117 HETATM 3573 C1 TAC A 301 142.798 157.196 166.399 1.00 46.06 C HETATM 3574 O1 TAC A 301 142.880 156.053 165.987 1.00 55.85 O HETATM 3575 C2 TAC A 301 142.271 158.163 165.665 1.00 50.57 C HETATM 3576 C21 TAC A 301 141.423 157.882 164.510 1.00 55.57 C HETATM 3577 O21 TAC A 301 141.408 158.688 163.595 1.00 57.03 O HETATM 3578 N21 TAC A 301 140.688 156.770 164.463 1.00 57.33 N HETATM 3579 C3 TAC A 301 142.528 159.423 165.996 1.00 54.68 C HETATM 3580 O3 TAC A 301 141.638 160.367 165.704 1.00 56.05 O HETATM 3581 C4 TAC A 301 143.807 159.805 166.691 1.00 44.36 C HETATM 3582 N4 TAC A 301 143.584 161.071 167.426 1.00 52.30 N HETATM 3583 C42 TAC A 301 144.865 161.664 167.843 1.00 51.92 C HETATM 3584 C43 TAC A 301 142.688 160.925 168.588 1.00 49.67 C HETATM 3585 C41 TAC A 301 144.332 158.667 167.575 1.00 41.12 C HETATM 3586 C5 TAC A 301 145.586 158.101 166.931 1.00 41.03 C HETATM 3587 C51 TAC A 301 146.233 156.990 167.750 1.00 38.73 C HETATM 3588 C6 TAC A 301 147.245 156.209 166.909 1.00 37.96 C HETATM 3589 C62 TAC A 301 148.341 157.124 166.365 1.00 48.35 C HETATM 3590 O6 TAC A 301 146.554 155.624 165.803 1.00 46.52 O HETATM 3591 C61 TAC A 301 147.834 155.102 167.747 1.00 39.23 C HETATM 3592 C7 TAC A 301 149.167 154.701 167.643 1.00 36.31 C HETATM 3593 C8 TAC A 301 149.650 153.672 168.439 1.00 30.89 C HETATM 3594 C9 TAC A 301 148.810 153.033 169.337 1.00 31.30 C HETATM 3595 C10 TAC A 301 147.487 153.429 169.439 1.00 39.33 C HETATM 3596 O10 TAC A 301 146.655 152.807 170.316 1.00 39.26 O HETATM 3597 C1A TAC A 301 147.008 154.452 168.644 1.00 45.98 C HETATM 3598 C11 TAC A 301 145.577 154.867 168.765 1.00 50.70 C HETATM 3599 O11 TAC A 301 144.758 154.117 169.267 1.00 54.94 O HETATM 3600 C1B TAC A 301 145.202 156.056 168.319 1.00 41.33 C HETATM 3601 C12 TAC A 301 143.916 156.371 168.436 1.00 45.36 C HETATM 3602 O12 TAC A 301 143.144 155.590 169.185 1.00 47.90 O HETATM 3603 C1C TAC A 301 143.303 157.568 167.761 1.00 43.74 C HETATM 3604 O1C TAC A 301 142.217 158.051 168.555 1.00 54.15 O HETATM 3605 HN21 TAC A 301 140.702 156.107 165.224 1.00 50.45 H HETATM 3606 HN22 TAC A 301 140.107 156.591 163.657 1.00 49.80 H HETATM 3607 H4 TAC A 301 144.561 159.986 165.913 1.00 46.42 H HETATM 3608 H421 TAC A 301 144.692 162.633 168.232 1.00 48.40 H HETATM 3609 H422 TAC A 301 145.511 161.734 167.007 1.00 47.59 H HETATM 3610 H423 TAC A 301 145.319 161.065 168.588 1.00 48.92 H HETATM 3611 H431 TAC A 301 142.462 161.887 168.969 1.00 47.47 H HETATM 3612 H432 TAC A 301 143.157 160.358 169.349 1.00 47.90 H HETATM 3613 H433 TAC A 301 141.787 160.452 168.296 1.00 48.81 H HETATM 3614 H41 TAC A 301 144.609 159.051 168.564 1.00 47.47 H HETATM 3615 H51A TAC A 301 146.302 158.918 166.820 1.00 47.96 H HETATM 3616 H52 TAC A 301 145.353 157.730 165.931 1.00 47.25 H HETATM 3617 H51 TAC A 301 146.778 157.454 168.582 1.00 46.68 H HETATM 3618 H621 TAC A 301 148.944 156.587 165.682 1.00 49.05 H HETATM 3619 H622 TAC A 301 148.938 157.478 167.165 1.00 48.07 H HETATM 3620 H623 TAC A 301 147.917 157.945 165.850 1.00 48.42 H HETATM 3621 HO6 TAC A 301 147.179 155.120 165.264 1.00 49.66 H HETATM 3622 H7 TAC A 301 149.848 155.178 166.953 1.00 47.48 H HETATM 3623 H8 TAC A 301 150.686 153.366 168.357 1.00 46.71 H HETATM 3624 H9 TAC A 301 149.188 152.230 169.958 1.00 46.36 H HETATM 3625 HOC TAC A 301 141.534 157.370 168.618 1.00 49.09 H HETATM 3626 MG MG A 302 143.169 154.161 170.307 1.00 49.91 MG HETATM 3627 MG MG A 303 152.743 145.472 176.414 1.00 27.88 MG HETATM 3628 MG MG A 304 147.797 151.825 179.487 1.00 9.62 MG HETATM 3629 MG MG A 305 159.577 162.630 115.976 1.00 45.87 MG HETATM 3630 MG MG A 306 158.033 166.343 120.612 1.00 49.26 MG HETATM 3631 MG MG A 307 154.239 164.604 125.549 1.00 40.33 MG HETATM 3632 MG MG A 308 156.940 150.923 194.042 1.00 47.77 MG HETATM 3633 MG MG A 309 155.231 144.633 129.220 1.00 43.75 MG HETATM 3634 MG MG A 310 151.246 143.020 179.172 1.00 62.49 MG HETATM 3635 MG MG A 311 148.761 143.429 167.708 1.00 55.78 MG HETATM 3636 MG MG A 312 153.764 145.941 178.506 1.00 53.33 MG HETATM 3637 MG MG A 313 144.837 140.236 129.106 1.00 41.35 MG HETATM 3638 MG MG A 314 149.132 143.812 161.073 1.00 57.02 MG HETATM 3639 MG MG A 315 171.171 152.460 200.357 1.00 66.89 MG HETATM 3640 MG MG A 316 133.450 163.501 173.249 1.00 58.19 MG HETATM 3641 O HOH A 401 154.841 147.479 178.294 1.00 30.36 O HETATM 3642 O HOH A 402 152.745 144.521 177.970 1.00 45.82 O CONECT 973 3629 CONECT 1541 3635 CONECT 1559 3627 3636 CONECT 1560 3627 CONECT 1561 3627 CONECT 1593 3627 3636 CONECT 1791 3640 CONECT 1985 3626 CONECT 2788 3634 CONECT 2789 3634 CONECT 2790 3634 CONECT 3573 3574 3575 3603 CONECT 3574 3573 CONECT 3575 3573 3576 3579 CONECT 3576 3575 3577 3578 CONECT 3577 3576 CONECT 3578 3576 3605 3606 CONECT 3579 3575 3580 3581 CONECT 3580 3579 CONECT 3581 3579 3582 3585 3607 CONECT 3582 3581 3583 3584 CONECT 3583 3582 3608 3609 3610 CONECT 3584 3582 3611 3612 3613 CONECT 3585 3581 3586 3603 3614 CONECT 3586 3585 3587 3615 3616 CONECT 3587 3586 3588 3600 3617 CONECT 3588 3587 3589 3590 3591 CONECT 3589 3588 3618 3619 3620 CONECT 3590 3588 3621 CONECT 3591 3588 3592 3597 CONECT 3592 3591 3593 3622 CONECT 3593 3592 3594 3623 CONECT 3594 3593 3595 3624 CONECT 3595 3594 3596 3597 CONECT 3596 3595 CONECT 3597 3591 3595 3598 CONECT 3598 3597 3599 3600 CONECT 3599 3598 3626 CONECT 3600 3587 3598 3601 CONECT 3601 3600 3602 3603 CONECT 3602 3601 3626 CONECT 3603 3573 3585 3601 3604 CONECT 3604 3603 3625 CONECT 3605 3578 CONECT 3606 3578 CONECT 3607 3581 CONECT 3608 3583 CONECT 3609 3583 CONECT 3610 3583 CONECT 3611 3584 CONECT 3612 3584 CONECT 3613 3584 CONECT 3614 3585 CONECT 3615 3586 CONECT 3616 3586 CONECT 3617 3587 CONECT 3618 3589 CONECT 3619 3589 CONECT 3620 3589 CONECT 3621 3590 CONECT 3622 3592 CONECT 3623 3593 CONECT 3624 3594 CONECT 3625 3604 CONECT 3626 1985 3599 3602 CONECT 3627 1559 1560 1561 1593 CONECT 3627 3642 CONECT 3629 973 CONECT 3634 2788 2789 2790 3642 CONECT 3635 1541 CONECT 3636 1559 1593 3641 3642 CONECT 3640 1791 CONECT 3641 3636 CONECT 3642 3627 3634 3636 MASTER 173 0 16 0 0 0 0 6 2427 1 74 10 END