HEADER RNA 12-FEB-25 9NAK TITLE RNA SCAFFOLD ATTACHED TO TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCAFFOLD ATTACHED TO TRNA; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS VIRAL RNA, SCAFFOLD, ENGINEERING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.P.JONES,A.R.FERRE-D'AMARE REVDAT 1 04-MAR-26 9NAK 0 JRNL AUTH C.P.JONES,A.R.FERRE-D'AMARE JRNL TITL SYMMETRIC SCAFFOLDS ENABLE DE NOVO MODELLING OF RNA BY JRNL TITL 2 CRYOEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.67 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) : 3.670 REMARK 3 NUMBER OF PARTICLES : 646397 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 9NAK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000292873. 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 : SCAFFOLD RNA ATTACHED TO TRNA 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 : 7.40 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 C A 144 REMARK 465 A A 145 REMARK 465 C A 146 REMARK 465 C A 147 REMARK 465 C A 148 REMARK 465 U A 149 REMARK 465 G A 150 REMARK 465 A A 151 REMARK 465 A A 152 REMARK 465 G A 153 REMARK 465 G A 154 REMARK 465 U A 155 REMARK 465 C C 5 REMARK 465 A C 6 REMARK 465 C C 7 REMARK 465 U C 8 REMARK 465 G C 9 REMARK 465 U C 10 REMARK 465 U C 11 REMARK 465 U C 12 REMARK 465 C C 13 REMARK 465 A C 14 REMARK 465 C C 15 REMARK 465 U C 16 REMARK 465 G C 17 REMARK 465 U C 18 REMARK 465 U C 19 REMARK 465 G C 20 REMARK 465 C C 21 REMARK 465 G C 22 REMARK 465 C C 23 REMARK 465 U C 24 REMARK 465 A C 25 REMARK 465 C C 26 REMARK 465 A C 27 REMARK 465 U C 28 REMARK 465 C C 29 REMARK 465 U C 30 REMARK 465 G C 31 REMARK 465 G C 32 REMARK 465 C C 33 REMARK 465 G C 34 REMARK 465 G C 35 REMARK 465 A C 36 REMARK 465 G C 37 REMARK 465 C C 38 REMARK 465 G C 39 REMARK 465 G C 40 REMARK 465 U C 41 REMARK 465 A C 42 REMARK 465 G C 43 REMARK 465 U C 44 REMARK 465 U C 45 REMARK 465 C C 46 REMARK 465 A C 47 REMARK 465 G C 48 REMARK 465 U C 49 REMARK 465 C C 50 REMARK 465 G C 51 REMARK 465 G C 52 REMARK 465 U C 53 REMARK 465 U C 54 REMARK 465 A C 55 REMARK 465 G C 56 REMARK 465 A C 57 REMARK 465 A C 58 REMARK 465 U C 59 REMARK 465 A C 60 REMARK 465 C C 61 REMARK 465 C C 62 REMARK 465 U C 63 REMARK 465 G C 64 REMARK 465 C C 65 REMARK 465 C C 66 REMARK 465 U C 67 REMARK 465 G C 68 REMARK 465 U C 69 REMARK 465 C C 70 REMARK 465 A C 71 REMARK 465 C C 72 REMARK 465 G C 73 REMARK 465 C C 74 REMARK 465 A C 75 REMARK 465 G C 76 REMARK 465 G C 77 REMARK 465 G C 78 REMARK 465 G C 79 REMARK 465 G C 80 REMARK 465 U C 81 REMARK 465 C C 82 REMARK 465 G C 83 REMARK 465 C C 84 REMARK 465 G C 85 REMARK 465 G C 86 REMARK 465 G C 87 REMARK 465 U C 88 REMARK 465 U C 89 REMARK 465 C C 90 REMARK 465 G C 91 REMARK 465 A C 92 REMARK 465 G C 93 REMARK 465 U C 94 REMARK 465 C C 95 REMARK 465 C C 96 REMARK 465 C C 97 REMARK 465 G C 98 REMARK 465 U C 99 REMARK 465 C C 100 REMARK 465 C C 101 REMARK 465 G C 102 REMARK 465 U C 103 REMARK 465 U C 104 REMARK 465 C C 105 REMARK 465 G C 106 REMARK 465 G C 107 REMARK 465 C C 108 REMARK 465 C C 109 REMARK 465 A C 110 REMARK 465 G C 111 REMARK 465 G C 112 REMARK 465 C C 113 REMARK 465 C C 114 REMARK 465 A C 115 REMARK 465 C C 116 REMARK 465 A C 117 REMARK 465 C C 118 REMARK 465 G C 119 REMARK 465 A C 120 REMARK 465 A C 121 REMARK 465 A C 122 REMARK 465 G C 123 REMARK 465 U C 124 REMARK 465 G C 125 REMARK 465 U C 126 REMARK 465 G C 127 REMARK 465 G C 128 REMARK 465 A C 129 REMARK 465 G C 130 REMARK 465 U C 131 REMARK 465 G C 132 REMARK 465 A C 133 REMARK 465 C C 134 REMARK 465 C C 135 REMARK 465 A C 136 REMARK 465 G C 137 REMARK 465 U C 138 REMARK 465 G C 139 REMARK 465 C C 144 REMARK 465 A C 145 REMARK 465 C C 146 REMARK 465 C C 147 REMARK 465 C C 148 REMARK 465 U C 149 REMARK 465 G C 150 REMARK 465 A C 151 REMARK 465 A C 152 REMARK 465 G C 153 REMARK 465 G C 154 REMARK 465 U C 155 REMARK 465 A C 156 REMARK 465 A C 157 REMARK 465 A C 158 REMARK 465 C C 159 REMARK 465 U C 160 REMARK 465 U C 161 REMARK 465 G C 162 REMARK 465 U C 163 REMARK 465 A C 164 REMARK 465 G C 165 REMARK 465 C C 166 REMARK 465 G C 167 REMARK 465 C C 168 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 OP2 A A 110 O HOH A 301 2.16 REMARK 500 OP1 U A 49 N2 G A 93 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 U A 11 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 U A 11 C6 - N1 - C1' ANGL. DEV. = -8.6 DEGREES REMARK 500 U A 11 C2 - N1 - C1' ANGL. DEV. = 11.3 DEGREES REMARK 500 C A 135 C2 - N1 - C1' ANGL. DEV. = 6.7 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 A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 304 O REMARK 620 2 HOH A 308 O 89.5 REMARK 620 3 HOH A 316 O 179.4 90.1 REMARK 620 4 HOH A 317 O 90.7 179.3 89.7 REMARK 620 5 HOH A 318 O 90.7 90.1 89.6 89.3 REMARK 620 6 HOH A 319 O 89.3 89.9 90.3 90.7 179.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 301 O REMARK 620 2 HOH A 302 O 89.5 REMARK 620 3 HOH A 303 O 179.6 90.1 REMARK 620 4 HOH A 310 O 90.4 90.4 89.6 REMARK 620 5 HOH A 314 O 89.8 90.1 90.2 179.5 REMARK 620 6 HOH A 315 O 90.6 179.8 89.8 89.4 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 301 O REMARK 620 2 HOH C 302 O 89.7 REMARK 620 3 HOH C 303 O 90.0 90.1 REMARK 620 4 HOH C 305 O 89.6 90.6 179.2 REMARK 620 5 HOH C 306 O 179.6 90.7 89.9 90.5 REMARK 620 6 HOH C 307 O 89.3 179.0 89.9 89.5 90.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49197 RELATED DB: EMDB REMARK 900 RNA SCAFFOLD ATTACHED TO TRNA DBREF 9NAK A 1 168 PDB 9NAK 9NAK 1 168 DBREF 9NAK C 1 168 PDB 9NAK 9NAK 1 168 SEQRES 1 A 168 G G G C C A C U G U U U C SEQRES 2 A 168 A C U G U U G C G C U A C SEQRES 3 A 168 A U C U G G C G G A G C G SEQRES 4 A 168 G U A G U U C A G U C G G SEQRES 5 A 168 U U A G A A U A C C U G C SEQRES 6 A 168 C U G U C A C G C A G G G SEQRES 7 A 168 G G U C G C G G G U U C G SEQRES 8 A 168 A G U C C C G U C C G U U SEQRES 9 A 168 C G G C C A G G C C A C A SEQRES 10 A 168 C G A A A G U G U G G A G SEQRES 11 A 168 U G A C C A G U G G C C C SEQRES 12 A 168 C A C C C U G A A G G U A SEQRES 13 A 168 A A C U U G U A G C G C SEQRES 1 C 168 G G G C C A C U G U U U C SEQRES 2 C 168 A C U G U U G C G C U A C SEQRES 3 C 168 A U C U G G C G G A G C G SEQRES 4 C 168 G U A G U U C A G U C G G SEQRES 5 C 168 U U A G A A U A C C U G C SEQRES 6 C 168 C U G U C A C G C A G G G SEQRES 7 C 168 G G U C G C G G G U U C G SEQRES 8 C 168 A G U C C C G U C C G U U SEQRES 9 C 168 C G G C C A G G C C A C A SEQRES 10 C 168 C G A A A G U G U G G A G SEQRES 11 C 168 U G A C C A G U G G C C C SEQRES 12 C 168 C A C C C U G A A G G U A SEQRES 13 C 168 A A C U U G U A G C G C HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET MG C 201 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 3 MG 3(MG 2+) FORMUL 5 K K 1+ FORMUL 7 HOH *26(H2 O) LINK MG MG A 201 O HOH A 304 1555 1555 2.18 LINK MG MG A 201 O HOH A 308 1555 1555 2.18 LINK MG MG A 201 O HOH A 316 1555 1555 2.18 LINK MG MG A 201 O HOH A 317 1555 1555 2.18 LINK MG MG A 201 O HOH A 318 1555 1555 2.18 LINK MG MG A 201 O HOH A 319 1555 1555 2.18 LINK MG MG A 202 O HOH A 301 1555 1555 2.18 LINK MG MG A 202 O HOH A 302 1555 1555 2.18 LINK MG MG A 202 O HOH A 303 1555 1555 2.18 LINK MG MG A 202 O HOH A 310 1555 1555 2.18 LINK MG MG A 202 O HOH A 314 1555 1555 2.18 LINK MG MG A 202 O HOH A 315 1555 1555 2.18 LINK MG MG C 201 O HOH C 301 1555 1555 2.17 LINK MG MG C 201 O HOH C 302 1555 1555 2.18 LINK MG MG C 201 O HOH C 303 1555 1555 2.18 LINK MG MG C 201 O HOH C 305 1555 1555 2.18 LINK MG MG C 201 O HOH C 306 1555 1555 2.18 LINK MG MG C 201 O HOH C 307 1555 1555 2.18 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 3499 3506 3510 3518 3519 CONECT 3499 3520 3521 CONECT 3500 3503 3504 3505 3512 CONECT 3500 3516 3517 CONECT 3502 3522 3523 3524 3526 CONECT 3502 3527 3528 CONECT 3503 3500 CONECT 3504 3500 CONECT 3505 3500 CONECT 3506 3499 CONECT 3510 3499 CONECT 3512 3500 CONECT 3516 3500 CONECT 3517 3500 CONECT 3518 3499 CONECT 3519 3499 CONECT 3520 3499 CONECT 3521 3499 CONECT 3522 3502 CONECT 3523 3502 CONECT 3524 3502 CONECT 3526 3502 CONECT 3527 3502 CONECT 3528 3502 MASTER 347 0 4 0 0 0 0 6 3526 2 24 26 END