HEADER RNA 11-FEB-25 9NA1 TITLE RNA SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (94-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: ENGINEERED KEYWDS VIRAL RNA, SCAFFOLD, ENGINEERING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.P.JONES,A.R.FERRE-D'AMARE REVDAT 1 04-MAR-26 9NA1 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. 3.51 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) : 3.510 REMARK 3 NUMBER OF PARTICLES : 393114 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 9NA1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000292847. 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 A A 76 REMARK 465 C A 77 REMARK 465 C A 78 REMARK 465 C A 79 REMARK 465 U A 80 REMARK 465 G A 81 REMARK 465 A A 82 REMARK 465 A A 83 REMARK 465 G A 84 REMARK 465 G A 85 REMARK 465 U A 86 REMARK 465 A B 76 REMARK 465 C B 77 REMARK 465 C B 78 REMARK 465 C B 79 REMARK 465 U B 80 REMARK 465 G B 81 REMARK 465 A B 82 REMARK 465 A B 83 REMARK 465 G B 84 REMARK 465 G B 85 REMARK 465 U B 86 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 O2' U B 34 O6 G B 37 2.08 REMARK 500 O2' U A 34 O6 G A 37 2.08 REMARK 500 O6 G B 68 O HOH B 201 2.09 REMARK 500 O6 G A 32 O HOH A 201 2.10 REMARK 500 O6 G A 68 O HOH A 202 2.13 REMARK 500 O6 G B 32 O HOH B 202 2.19 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 203 O 90.0 REMARK 620 3 HOH A 204 O 89.2 90.1 REMARK 620 4 HOH A 209 O 90.3 89.9 179.5 REMARK 620 5 HOH A 214 O 179.7 90.2 90.6 89.9 REMARK 620 6 HOH A 223 O 90.3 179.7 90.1 89.9 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 205 O REMARK 620 2 HOH A 206 O 88.5 REMARK 620 3 HOH A 211 O 89.8 90.6 REMARK 620 4 HOH A 218 O 179.5 91.0 90.4 REMARK 620 5 HOH A 220 O 91.1 89.9 178.9 88.7 REMARK 620 6 HOH A 222 O 91.2 179.7 89.2 89.3 90.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 202 O REMARK 620 2 HOH A 207 O 89.9 REMARK 620 3 HOH A 210 O 90.1 89.7 REMARK 620 4 HOH A 215 O 90.3 90.6 179.5 REMARK 620 5 HOH A 216 O 89.8 179.6 90.0 89.7 REMARK 620 6 HOH A 221 O 179.6 90.5 90.1 89.5 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 208 O REMARK 620 2 HOH A 212 O 179.7 REMARK 620 3 HOH A 213 O 90.0 90.2 REMARK 620 4 HOH A 217 O 90.7 89.1 89.9 REMARK 620 5 HOH A 219 O 90.5 89.3 179.5 90.1 REMARK 620 6 HOH A 224 O 89.8 90.4 90.0 179.5 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 202 O REMARK 620 2 HOH B 204 O 89.8 REMARK 620 3 HOH B 208 O 90.1 89.9 REMARK 620 4 HOH B 210 O 179.7 90.3 90.2 REMARK 620 5 HOH B 221 O 90.0 90.0 179.9 89.7 REMARK 620 6 HOH B 223 O 90.4 179.9 90.2 89.6 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 203 O REMARK 620 2 HOH B 205 O 88.5 REMARK 620 3 HOH B 214 O 89.9 90.6 REMARK 620 4 HOH B 216 O 179.6 91.1 90.3 REMARK 620 5 HOH B 218 O 91.0 89.9 179.0 88.8 REMARK 620 6 HOH B 220 O 91.2 179.7 89.3 89.2 90.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 201 O REMARK 620 2 HOH B 206 O 90.7 REMARK 620 3 HOH B 207 O 89.9 89.2 REMARK 620 4 HOH B 213 O 89.7 179.5 90.4 REMARK 620 5 HOH B 219 O 179.3 89.8 90.5 89.8 REMARK 620 6 HOH B 222 O 89.8 90.3 179.5 90.0 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 209 O REMARK 620 2 HOH B 211 O 90.0 REMARK 620 3 HOH B 212 O 179.8 90.2 REMARK 620 4 HOH B 215 O 90.7 89.9 89.2 REMARK 620 5 HOH B 217 O 90.5 179.5 89.3 90.2 REMARK 620 6 HOH B 224 O 89.7 90.0 90.4 179.5 90.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49180 RELATED DB: EMDB REMARK 900 RNA SCAFFOLD DBREF 9NA1 A 1 99 PDB 9NA1 9NA1 1 99 DBREF 9NA1 B 1 99 PDB 9NA1 9NA1 1 99 SEQRES 1 A 99 G G G C C A C U G U U U C SEQRES 2 A 99 A C U G U U G C G C U A C SEQRES 3 A 99 A U C U G G C U U C G G C SEQRES 4 A 99 C A G G C C A C A C G A A SEQRES 5 A 99 A G U G U G G A G U G A C SEQRES 6 A 99 C A G U G G C C C C A C C SEQRES 7 A 99 C U G A A G G U A A A C U SEQRES 8 A 99 U G U A G C G C SEQRES 1 B 99 G G G C C A C U G U U U C SEQRES 2 B 99 A C U G U U G C G C U A C SEQRES 3 B 99 A U C U G G C U U C G G C SEQRES 4 B 99 C A G G C C A C A C G A A SEQRES 5 B 99 A G U G U G G A G U G A C SEQRES 6 B 99 C A G U G G C C C C A C C SEQRES 7 B 99 C U G A A G G U A A A C U SEQRES 8 B 99 U G U A G C G C HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG B 101 1 HET MG B 102 1 HET MG B 103 1 HET MG B 104 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 8(MG 2+) FORMUL 11 HOH *48(H2 O) LINK MG MG A 101 O HOH A 201 1555 1555 2.18 LINK MG MG A 101 O HOH A 203 1555 1555 2.18 LINK MG MG A 101 O HOH A 204 1555 1555 2.18 LINK MG MG A 101 O HOH A 209 1555 1555 2.18 LINK MG MG A 101 O HOH A 214 1555 1555 2.18 LINK MG MG A 101 O HOH A 223 1555 1555 2.18 LINK MG MG A 102 O HOH A 205 1555 1555 2.18 LINK MG MG A 102 O HOH A 206 1555 1555 2.18 LINK MG MG A 102 O HOH A 211 1555 1555 2.17 LINK MG MG A 102 O HOH A 218 1555 1555 2.18 LINK MG MG A 102 O HOH A 220 1555 1555 2.18 LINK MG MG A 102 O HOH A 222 1555 1555 2.18 LINK MG MG A 103 O HOH A 202 1555 1555 2.18 LINK MG MG A 103 O HOH A 207 1555 1555 2.18 LINK MG MG A 103 O HOH A 210 1555 1555 2.18 LINK MG MG A 103 O HOH A 215 1555 1555 2.18 LINK MG MG A 103 O HOH A 216 1555 1555 2.18 LINK MG MG A 103 O HOH A 221 1555 1555 2.18 LINK MG MG A 104 O HOH A 208 1555 1555 2.18 LINK MG MG A 104 O HOH A 212 1555 1555 2.18 LINK MG MG A 104 O HOH A 213 1555 1555 2.18 LINK MG MG A 104 O HOH A 217 1555 1555 2.18 LINK MG MG A 104 O HOH A 219 1555 1555 2.18 LINK MG MG A 104 O HOH A 224 1555 1555 2.18 LINK MG MG B 101 O HOH B 202 1555 1555 2.18 LINK MG MG B 101 O HOH B 204 1555 1555 2.18 LINK MG MG B 101 O HOH B 208 1555 1555 2.18 LINK MG MG B 101 O HOH B 210 1555 1555 2.18 LINK MG MG B 101 O HOH B 221 1555 1555 2.18 LINK MG MG B 101 O HOH B 223 1555 1555 2.18 LINK MG MG B 102 O HOH B 203 1555 1555 2.18 LINK MG MG B 102 O HOH B 205 1555 1555 2.18 LINK MG MG B 102 O HOH B 214 1555 1555 2.18 LINK MG MG B 102 O HOH B 216 1555 1555 2.18 LINK MG MG B 102 O HOH B 218 1555 1555 2.18 LINK MG MG B 102 O HOH B 220 1555 1555 2.18 LINK MG MG B 103 O HOH B 201 1555 1555 2.18 LINK MG MG B 103 O HOH B 206 1555 1555 2.18 LINK MG MG B 103 O HOH B 207 1555 1555 2.18 LINK MG MG B 103 O HOH B 213 1555 1555 2.18 LINK MG MG B 103 O HOH B 219 1555 1555 2.18 LINK MG MG B 103 O HOH B 222 1555 1555 2.18 LINK MG MG B 104 O HOH B 209 1555 1555 2.18 LINK MG MG B 104 O HOH B 211 1555 1555 2.18 LINK MG MG B 104 O HOH B 212 1555 1555 2.18 LINK MG MG B 104 O HOH B 215 1555 1555 2.18 LINK MG MG B 104 O HOH B 217 1555 1555 2.18 LINK MG MG B 104 O HOH B 224 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 3741 3749 3751 3752 3757 CONECT 3741 3762 3771 CONECT 3742 3753 3754 3759 3766 CONECT 3742 3768 3770 CONECT 3743 3750 3755 3758 3763 CONECT 3743 3764 3769 CONECT 3744 3756 3760 3761 3765 CONECT 3744 3767 3772 CONECT 3745 3774 3776 3780 3782 CONECT 3745 3793 3795 CONECT 3746 3775 3777 3786 3788 CONECT 3746 3790 3792 CONECT 3747 3773 3778 3779 3785 CONECT 3747 3791 3794 CONECT 3748 3781 3783 3784 3787 CONECT 3748 3789 3796 CONECT 3749 3741 CONECT 3750 3743 CONECT 3751 3741 CONECT 3752 3741 CONECT 3753 3742 CONECT 3754 3742 CONECT 3755 3743 CONECT 3756 3744 CONECT 3757 3741 CONECT 3758 3743 CONECT 3759 3742 CONECT 3760 3744 CONECT 3761 3744 CONECT 3762 3741 CONECT 3763 3743 CONECT 3764 3743 CONECT 3765 3744 CONECT 3766 3742 CONECT 3767 3744 CONECT 3768 3742 CONECT 3769 3743 CONECT 3770 3742 CONECT 3771 3741 CONECT 3772 3744 CONECT 3773 3747 CONECT 3774 3745 CONECT 3775 3746 CONECT 3776 3745 CONECT 3777 3746 CONECT 3778 3747 CONECT 3779 3747 CONECT 3780 3745 CONECT 3781 3748 CONECT 3782 3745 CONECT 3783 3748 CONECT 3784 3748 CONECT 3785 3747 CONECT 3786 3746 CONECT 3787 3748 CONECT 3788 3746 CONECT 3789 3748 CONECT 3790 3746 CONECT 3791 3747 CONECT 3792 3746 CONECT 3793 3745 CONECT 3794 3747 CONECT 3795 3745 CONECT 3796 3748 MASTER 236 0 8 0 0 0 0 6 3794 2 64 16 END