HEADER RNA 11-FEB-25 9NA7 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 KEYWDS VIRAL RNA, SCAFFOLD, ENGINEERING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.P.JONES,A.R.FERRE-D'AMARE REVDAT 1 04-MAR-26 9NA7 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. 3.56 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) : 3.560 REMARK 3 NUMBER OF PARTICLES : 659034 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 9NA7 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_1000292866. 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 U A 79 REMARK 465 U A 80 REMARK 465 G A 81 REMARK 465 A A 82 REMARK 465 A A 83 REMARK 465 U B 79 REMARK 465 U B 80 REMARK 465 G B 81 REMARK 465 A B 82 REMARK 465 A B 83 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 10 N4 C A 65 2.16 REMARK 500 O4 U B 10 N4 C B 65 2.16 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 C A 78 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 C B 78 N3 - C2 - O2 ANGL. DEV. = -4.6 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 206 O 179.8 REMARK 620 3 HOH A 212 O 90.1 90.1 REMARK 620 4 HOH A 214 O 89.9 89.9 180.0 REMARK 620 5 HOH A 215 O 90.1 89.8 89.5 90.5 REMARK 620 6 HOH A 218 O 90.0 90.1 90.5 89.5 179.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 202 O REMARK 620 2 HOH A 205 O 89.5 REMARK 620 3 HOH A 208 O 90.5 179.8 REMARK 620 4 HOH A 209 O 90.4 89.8 90.0 REMARK 620 5 HOH A 213 O 89.8 90.2 89.9 179.8 REMARK 620 6 HOH A 217 O 179.7 90.3 89.8 89.7 90.1 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 201 O REMARK 620 2 HOH A 204 O 89.5 REMARK 620 3 HOH A 207 O 90.0 90.3 REMARK 620 4 HOH A 210 O 90.6 179.8 89.5 REMARK 620 5 HOH A 211 O 90.5 89.7 179.5 90.5 REMARK 620 6 HOH A 216 O 179.8 90.3 89.9 89.6 89.6 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 204 O REMARK 620 2 HOH B 205 O 179.9 REMARK 620 3 HOH B 208 O 90.0 90.0 REMARK 620 4 HOH B 214 O 89.9 90.0 89.4 REMARK 620 5 HOH B 216 O 90.1 90.0 90.5 179.9 REMARK 620 6 HOH B 217 O 89.9 90.0 179.9 90.5 89.5 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 202 O REMARK 620 2 HOH B 206 O 89.5 REMARK 620 3 HOH B 209 O 90.5 179.9 REMARK 620 4 HOH B 210 O 90.4 89.8 90.0 REMARK 620 5 HOH B 213 O 89.9 90.2 89.9 179.7 REMARK 620 6 HOH B 218 O 179.8 90.3 89.7 89.7 90.1 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 203 O 89.5 REMARK 620 3 HOH B 207 O 90.0 90.3 REMARK 620 4 HOH B 211 O 90.5 89.7 179.6 REMARK 620 5 HOH B 212 O 90.5 179.8 89.5 90.5 REMARK 620 6 HOH B 215 O 179.7 90.3 89.9 89.6 89.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49181 RELATED DB: EMDB REMARK 900 RNA SCAFFOLD DBREF 9NA7 A 1 99 PDB 9NA7 9NA7 1 99 DBREF 9NA7 B 1 99 PDB 9NA7 9NA7 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 A 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 A A C C SEQRES 7 A 99 U 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 A 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 A A C C SEQRES 7 B 99 U 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 B 101 1 HET MG B 102 1 HET MG B 103 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 6(MG 2+) FORMUL 9 HOH *36(H2 O) LINK MG MG A 101 O HOH A 203 1555 1555 2.18 LINK MG MG A 101 O HOH A 206 1555 1555 2.18 LINK MG MG A 101 O HOH A 212 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 215 1555 1555 2.18 LINK MG MG A 101 O HOH A 218 1555 1555 2.18 LINK MG MG A 102 O HOH A 202 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 208 1555 1555 2.18 LINK MG MG A 102 O HOH A 209 1555 1555 2.18 LINK MG MG A 102 O HOH A 213 1555 1555 2.18 LINK MG MG A 102 O HOH A 217 1555 1555 2.18 LINK MG MG A 103 O HOH A 201 1555 1555 2.18 LINK MG MG A 103 O HOH A 204 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 211 1555 1555 2.18 LINK MG MG A 103 O HOH A 216 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 205 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 214 1555 1555 2.18 LINK MG MG B 101 O HOH B 216 1555 1555 2.18 LINK MG MG B 101 O HOH B 217 1555 1555 2.18 LINK MG MG B 102 O HOH B 202 1555 1555 2.18 LINK MG MG B 102 O HOH B 206 1555 1555 2.18 LINK MG MG B 102 O HOH B 209 1555 1555 2.18 LINK MG MG B 102 O HOH B 210 1555 1555 2.18 LINK MG MG B 102 O HOH B 213 1555 1555 2.18 LINK MG MG B 102 O HOH B 218 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 203 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 211 1555 1555 2.18 LINK MG MG B 103 O HOH B 212 1555 1555 2.18 LINK MG MG B 103 O HOH B 215 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 3999 4007 4010 4016 4018 CONECT 3999 4019 4022 CONECT 4000 4006 4009 4012 4013 CONECT 4000 4017 4021 CONECT 4001 4005 4008 4011 4014 CONECT 4001 4015 4020 CONECT 4002 4026 4027 4030 4036 CONECT 4002 4038 4039 CONECT 4003 4024 4028 4031 4032 CONECT 4003 4035 4040 CONECT 4004 4023 4025 4029 4033 CONECT 4004 4034 4037 CONECT 4005 4001 CONECT 4006 4000 CONECT 4007 3999 CONECT 4008 4001 CONECT 4009 4000 CONECT 4010 3999 CONECT 4011 4001 CONECT 4012 4000 CONECT 4013 4000 CONECT 4014 4001 CONECT 4015 4001 CONECT 4016 3999 CONECT 4017 4000 CONECT 4018 3999 CONECT 4019 3999 CONECT 4020 4001 CONECT 4021 4000 CONECT 4022 3999 CONECT 4023 4004 CONECT 4024 4003 CONECT 4025 4004 CONECT 4026 4002 CONECT 4027 4002 CONECT 4028 4003 CONECT 4029 4004 CONECT 4030 4002 CONECT 4031 4003 CONECT 4032 4003 CONECT 4033 4004 CONECT 4034 4004 CONECT 4035 4003 CONECT 4036 4002 CONECT 4037 4004 CONECT 4038 4002 CONECT 4039 4002 CONECT 4040 4003 MASTER 218 0 6 0 0 0 0 6 4038 2 48 16 END