HEADER RNA 18-FEB-25 9NDD TITLE RNA SCAFFOLD ATTACHED TO 8-OXOGUANINE RIBOSWITCH APTAMER, COMBINED TITLE 2 CORE PLUS APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (160-MER); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RIBOSWITCH, RNA, APTAMER, ENGINEERING EXPDTA ELECTRON MICROSCOPY AUTHOR C.P.JONES,A.R.FERRE-D'AMARE REVDAT 1 04-MAR-26 9NDD 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. 2.67 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) : 2.670 REMARK 3 NUMBER OF PARTICLES : 465913 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 9NDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293050. 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 : RNA SCAFFOLD ATTACHED TO 8 REMARK 245 -OXOGUANINE RIBOSWITCH APTAMER, REMARK 245 COMBINED CORE PLUS APTAMER 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) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 3915.00 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 U A 80 C2 O2 N3 C4 O4 C5 C6 REMARK 470 U B 80 C2 O2 N3 C4 O4 C5 C6 REMARK 470 U C 80 C2 O2 N3 C4 O4 C5 C6 REMARK 470 U D 80 C2 O2 N3 C4 O4 C5 C6 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' C B 4 O6 G B 142 2.06 REMARK 500 O2 U D 66 O2' A D 93 2.15 REMARK 500 O2 U B 66 O2' A B 93 2.17 REMARK 500 O2 U D 33 O6 G D 99 2.17 REMARK 500 O2 U A 66 O2' A A 93 2.17 REMARK 500 O2 U A 33 N1 G A 99 2.17 REMARK 500 O2 U C 66 O2' A C 93 2.18 REMARK 500 O2' C C 4 O6 G C 142 2.18 REMARK 500 O2' C D 4 O6 G D 142 2.18 REMARK 500 O2' C A 4 O6 G A 142 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49272 RELATED DB: EMDB REMARK 900 RNA SCAFFOLD ATTACHED TO 8-OXOGUANINE RIBOSWITCH APTAMER, COMBINED REMARK 900 CORE PLUS APTAMER DBREF 9NDD A 1 160 PDB 9NDD 9NDD 1 160 DBREF 9NDD B 1 160 PDB 9NDD 9NDD 1 160 DBREF 9NDD C 1 160 PDB 9NDD 9NDD 1 160 DBREF 9NDD D 1 160 PDB 9NDD 9NDD 1 160 SEQRES 1 A 160 G G G C C A C U G U U U C SEQRES 2 A 160 A C U G U U G C G C U A C SEQRES 3 A 160 A U C U C C U G U U C G U SEQRES 4 A 160 A U A A C C C C G A U A A SEQRES 5 A 160 U C G G U U C G G G G G C SEQRES 6 A 160 U C U A C U G G G G U C C SEQRES 7 A 160 G U A A A A U C C U A A C SEQRES 8 A 160 U A C G A A C G G G A G G SEQRES 9 A 160 C C A C A C G A A A G U G SEQRES 10 A 160 U G G A G U G A C C A G U SEQRES 11 A 160 G G C C C C A C C C U G A SEQRES 12 A 160 A G G U A A A C U U G U A SEQRES 13 A 160 G C G C SEQRES 1 B 160 G G G C C A C U G U U U C SEQRES 2 B 160 A C U G U U G C G C U A C SEQRES 3 B 160 A U C U C C U G U U C G U SEQRES 4 B 160 A U A A C C C C G A U A A SEQRES 5 B 160 U C G G U U C G G G G G C SEQRES 6 B 160 U C U A C U G G G G U C C SEQRES 7 B 160 G U A A A A U C C U A A C SEQRES 8 B 160 U A C G A A C G G G A G G SEQRES 9 B 160 C C A C A C G A A A G U G SEQRES 10 B 160 U G G A G U G A C C A G U SEQRES 11 B 160 G G C C C C A C C C U G A SEQRES 12 B 160 A G G U A A A C U U G U A SEQRES 13 B 160 G C G C SEQRES 1 C 160 G G G C C A C U G U U U C SEQRES 2 C 160 A C U G U U G C G C U A C SEQRES 3 C 160 A U C U C C U G U U C G U SEQRES 4 C 160 A U A A C C C C G A U A A SEQRES 5 C 160 U C G G U U C G G G G G C SEQRES 6 C 160 U C U A C U G G G G U C C SEQRES 7 C 160 G U A A A A U C C U A A C SEQRES 8 C 160 U A C G A A C G G G A G G SEQRES 9 C 160 C C A C A C G A A A G U G SEQRES 10 C 160 U G G A G U G A C C A G U SEQRES 11 C 160 G G C C C C A C C C U G A SEQRES 12 C 160 A G G U A A A C U U G U A SEQRES 13 C 160 G C G C SEQRES 1 D 160 G G G C C A C U G U U U C SEQRES 2 D 160 A C U G U U G C G C U A C SEQRES 3 D 160 A U C U C C U G U U C G U SEQRES 4 D 160 A U A A C C C C G A U A A SEQRES 5 D 160 U C G G U U C G G G G G C SEQRES 6 D 160 U C U A C U G G G G U C C SEQRES 7 D 160 G U A A A A U C C U A A C SEQRES 8 D 160 U A C G A A C G G G A G G SEQRES 9 D 160 C C A C A C G A A A G U G SEQRES 10 D 160 U G G A G U G A C C A G U SEQRES 11 D 160 G G C C C C A C C C U G A SEQRES 12 D 160 A G G U A A A C U U G U A SEQRES 13 D 160 G C G C HET OXG A 201 12 HET OXG B 201 12 HET OXG C 201 12 HET OXG D 201 12 HETNAM OXG 8-OXOGUANINE FORMUL 5 OXG 4(C5 H3 N5 O2) 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 CONECT139291393013939 CONECT13930139291393113940 CONECT139311393013932 CONECT13932139311393313939 CONECT13933139321393413935 CONECT1393413933 CONECT139351393313936 CONECT13936139351393713938 CONECT1393713936 CONECT139381393613939 CONECT13939139291393213938 CONECT1394013930 CONECT139411394213951 CONECT13942139411394313952 CONECT139431394213944 CONECT13944139431394513951 CONECT13945139441394613947 CONECT1394613945 CONECT139471394513948 CONECT13948139471394913950 CONECT1394913948 CONECT139501394813951 CONECT13951139411394413950 CONECT1395213942 CONECT139531395413963 CONECT13954139531395513964 CONECT139551395413956 CONECT13956139551395713963 CONECT13957139561395813959 CONECT1395813957 CONECT139591395713960 CONECT13960139591396113962 CONECT1396113960 CONECT139621396013963 CONECT13963139531395613962 CONECT1396413954 CONECT139651396613975 CONECT13966139651396713976 CONECT139671396613968 CONECT13968139671396913975 CONECT13969139681397013971 CONECT1397013969 CONECT139711396913972 CONECT13972139711397313974 CONECT1397313972 CONECT139741397213975 CONECT13975139651396813974 CONECT1397613966 MASTER 130 0 4 0 0 0 0 613624 4 48 52 END