HEADER RNA 05-SEP-24 9DIG TITLE ROUS SARCOMA VIRUS FRAMESHIFTING PSEUDOKNOT RNA EM STRAIGHT DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRAMESHIFTING PSEUDOKNOT RNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROUS SARCOMA VIRUS - PRAGUE C; SOURCE 3 ORGANISM_TAXID: 11888; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS PSEUDOKNOT, RETROVIRAL RNA, FRAMESHIFTING, TRANSLATION REGULATION, KEYWDS 2 RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.P.JONES,A.R.FERRE-D'AMARE REVDAT 2 16-APR-25 9DIG 1 JRNL REVDAT 1 09-APR-25 9DIG 0 JRNL AUTH C.P.JONES,A.R.FERRE-D'AMARE JRNL TITL STRUCTURAL SWITCHING DYNAMICALLY CONTROLS THE DOUBLY JRNL TITL 2 PSEUDOKNOTTED ROUS SARCOMA VIRUS-PROGRAMMED RIBOSOMAL JRNL TITL 3 FRAMESHIFTING ELEMENT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 18122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40172966 JRNL DOI 10.1073/PNAS.2418418122 REMARK 2 REMARK 2 RESOLUTION. 3.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, SERIALEM, CTFFIND, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, RELION, CRYOSPARC, REMARK 3 PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9DIB REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 116.700 REMARK 3 REMARK 3 FITTING PROCEDURE : PHENIX REAL-SPACE REFINEMENT, USING REAL-SPACE REMARK 3 REFINEMENT, SIMULATED ANNEALING ON THE FIRST STEP, B-FACTOR, REMARK 3 OCCUPANCY, AND GLOBAL MINIMIZATION WITH NCS AND SECONDARY REMARK 3 STRUCTURE RESTRAINTS 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) : 3.220 REMARK 3 NUMBER OF PARTICLES : 88523 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 9DIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288192. 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 : DIMERIC RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : PELCO EASIGLOW FROM TED PELLA REMARK 245 (REDDING, CA) REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : FOLDED RNA SPECIMEN PREPARED BY REMARK 245 IN VITRO TRANSCRIPTION REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7874 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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) : 5440.00 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, 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 C A 12 REMARK 465 U A 37 REMARK 465 U A 38 REMARK 465 C A 39 REMARK 465 G A 40 REMARK 465 G A 41 REMARK 465 A A 42 REMARK 465 A A 43 REMARK 465 A A 44 REMARK 465 U A 45 REMARK 465 G A 46 REMARK 465 G A 62 REMARK 465 A A 63 REMARK 465 A A 64 REMARK 465 A A 65 REMARK 465 C B 12 REMARK 465 U B 37 REMARK 465 U B 38 REMARK 465 C B 39 REMARK 465 G B 40 REMARK 465 G B 41 REMARK 465 A B 42 REMARK 465 A B 43 REMARK 465 A B 44 REMARK 465 U B 45 REMARK 465 G B 46 REMARK 465 G B 62 REMARK 465 A B 63 REMARK 465 A B 64 REMARK 465 A B 65 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 13 P OP1 OP2 REMARK 470 U B 13 P OP1 OP2 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 N4 C A 16 O4 U A 73 2.13 REMARK 500 N4 C B 16 O4 U B 73 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9DIB RELATED DB: PDB REMARK 900 ROUS SARCOMA VIRUS FRAMESHIFTING PSEUDOKNOT RNA EM STRAIGHT DIMER, REMARK 900 CRYSTAL STRUCTURE REMARK 900 RELATED ID: EMD-46905 RELATED DB: EMDB REMARK 900 ROUS SARCOMA VIRUS FRAMESHIFTING PSEUDOKNOT RNA EM STRAIGHT DIMER DBREF 9DIG A 1 111 GB 210171 J02342.1 2722 2835 DBREF 9DIG B 1 111 GB 210171 J02342.1 2722 2835 SEQADV 9DIG U A 36 GB 210171 A 2757 CONFLICT SEQADV 9DIG G A 40 GB 210171 C 2761 CONFLICT SEQADV 9DIG A GB 210171 C 2763 DELETION SEQADV 9DIG A GB 210171 U 2764 DELETION SEQADV 9DIG A GB 210171 C 2765 DELETION SEQADV 9DIG A A 63 GB 210171 C 2787 CONFLICT SEQADV 9DIG A A 64 GB 210171 C 2788 CONFLICT SEQADV 9DIG A A 65 GB 210171 U 2789 CONFLICT SEQADV 9DIG U B 36 GB 210171 A 2757 CONFLICT SEQADV 9DIG G B 40 GB 210171 C 2761 CONFLICT SEQADV 9DIG B GB 210171 C 2763 DELETION SEQADV 9DIG B GB 210171 U 2764 DELETION SEQADV 9DIG B GB 210171 C 2765 DELETION SEQADV 9DIG A B 63 GB 210171 C 2787 CONFLICT SEQADV 9DIG A B 64 GB 210171 C 2788 CONFLICT SEQADV 9DIG A B 65 GB 210171 U 2789 CONFLICT SEQRES 1 A 111 G G G C C A C U G U U C U SEQRES 2 A 111 C A C U G U U G C G C U A SEQRES 3 A 111 C A U C U G G C U U U U C SEQRES 4 A 111 G G A A A U G G A A G C C SEQRES 5 A 111 A G A C C A C A C G A A A SEQRES 6 A 111 G U G U G G A U U G A C C SEQRES 7 A 111 A G U G G C C C C U C C C SEQRES 8 A 111 U G A A G G U A A A C U U SEQRES 9 A 111 G U A G C G C SEQRES 1 B 111 G G G C C A C U G U U C U SEQRES 2 B 111 C A C U G U U G C G C U A SEQRES 3 B 111 C A U C U G G C U U U U C SEQRES 4 B 111 G G A A A U G G A A G C C SEQRES 5 B 111 A G A C C A C A C G A A A SEQRES 6 B 111 G U G U G G A U U G A C C SEQRES 7 B 111 A G U G G C C C C U C C C SEQRES 8 B 111 U G A A G G U A A A C U U SEQRES 9 B 111 G U A G C G C HET K A 201 1 HET K A 202 1 HET MG A 203 1 HET K B 201 1 HET K B 202 1 HET MG B 203 1 HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION FORMUL 3 K 4(K 1+) FORMUL 5 MG 2(MG 2+) LINK OP2 A A 94 K K A 201 1555 1555 2.55 LINK OP2 A B 94 K K B 201 1555 1555 2.50 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