HEADER RNA 13-NOV-23 8UYP TITLE SARS-COV-1 5' PROXIMAL STEM-LOOP 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARS-COV-1 5' PROXIMAL STEM-LOOP 5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS TOR2; SOURCE 4 ORGANISM_TAXID: 227984 KEYWDS SL5, CORONAVIRUS, 5' UTR, RNA EXPDTA ELECTRON MICROSCOPY NUMMDL 20 AUTHOR R.C.KRETSCH,L.XU,I.N.ZHELUDEV,X.ZHOU,R.HUANG,G.NYE,S.LI,K.ZHANG, AUTHOR 2 W.CHIU,R.DAS REVDAT 2 13-MAR-24 8UYP 1 JRNL REVDAT 1 20-DEC-23 8UYP 0 JRNL AUTH R.C.KRETSCH,L.XU,I.N.ZHELUDEV,X.ZHOU,R.HUANG,G.NYE,S.LI, JRNL AUTH 2 K.ZHANG,W.CHIU,R.DAS JRNL TITL TERTIARY FOLDS OF THE SL5 RNA FROM THE 5' PROXIMAL REGION OF JRNL TITL 2 SARS-COV-2 AND RELATED CORONAVIRUSES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 93121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38427602 JRNL DOI 10.1073/PNAS.2320493121 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.C.KRETSCH,L.XU,I.N.ZHELUDEV,X.ZHOU,R.HUANG,G.NYE,S.LI, REMARK 1 AUTH 2 K.ZHANG,W.CHIU,R.DAS REMARK 1 TITL TERTIARY FOLDS OF THE SL5 RNA FROM THE 5' PROXIMAL REGION OF REMARK 1 TITL 2 SARS-COV-2 AND RELATED CORONAVIRUSES. REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 38076883 REMARK 1 DOI 10.1101/2023.11.22.567964 REMARK 2 REMARK 2 RESOLUTION. 7.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, ROSETTA, REMARK 3 ERRASER, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER 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) : 7.100 REMARK 3 NUMBER OF PARTICLES : 220917 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 8UYP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000279181. 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 : SARS-COV-1 5' PROXIMAL STEM REMARK 245 -LOOP 5 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.38 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 10376 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 OP1 G A 150 C5 G A 284 1.35 REMARK 500 OP1 G A 150 C6 G A 284 1.56 REMARK 500 OP1 G A 150 N7 G A 284 1.73 REMARK 500 OP1 G A 150 O6 G A 284 1.96 REMARK 500 O5' G A 150 O6 G A 284 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42809 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42810 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42811 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42801 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42805 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42802 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42808 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42803 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42813 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-42814 RELATED DB: EMDB REMARK 900 RELATED ID: 8UYK RELATED DB: PDB REMARK 900 RELATED ID: 8UYL RELATED DB: PDB REMARK 900 RELATED ID: 8UYM RELATED DB: PDB REMARK 900 RELATED ID: 8UYE RELATED DB: PDB REMARK 900 RELATED ID: 8UYG RELATED DB: PDB REMARK 900 RELATED ID: 8UYJ RELATED DB: PDB REMARK 900 RELATED ID: EMD-42816 RELATED DB: EMDB REMARK 900 SARS-COV-1 5' PROXIMAL STEM-LOOP 5 DBREF1 8UYP A 150 292 GB NC_004718.3 DBREF2 8UYP A NC_004718.3 150 292 SEQADV 8UYP G A 150 GB NC_004718 C 150 CONFLICT SEQADV 8UYP C A 292 GB NC_004718 G 292 CONFLICT SEQRES 1 A 143 G G U U G A C A A G A A A SEQRES 2 A 143 C G A G U A A C U C G U C SEQRES 3 A 143 C C U C U U C U G C A G A SEQRES 4 A 143 C U G C U U A C G G U U U SEQRES 5 A 143 C G U C C G U G U U G C A SEQRES 6 A 143 G U C G A U C A U C A G C SEQRES 7 A 143 A U A C C U A G G U U U C SEQRES 8 A 143 G U C C G G G U G U G A C SEQRES 9 A 143 C G A A A G G U A A G A U SEQRES 10 A 143 G G A G A G C C U U G U U SEQRES 11 A 143 C U U G G U G U C A A C C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1