HEADER RNA 04-JUL-19 6POM TITLE CRYO-EM STRUCTURE OF THE FULL-LENGTH BACILLUS SUBTILIS GLYQS T-BOX TITLE 2 RIBOSWITCH IN COMPLEX WITH TRNA-GLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-BOX GLYQS LEADER (155-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRNAGLY (75-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: GLYQS; SOURCE 5 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 905931; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 9 ORGANISM_TAXID: 1423; SOURCE 10 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RNA COMPLEX, RIBOSWITCH, TRANSCRIPTION ATTENUATION, STACKING., RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.LI,Z.SU,J.ZHANG,W.CHIU REVDAT 5 20-MAR-24 6POM 1 REMARK REVDAT 4 08-JAN-20 6POM 1 REMARK REVDAT 3 18-DEC-19 6POM 1 JRNL REVDAT 2 04-DEC-19 6POM 1 JRNL REVDAT 1 20-NOV-19 6POM 0 JRNL AUTH S.LI,Z.SU,J.LEHMANN,V.STAMATOPOULOU,N.GIARIMOGLOU, JRNL AUTH 2 F.E.HENDERSON,L.FAN,G.D.PINTILIE,K.ZHANG,M.CHEN,S.J.LUDTKE, JRNL AUTH 3 Y.X.WANG,C.STATHOPOULOS,W.CHIU,J.ZHANG JRNL TITL STRUCTURAL BASIS OF AMINO ACID SURVEILLANCE BY HIGHER-ORDER JRNL TITL 2 TRNA-MRNA INTERACTIONS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 26 1094 2019 JRNL REFN ESSN 1545-9985 JRNL PMID 31740854 JRNL DOI 10.1038/S41594-019-0326-7 REMARK 2 REMARK 2 RESOLUTION. 4.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, RELION, UCSF CHIMERA, REMARK 3 RELION, RELION, RELION, CRYOSPARC, REMARK 3 RELION, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4LCK REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : MODEL MAP CROSS CORRELATION 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) : 4.900 REMARK 3 NUMBER OF PARTICLES : 189361 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6POM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242805. 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 : T-BOX-TRNAGLY COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.25 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 3 UL SAMPLE BLOT ONCE FOR 3S 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 : 5600 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 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) : 3800.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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 87 REMARK 465 U A 115 REMARK 465 U A 116 REMARK 465 U A 117 REMARK 465 U A 134 REMARK 465 U A 135 REMARK 465 U A 136 REMARK 465 U A 137 REMARK 465 G A 138 REMARK 465 U A 139 REMARK 465 G A 168 REMARK 465 A A 169 REMARK 465 A A 170 REMARK 465 C A 171 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6PMO RELATED DB: PDB REMARK 900 6PMO IS THE CRYSTAL STRUCTURE OF T-BOX DISCRIMINATOR IN COMPLEX REMARK 900 WITH TRNAGLY REMARK 900 RELATED ID: EMD-20416 RELATED DB: EMDB REMARK 900 T-BOX LEADER COMPLEX DBREF1 6POM A 13 182 GB D84432.1 DBREF2 6POM A 2627063 110701 110870 DBREF1 6POM B 1 75 GB CP035163.1 DBREF2 6POM B 1560688081 95217 95291 SEQRES 1 A 169 G U U G C A G U G A G A G SEQRES 2 A 169 A A A G A A G U A C U U G SEQRES 3 A 169 C G U U A C C U C A U G A SEQRES 4 A 169 A A G C G A C C U U A G G SEQRES 5 A 169 G C G G U G U A A G C U A SEQRES 6 A 169 A G G A U G A G C A C G C SEQRES 7 A 169 A A C G A A A G G C A U U SEQRES 8 A 169 C U U G A G C A A U U U U SEQRES 9 A 169 A A A A A A G A G G C U G SEQRES 10 A 169 G G A U U U U G U U C U C SEQRES 11 A 169 A G C A A C U A G G G U G SEQRES 12 A 169 G A A C C G C G G G A G A SEQRES 13 A 169 A C U C U C G U C C C U A SEQRES 1 B 75 G C G G A A G U A G U U C SEQRES 2 B 75 A G U G G U A G A A C A C SEQRES 3 B 75 C A C C U U G C C A A G G SEQRES 4 B 75 U G G G G G U C G C G G G SEQRES 5 B 75 U U C G A A U C C C G U C SEQRES 6 B 75 U U C C G C U C C A 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