HEADER RNA 31-JAN-25 9N3I TITLE VIBRIO CHOLERAE GLYCINE RIBOSWITCH - GLYCINE BOUND AT 2.9A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINE RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 4 ORGANISM_TAXID: 666 KEYWDS RIBOSWITCH, GLYCINE, MAGNESIUM, HOLO, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR N.JESPERSEN,A.SINGHAL,J.D.PRAJAPATI,K.SANBONMATSU REVDAT 1 29-JUL-26 9N3I 0 JRNL AUTH N.JESPERSEN,A.SINGHAL,J.D.PRAJAPATI,K.SANBONMATSU JRNL TITL VIBRIO CHOLERAE GLYCINE RIBOSWITCH - GLYCINE BOUND AT 2.9A JRNL TITL 2 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6WLT 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) : 2.860 REMARK 3 NUMBER OF PARTICLES : 215269 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 9N3I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000290938. 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 : HOLO STRUCTURE OF THE GLYCINE REMARK 245 RIBOSWITCH WITH 10MM MAGNESIUM REMARK 245 AND 2MM GLYCINE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : 15MA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5338 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) : 2300.00 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) : 5900.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 G A 0 REMARK 465 U A 231 REMARK 465 G A 232 REMARK 465 A A 233 REMARK 465 A A 234 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 310 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 66 O2' REMARK 620 2 A A 67 OP2 73.1 REMARK 620 3 C A 78 OP2 156.2 83.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 68 OP1 REMARK 620 2 G A 69 OP2 102.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 73 O4 REMARK 620 2 A A 76 OP2 102.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 314 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 82 OP2 REMARK 620 2 A A 83 OP2 110.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 173 O2' REMARK 620 2 A A 174 OP2 76.5 REMARK 620 3 C A 207 OP2 155.7 81.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 315 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 175 OP1 REMARK 620 2 G A 176 OP2 88.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 308 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 211 OP2 REMARK 620 2 A A 212 OP2 111.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48851 RELATED DB: EMDB REMARK 900 VIBRIO CHOLERAE GLYCINE RIBOSWITCH - GLYCINE BOUND AT 2.9A REMARK 900 RESOLUTION DBREF1 9N3I A 1 234 GB CP160480.1 DBREF2 9N3I A 2772158317 1842282 1842049 SEQADV 9N3I G A 0 GB 277215831 EXPRESSION TAG SEQRES 1 A 235 G U C C G U U G A A G A C SEQRES 2 A 235 U G C A G G A G A G U G G SEQRES 3 A 235 U U G U U A A C C A G A U SEQRES 4 A 235 U U U A A C A U C U G A G SEQRES 5 A 235 C C A A A U A A C C C G C SEQRES 6 A 235 C G A A G A A G U A A A U SEQRES 7 A 235 C U U U C A G G U G C A U SEQRES 8 A 235 U A U U C U U A G C C A U SEQRES 9 A 235 A U A U U G G C A A C G A SEQRES 10 A 235 A U A A G C G A G G A C U SEQRES 11 A 235 G U A G U U G G A G G A A SEQRES 12 A 235 C C U C U G G A G A G A A SEQRES 13 A 235 C C G U U U A A U C G G U SEQRES 14 A 235 C G C C G A A G G A G C A SEQRES 15 A 235 A G C U C U G C G C A U A SEQRES 16 A 235 U G C A G A G U G A A A C SEQRES 17 A 235 U C U C A G G C A A A A G SEQRES 18 A 235 G A C A G A G G A G U G A SEQRES 19 A 235 A HET GLY A 301 10 HET GLY A 302 10 HET MG A 303 1 HET MG A 304 1 HET MG A 305 1 HET MG A 306 1 HET MG A 307 1 HET MG A 308 1 HET MG A 309 1 HET MG A 310 1 HET MG A 311 1 HET MG A 312 1 HET MG A 313 1 HET MG A 314 1 HET MG A 315 1 HET MG A 316 1 HETNAM GLY GLYCINE HETNAM MG MAGNESIUM ION FORMUL 2 GLY 2(C2 H5 N O2) FORMUL 4 MG 14(MG 2+) LINK O6 G A 18 MG MG A 311 1555 1555 2.81 LINK O2' G A 66 MG MG A 310 1555 1555 1.93 LINK OP2 A A 67 MG MG A 310 1555 1555 1.94 LINK OP1 A A 68 MG MG A 312 1555 1555 1.99 LINK OP2 G A 69 MG MG A 312 1555 1555 1.92 LINK O4 U A 73 MG MG A 304 1555 1555 1.78 LINK OP2 U A 73 MG MG A 313 1555 1555 2.61 LINK OP2 A A 76 MG MG A 304 1555 1555 1.78 LINK OP2 C A 78 MG MG A 310 1555 1555 2.07 LINK OP2 C A 82 MG MG A 314 1555 1555 1.88 LINK OP2 A A 83 MG MG A 314 1555 1555 1.78 LINK O2' G A 173 MG MG A 307 1555 1555 2.13 LINK OP2 A A 174 MG MG A 307 1555 1555 2.03 LINK OP1 A A 175 MG MG A 315 1555 1555 2.23 LINK OP2 G A 176 MG MG A 315 1555 1555 2.19 LINK OP2 C A 207 MG MG A 307 1555 1555 2.08 LINK OP2 C A 211 MG MG A 308 1555 1555 1.92 LINK OP2 A A 212 MG MG A 308 1555 1555 1.82 LINK OP2 A A 219 MG MG A 309 1555 1555 1.95 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 564 7439 CONECT 2093 7438 CONECT 2119 7438 CONECT 2151 7440 CONECT 2185 7440 CONECT 2319 7441 CONECT 2334 7432 CONECT 2415 7432 CONECT 2478 7438 CONECT 2599 7442 CONECT 2630 7442 CONECT 5530 7435 CONECT 5556 7435 CONECT 5588 7443 CONECT 5622 7443 CONECT 6628 7435 CONECT 6750 7436 CONECT 6781 7436 CONECT 7012 7437 CONECT 7432 2334 2415 CONECT 7435 5530 5556 6628 CONECT 7436 6750 6781 CONECT 7437 7012 CONECT 7438 2093 2119 2478 CONECT 7439 564 CONECT 7440 2151 2185 CONECT 7441 2319 CONECT 7442 2599 2630 CONECT 7443 5588 5622 MASTER 171 0 16 0 0 0 0 6 4954 1 29 19 END