HEADER RNA 06-JAN-25 9MQS TITLE CRYOEM STRUCTURE OF THE CANDIDA ALBICANS GROUP I INTRON-GMP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (332-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS; SOURCE 3 ORGANISM_TAXID: 5476; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTRON, GROUP I, SPLICING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR K.CHUNG,L.XU,T.LIU,A.PYLE REVDAT 2 28-MAY-25 9MQS 1 JRNL REVDAT 1 30-APR-25 9MQS 0 JRNL AUTH T.LIU,L.XU,K.CHUNG,L.J.SISTO,J.HWANG,C.ZHANG,M.C.VAN ZANDT, JRNL AUTH 2 A.M.PYLE JRNL TITL MOLECULAR INSIGHTS INTO DE NOVO SMALL-MOLECULE RECOGNITION JRNL TITL 2 BY AN INTRON RNA STRUCTURE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 25122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40339124 JRNL DOI 10.1073/PNAS.2502425122 REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 389832 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 9MQS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000287579. 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 : COMPLEX OF GROUP I INTRON WITH REMARK 245 GMP SUBSTRATE 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 : 7.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5930.00 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 C A -9 REMARK 465 G A -8 REMARK 465 C A -7 REMARK 465 U A -6 REMARK 465 C A 4 REMARK 465 U A 5 REMARK 465 G A 6 REMARK 465 U A 36 REMARK 465 A A 37 REMARK 465 A A 38 REMARK 465 A A 58 REMARK 465 A A 59 REMARK 465 U A 60 REMARK 465 A A 61 REMARK 465 C A 62 REMARK 465 C A 63 REMARK 465 A A 64 REMARK 465 C A 65 REMARK 465 C A 66 REMARK 465 C A 67 REMARK 465 A A 68 REMARK 465 C A 69 REMARK 465 C A 70 REMARK 465 U A 71 REMARK 465 C A 72 REMARK 465 C A 73 REMARK 465 U A 74 REMARK 465 U A 75 REMARK 465 U A 76 REMARK 465 G A 77 REMARK 465 G A 78 REMARK 465 A A 79 REMARK 465 G A 80 REMARK 465 G A 81 REMARK 465 U A 82 REMARK 465 G A 83 REMARK 465 G A 84 REMARK 465 G A 85 REMARK 465 U A 86 REMARK 465 G A 87 REMARK 465 A A 88 REMARK 465 C A 89 REMARK 465 A A 90 REMARK 465 A A 91 REMARK 465 A A 120 REMARK 465 A A 121 REMARK 465 U A 122 REMARK 465 A A 123 REMARK 465 A A 124 REMARK 465 A A 125 REMARK 465 A A 126 REMARK 465 U A 127 REMARK 465 A A 128 REMARK 465 U A 129 REMARK 465 U A 130 REMARK 465 A A 212 REMARK 465 C A 213 REMARK 465 C A 214 REMARK 465 A A 215 REMARK 465 A A 216 REMARK 465 C A 217 REMARK 465 A A 218 REMARK 465 A A 219 REMARK 465 U A 220 REMARK 465 U A 221 REMARK 465 A A 222 REMARK 465 C A 223 REMARK 465 A A 224 REMARK 465 A A 225 REMARK 465 U A 226 REMARK 465 U A 227 REMARK 465 A A 228 REMARK 465 A A 229 REMARK 465 U A 230 REMARK 465 U A 231 REMARK 465 A A 232 REMARK 465 A A 233 REMARK 465 A A 234 REMARK 465 G A 235 REMARK 465 G A 236 REMARK 465 U A 237 REMARK 465 C A 238 REMARK 465 G A 316 REMARK 465 A A 317 REMARK 465 A A 318 REMARK 465 C A 319 REMARK 465 A A 320 REMARK 465 G A 321 REMARK 465 G A 322 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 U A 47 N1 U A 47 C2 -0.056 REMARK 500 A A 49 N9 A A 49 C4 -0.036 REMARK 500 A A 50 N3 A A 50 C4 -0.044 REMARK 500 A A 101 N9 A A 101 C4 -0.045 REMARK 500 A A 102 N3 A A 102 C4 -0.039 REMARK 500 A A 102 N9 A A 102 C4 -0.036 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G A 260 C4' - C3' - O3' ANGL. DEV. = 15.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A -1 O2' REMARK 620 2 A A 251 OP1 71.5 REMARK 620 3 A A 253 OP2 140.9 94.9 REMARK 620 4 U A 254 OP1 139.8 79.6 67.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 0 OP1 REMARK 620 2 5GP A 409 O3' 158.5 REMARK 620 3 HOH A 501 O 108.5 92.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 408 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 46 O6 REMARK 620 2 U A 47 O4 73.6 REMARK 620 3 G A 48 O6 119.9 66.4 REMARK 620 4 G A 195 O6 73.2 67.6 51.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 407 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 148 OP2 REMARK 620 2 U A 149 O4 63.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48538 RELATED DB: EMDB REMARK 900 CRYOEM COMPLEX 1 - GMP DBREF1 9MQS A -9 322 GB NC_018046.1 DBREF2 9MQS A 391224033 2092 2423 SEQADV 9MQS U A 9 GB 391224033 A 2110 CONFLICT SEQRES 1 A 332 C G C U A G G G A U A A A SEQRES 2 A 332 C U G U U U G U C C C U U SEQRES 3 A 332 U A U A U A G A G A U A U SEQRES 4 A 332 A U A G A A U A A C A A U SEQRES 5 A 332 C G G G U G A A U U G C A SEQRES 6 A 332 A G A A U A C C A C C C A SEQRES 7 A 332 C C U C C U U U G G A G G SEQRES 8 A 332 U G G G U G A C A A U U U SEQRES 9 A 332 G C A G C G A A G U A U A SEQRES 10 A 332 U A U U A G C U U A A U A SEQRES 11 A 332 A U A A A A U A U U A U U SEQRES 12 A 332 U A G A U A U A U A A A C SEQRES 13 A 332 G U U C A A C G A C U A G SEQRES 14 A 332 A A G G U G A G U A A G C SEQRES 15 A 332 U A A C A A U A A C C C U SEQRES 16 A 332 U C C A C G A G C G C C C SEQRES 17 A 332 G A C A U C U U A A U G A SEQRES 18 A 332 A C C A A C A A U U A C A SEQRES 19 A 332 A U U A A U U A A A G G U SEQRES 20 A 332 C A U U A U G A U G A U G SEQRES 21 A 332 A C A U A G U C U G A A C SEQRES 22 A 332 U A A A U A G U G A U A U SEQRES 23 A 332 U U A G A U A U A A U A U SEQRES 24 A 332 U U A A A U G A U A U U A SEQRES 25 A 332 U G A U A A C A A A A U U SEQRES 26 A 332 G A A C A G G HET CA A 401 1 HET CA A 402 1 HET CA A 403 1 HET CA A 404 1 HET CA A 405 1 HET CA A 406 1 HET CA A 407 1 HET K A 408 1 HET 5GP A 409 24 HETNAM CA CALCIUM ION HETNAM K POTASSIUM ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 CA 7(CA 2+) FORMUL 9 K K 1+ FORMUL 10 5GP C10 H14 N5 O8 P FORMUL 11 HOH *(H2 O) LINK O2' A A -1 CA CA A 403 1555 1555 3.12 LINK OP1 U A 0 CA CA A 401 1555 1555 3.02 LINK O6 G A 46 K K A 408 1555 1555 3.18 LINK O4 U A 47 K K A 408 1555 1555 2.12 LINK O6 G A 48 K K A 408 1555 1555 3.43 LINK OP1 U A 148 CA CA A 405 1555 1555 2.35 LINK OP2 U A 148 CA CA A 407 1555 1555 2.76 LINK OP1 U A 149 CA CA A 406 1555 1555 2.79 LINK O4 U A 149 CA CA A 407 1555 1555 2.70 LINK O6 G A 195 K K A 408 1555 1555 3.35 LINK OP1 A A 251 CA CA A 403 1555 1555 2.96 LINK O2' A A 253 CA CA A 402 1555 1555 2.94 LINK OP2 A A 253 CA CA A 403 1555 1555 2.40 LINK OP1 U A 254 CA CA A 403 1555 1555 2.88 LINK OP1 A A 255 CA CA A 404 1555 1555 2.19 LINK CA CA A 401 O3' 5GP A 409 1555 1555 2.08 LINK CA CA A 401 O HOH A 501 1555 1555 3.17 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 TER 5175 U A 315 HETATM 5176 CA CA A 401 119.733 125.898 103.873 1.00 50.00 CA HETATM 5177 CA CA A 402 119.103 117.832 108.443 1.00 30.00 CA HETATM 5178 CA CA A 403 116.779 125.284 108.347 1.00 30.00 CA HETATM 5179 CA CA A 404 124.524 124.267 110.084 1.00 30.00 CA HETATM 5180 CA CA A 405 111.094 118.910 114.418 1.00 30.00 CA HETATM 5181 CA CA A 406 108.169 113.765 109.633 1.00 30.00 CA HETATM 5182 CA CA A 407 106.244 122.981 117.252 1.00 30.00 CA HETATM 5183 K K A 408 119.724 115.768 125.359 1.00 30.00 K HETATM 5184 P 5GP A 409 120.062 123.415 100.015 1.00 17.31 P HETATM 5185 O1P 5GP A 409 120.181 123.830 98.584 1.00 11.71 O HETATM 5186 O2P 5GP A 409 120.981 122.305 100.442 1.00 7.14 O HETATM 5187 O3P 5GP A 409 120.092 124.613 100.920 1.00 11.76 O HETATM 5188 O5' 5GP A 409 118.568 122.844 100.143 1.00 14.81 O HETATM 5189 C5' 5GP A 409 117.514 123.785 100.236 1.00 20.04 C HETATM 5190 C4' 5GP A 409 116.869 123.664 101.600 1.00 22.20 C HETATM 5191 O4' 5GP A 409 116.437 122.319 101.743 1.00 17.15 O HETATM 5192 C3' 5GP A 409 117.790 123.903 102.779 1.00 18.24 C HETATM 5193 O3' 5GP A 409 117.858 125.268 103.231 1.00 11.54 O HETATM 5194 C2' 5GP A 409 117.188 123.010 103.832 1.00 18.14 C HETATM 5195 O2' 5GP A 409 116.289 123.782 104.609 1.00 15.15 O HETATM 5196 C1' 5GP A 409 116.421 121.927 103.109 1.00 18.97 C HETATM 5197 N9 5GP A 409 117.097 120.627 103.314 1.00 17.08 N HETATM 5198 C8 5GP A 409 118.412 120.498 103.479 1.00 18.48 C HETATM 5199 N7 5GP A 409 118.768 119.210 103.660 1.00 15.47 N HETATM 5200 C5 5GP A 409 117.656 118.476 103.611 1.00 16.70 C HETATM 5201 C6 5GP A 409 117.338 117.043 103.724 1.00 20.29 C HETATM 5202 O6 5GP A 409 118.220 116.191 103.923 1.00 17.98 O HETATM 5203 N1 5GP A 409 116.085 116.663 103.614 1.00 10.42 N HETATM 5204 C2 5GP A 409 115.125 117.547 103.413 1.00 18.43 C HETATM 5205 N2 5GP A 409 113.877 117.063 103.318 1.00 15.53 N HETATM 5206 N3 5GP A 409 115.336 118.875 103.302 1.00 17.35 N HETATM 5207 C4 5GP A 409 116.563 119.408 103.391 1.00 16.66 C HETATM 5208 O HOH A 501 120.442 127.172 101.059 1.00 50.00 O CONECT 102 5178 CONECT 115 5176 CONECT 979 5183 CONECT 1002 5183 CONECT 1022 5183 CONECT 2178 5180 CONECT 2179 5182 CONECT 2198 5181 CONECT 2214 5182 CONECT 3195 5183 CONECT 3795 5178 CONECT 3838 5178 CONECT 3846 5177 CONECT 3859 5178 CONECT 3879 5179 CONECT 5176 115 5193 5208 CONECT 5177 3846 CONECT 5178 102 3795 3838 3859 CONECT 5179 3879 CONECT 5180 2178 CONECT 5181 2198 CONECT 5182 2179 2214 CONECT 5183 979 1002 1022 3195 CONECT 5184 5185 5186 5187 5188 CONECT 5185 5184 CONECT 5186 5184 CONECT 5187 5184 CONECT 5188 5184 5189 CONECT 5189 5188 5190 CONECT 5190 5189 5191 5192 CONECT 5191 5190 5196 CONECT 5192 5190 5193 5194 CONECT 5193 5176 5192 CONECT 5194 5192 5195 5196 CONECT 5195 5194 CONECT 5196 5191 5194 5197 CONECT 5197 5196 5198 5207 CONECT 5198 5197 5199 CONECT 5199 5198 5200 CONECT 5200 5199 5201 5207 CONECT 5201 5200 5202 5203 CONECT 5202 5201 CONECT 5203 5201 5204 CONECT 5204 5203 5205 5206 CONECT 5205 5204 CONECT 5206 5204 5207 CONECT 5207 5197 5200 5206 CONECT 5208 5176 MASTER 276 0 9 0 0 0 0 6 5207 1 48 26 END