HEADER LIGASE 06-FEB-25 9I8V TITLE CRYO-EM STRUCTURE OF THE DANIO RERIO TRNA LIGASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE; COMPND 3 CHAIN: B; COMPND 4 EC: 3.6.4.13; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: TRUNCATED VARIANT (AA 693-740); COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA-SPLICING LIGASE RTCB HOMOLOG; COMPND 9 CHAIN: C; COMPND 10 SYNONYM: 3'-PHOSPHATE/5'-HYDROXY NUCLEIC ACID LIGASE; COMPND 11 EC: 6.5.1.8; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: HIS-TEV-RTCB; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: FAMILY WITH SEQUENCE SIMILARITY 98, MEMBER B; COMPND 16 CHAIN: D; COMPND 17 SYNONYM: PROTEIN FAM98B; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: TRUNCATED VARIANT (AA 1-296); COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: RNA TRANSCRIPTION, TRANSLATION AND TRANSPORT FACTOR COMPND 22 PROTEIN; COMPND 23 CHAIN: E; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 5; COMPND 26 MOLECULE: ASHWIN; COMPND 27 CHAIN: F; COMPND 28 ENGINEERED: YES; COMPND 29 OTHER_DETAILS: TRUNCATED VARIANT (AA 1-83) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: DDX1, SI:CH211-214K9.2, SI:DKEY-161F12.1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7106; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 10 ORGANISM_COMMON: ZEBRAFISH; SOURCE 11 ORGANISM_TAXID: 7955; SOURCE 12 GENE: RTCB, ZGC:76871; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7106; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 17 ORGANISM_COMMON: ZEBRAFISH; SOURCE 18 ORGANISM_TAXID: 7955; SOURCE 19 GENE: FAM98B, ZGC:158382; SOURCE 20 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 7106; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 24 ORGANISM_COMMON: ZEBRAFISH; SOURCE 25 ORGANISM_TAXID: 7955; SOURCE 26 GENE: RTRAF, ZGC:56576; SOURCE 27 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 7106; SOURCE 29 MOL_ID: 5; SOURCE 30 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 31 ORGANISM_COMMON: ZEBRAFISH; SOURCE 32 ORGANISM_TAXID: 7955; SOURCE 33 GENE: IM:6907446, SI:DKEYP-118H3.6; SOURCE 34 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 35 EXPRESSION_SYSTEM_TAXID: 7106 KEYWDS TRNA LIGASE COMPLEX, RTCB, TRNA, TRNA MATURATION, TRNA SPLICING, KEYWDS 2 LIGASE, RNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.CHAMERA,W.ZAJKO,M.CZARNOCKI-CIECIURA,M.JACIUK,L.KOZIEJ,J.NOWAK, AUTHOR 2 K.WYCISK,M.SROKA,A.CHRAMIEC-GLABIK,M.SMIETANSKI,F.GOLEBIOWSKI, AUTHOR 3 M.WARMINSKI,J.JEMIELITY,S.GLATT,M.NOWOTNY REVDAT 2 21-MAY-25 9I8V 1 JRNL REVDAT 1 23-APR-25 9I8V 0 JRNL AUTH S.CHAMERA,W.ZAJKO,M.CZARNOCKI-CIECIURA,M.JACIUK,L.KOZIEJ, JRNL AUTH 2 J.NOWAK,K.WYCISK,M.SROKA,A.CHRAMIEC-GLABIK,M.SMIETANSKI, JRNL AUTH 3 F.GOLEBIOWSKI,M.WARMINSKI,J.JEMIELITY,S.GLATT,M.NOWOTNY JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE 3'-5' JRNL TITL 2 TRNA SPLICING LIGASES. JRNL REF J.BIOL.CHEM. V. 301 08506 2025 JRNL REFN ESSN 1083-351X JRNL PMID 40220997 JRNL DOI 10.1016/J.JBC.2025.108506 REMARK 2 REMARK 2 RESOLUTION. 3.33 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 : REAL 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) : 3.330 REMARK 3 NUMBER OF PARTICLES : 179455 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 9I8V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1292145143. 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 : TRNA LIGASE COMPLEX FROM D. REMARK 245 RERIO REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.97 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 : 9942 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) : 1500.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4109.00 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 : STAGE TILT 20 DEG 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, E, F 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 ARG B 693 REMARK 465 ARG B 694 REMARK 465 ALA B 695 REMARK 465 THR B 696 REMARK 465 GLY B 697 REMARK 465 GLY B 698 REMARK 465 GLY B 699 REMARK 465 LEU B 700 REMARK 465 TYR B 701 REMARK 465 LYS B 702 REMARK 465 GLY B 703 REMARK 465 HIS B 704 REMARK 465 VAL B 705 REMARK 465 ASN B 734 REMARK 465 GLN B 735 REMARK 465 LEU B 736 REMARK 465 PHE B 737 REMARK 465 LYS B 738 REMARK 465 ALA B 739 REMARK 465 PHE B 740 REMARK 465 MET C -13 REMARK 465 HIS C -12 REMARK 465 HIS C -11 REMARK 465 HIS C -10 REMARK 465 HIS C -9 REMARK 465 HIS C -8 REMARK 465 HIS C -7 REMARK 465 GLU C -6 REMARK 465 ASN C -5 REMARK 465 LEU C -4 REMARK 465 TYR C -3 REMARK 465 PHE C -2 REMARK 465 GLN C -1 REMARK 465 GLY C 0 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 GLY C 56 REMARK 465 GLY C 57 REMARK 465 GLY C 58 REMARK 465 PHE C 59 REMARK 465 ALA C 433 REMARK 465 LEU C 434 REMARK 465 SER C 435 REMARK 465 ARG C 436 REMARK 465 ALA C 437 REMARK 465 LYS C 438 REMARK 465 SER C 439 REMARK 465 ARG C 440 REMARK 465 ARG C 441 REMARK 465 ASN C 442 REMARK 465 LEU C 443 REMARK 465 ASP C 444 REMARK 465 PHE C 445 REMARK 465 GLN C 446 REMARK 465 ASP C 447 REMARK 465 VAL C 448 REMARK 465 LEU C 449 REMARK 465 ASP C 450 REMARK 465 LYS C 451 REMARK 465 LEU C 452 REMARK 465 ALA C 453 REMARK 465 ASP C 454 REMARK 465 MET C 455 REMARK 465 GLY C 456 REMARK 465 ILE C 457 REMARK 465 ALA C 458 REMARK 465 ILE C 459 REMARK 465 ARG C 460 REMARK 465 VAL C 461 REMARK 465 ALA C 462 REMARK 465 SER C 463 REMARK 465 PRO C 464 REMARK 465 LYS C 465 REMARK 465 LEU C 466 REMARK 465 VAL C 467 REMARK 465 MET C 468 REMARK 465 GLU C 469 REMARK 465 GLU C 470 REMARK 465 ALA C 471 REMARK 465 PRO C 472 REMARK 465 GLU C 473 REMARK 465 SER C 474 REMARK 465 TYR C 475 REMARK 465 THR D 56 REMARK 465 GLN D 57 REMARK 465 ASP D 58 REMARK 465 GLU D 59 REMARK 465 ILE D 60 REMARK 465 ILE D 61 REMARK 465 MET D 267 REMARK 465 VAL D 268 REMARK 465 LYS D 269 REMARK 465 THR D 270 REMARK 465 SER D 271 REMARK 465 SER D 272 REMARK 465 GLY D 273 REMARK 465 SER D 274 REMARK 465 SER D 275 REMARK 465 ARG D 276 REMARK 465 GLN D 277 REMARK 465 ASN D 278 REMARK 465 THR D 279 REMARK 465 SER D 280 REMARK 465 CYS D 281 REMARK 465 ALA D 282 REMARK 465 VAL D 283 REMARK 465 ASN D 284 REMARK 465 ARG D 285 REMARK 465 ILE D 286 REMARK 465 LEU D 287 REMARK 465 MET D 288 REMARK 465 GLY D 289 REMARK 465 ARG D 290 REMARK 465 VAL D 291 REMARK 465 PRO D 292 REMARK 465 ASP D 293 REMARK 465 ARG D 294 REMARK 465 GLY D 295 REMARK 465 GLY D 296 REMARK 465 THR E 106 REMARK 465 GLU E 107 REMARK 465 THR E 108 REMARK 465 ASN E 109 REMARK 465 ASP E 110 REMARK 465 VAL E 111 REMARK 465 GLN E 112 REMARK 465 LYS E 113 REMARK 465 SER E 114 REMARK 465 ALA E 115 REMARK 465 ASP E 116 REMARK 465 PRO E 117 REMARK 465 LEU E 118 REMARK 465 ILE E 119 REMARK 465 ASN E 120 REMARK 465 LEU E 121 REMARK 465 ASP E 122 REMARK 465 SER E 123 REMARK 465 GLN E 172 REMARK 465 ALA E 173 REMARK 465 LYS E 174 REMARK 465 GLU E 175 REMARK 465 GLY E 176 REMARK 465 LEU E 177 REMARK 465 PRO E 178 REMARK 465 ALA E 229 REMARK 465 ASP E 230 REMARK 465 PRO E 231 REMARK 465 LYS E 232 REMARK 465 THR E 233 REMARK 465 ASP E 234 REMARK 465 HIS E 235 REMARK 465 ARG E 236 REMARK 465 LEU E 237 REMARK 465 GLY E 238 REMARK 465 LYS E 239 REMARK 465 VAL E 240 REMARK 465 GLY E 241 REMARK 465 ARG E 242 REMARK 465 MET F 1 REMARK 465 ALA F 2 REMARK 465 SER F 3 REMARK 465 HIS F 4 REMARK 465 ARG F 5 REMARK 465 THR F 6 REMARK 465 ASP F 7 REMARK 465 ARG F 8 REMARK 465 THR F 9 REMARK 465 LYS F 10 REMARK 465 ASN F 11 REMARK 465 PRO F 12 REMARK 465 THR F 13 REMARK 465 SER F 14 REMARK 465 ASN F 15 REMARK 465 GLY F 16 REMARK 465 ASP F 17 REMARK 465 SER F 83 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 ASP B 706 CG OD1 OD2 REMARK 470 ILE B 707 CG1 CG2 CD1 REMARK 470 LYS C 44 CG CD CE NZ REMARK 470 GLU C 49 CG CD OE1 OE2 REMARK 470 ASP C 103 CG OD1 OD2 REMARK 470 ASP C 132 CG OD1 OD2 REMARK 470 GLU C 133 CG CD OE1 OE2 REMARK 470 LYS C 140 CG CD CE NZ REMARK 470 GLN C 145 CG CD OE1 NE2 REMARK 470 ASP C 149 CG OD1 OD2 REMARK 470 LYS C 158 CG CD CE NZ REMARK 470 ASP C 167 CG OD1 OD2 REMARK 470 GLU C 173 CG CD OE1 OE2 REMARK 470 GLU C 195 CG CD OE1 OE2 REMARK 470 GLN C 218 CG CD OE1 NE2 REMARK 470 ASN C 226 CG OD1 ND2 REMARK 470 ASP C 235 CG OD1 OD2 REMARK 470 GLU C 236 CG CD OE1 OE2 REMARK 470 ILE C 286 CG1 CG2 CD1 REMARK 470 ARG C 291 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 301 CG CD OE1 OE2 REMARK 470 GLU C 359 CG CD OE1 OE2 REMARK 470 MET C 405 CG SD CE REMARK 470 HIS C 428 CG ND1 CD2 CE1 NE2 REMARK 470 GLU D 2 CG CD OE1 OE2 REMARK 470 ASP D 4 CG OD1 OD2 REMARK 470 GLU D 10 CG CD OE1 OE2 REMARK 470 ASP D 15 CG OD1 OD2 REMARK 470 GLU D 20 CG CD OE1 OE2 REMARK 470 GLU D 21 CG CD OE1 OE2 REMARK 470 GLU D 27 CG CD OE1 OE2 REMARK 470 ARG D 30 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 39 CG OD1 ND2 REMARK 470 GLU D 53 CG CD OE1 OE2 REMARK 470 ASP D 64 CG OD1 OD2 REMARK 470 LEU D 66 CG CD1 CD2 REMARK 470 ARG D 70 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 73 CG CD CE NZ REMARK 470 ASP D 74 CG OD1 OD2 REMARK 470 GLU D 80 CG CD OE1 OE2 REMARK 470 LYS D 92 CG CD CE NZ REMARK 470 HIS D 97 CG ND1 CD2 CE1 NE2 REMARK 470 GLU D 107 CG CD OE1 OE2 REMARK 470 GLU D 126 CG CD OE1 OE2 REMARK 470 GLN D 134 CG CD OE1 NE2 REMARK 470 ASP D 135 CG OD1 OD2 REMARK 470 ASP D 152 CG OD1 OD2 REMARK 470 ASP D 159 CG OD1 OD2 REMARK 470 ARG D 183 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 188 CG CD OE1 OE2 REMARK 470 GLU D 191 CG CD OE1 OE2 REMARK 470 ARG D 262 CG CD NE CZ NH1 NH2 REMARK 470 GLU E 22 CG CD OE1 OE2 REMARK 470 LYS E 58 CG CD CE NZ REMARK 470 GLU E 75 CG CD OE1 OE2 REMARK 470 GLU E 91 CG CD OE1 OE2 REMARK 470 ASP E 94 CG OD1 OD2 REMARK 470 LYS E 129 CG CD CE NZ REMARK 470 ARG E 143 CG CD NE CZ NH1 NH2 REMARK 470 GLU E 160 CG CD OE1 OE2 REMARK 470 ASP E 165 CG OD1 OD2 REMARK 470 LEU E 181 CG CD1 CD2 REMARK 470 ASP E 182 CG OD1 OD2 REMARK 470 GLU F 50 CG CD OE1 OE2 REMARK 470 ASP F 51 CG OD1 OD2 REMARK 470 ARG F 75 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 82 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS C 19 116.58 -160.49 REMARK 500 HIS C 80 -129.40 58.66 REMARK 500 PRO C 86 -2.43 -57.95 REMARK 500 LEU C 131 -169.86 -79.00 REMARK 500 GLU C 195 17.68 56.17 REMARK 500 ALA C 202 139.52 -170.16 REMARK 500 ARG C 263 -123.24 63.66 REMARK 500 MET C 345 53.36 -91.41 REMARK 500 THR D 144 59.90 36.88 REMARK 500 GLU E 22 -61.66 -92.90 REMARK 500 ILE E 37 -55.46 -123.59 REMARK 500 ARG E 45 1.57 -68.02 REMARK 500 ASP F 48 70.14 39.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50108 RELATED DB: EMDB REMARK 900 MEDIUM RESOLUTION CRYO-EM MAP OF THE DANIO RERIO TRNA LIGASE COMPLEX REMARK 900 RELATED ID: EMD-52744 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE DANIO RERIO TRNA LIGASE COMPLEX DBREF 9I8V B 693 740 UNP F1R2L8 F1R2L8_DANRE 693 740 DBREF 9I8V C 1 505 UNP Q6NZS4 RTCB_DANRE 1 505 DBREF 9I8V D 1 296 UNP A0PJS3 A0PJS3_DANRE 1 296 DBREF 9I8V E 1 242 UNP Q7ZUH1 RTRAF_DANRE 1 242 DBREF 9I8V F 1 83 UNP Q32LR5 ASHWN_DANRE 1 83 SEQADV 9I8V MET C -13 UNP Q6NZS4 INITIATING METHIONINE SEQADV 9I8V HIS C -12 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V HIS C -11 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V HIS C -10 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V HIS C -9 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V HIS C -8 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V HIS C -7 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V GLU C -6 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V ASN C -5 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V LEU C -4 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V TYR C -3 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V PHE C -2 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V GLN C -1 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V GLY C 0 UNP Q6NZS4 EXPRESSION TAG SEQADV 9I8V ILE E 201 UNP Q7ZUH1 VAL 201 VARIANT SEQRES 1 B 48 ARG ARG ALA THR GLY GLY GLY LEU TYR LYS GLY HIS VAL SEQRES 2 B 48 ASP ILE LEU ALA PRO THR VAL GLN GLU LEU ALA ASN LEU SEQRES 3 B 48 GLU ARG GLU ALA GLN THR SER PHE LEU HIS LEU GLY TYR SEQRES 4 B 48 LEU PRO ASN GLN LEU PHE LYS ALA PHE SEQRES 1 C 519 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 C 519 GLY MET SER ARG SER TYR ASN ASP GLU LEU GLN TYR LEU SEQRES 3 C 519 ASP LYS ILE HIS LYS ASN CYS TRP ARG ILE LYS LYS GLY SEQRES 4 C 519 PHE VAL PRO ASN MET LEU VAL GLU GLY VAL PHE TYR VAL SEQRES 5 C 519 ASN ASP PRO LEU GLU LYS LEU MET PHE GLU GLU LEU ARG SEQRES 6 C 519 ASN ALA CYS ARG GLY GLY GLY PHE GLY GLY PHE LEU PRO SEQRES 7 C 519 ALA MET LYS GLN ILE GLY ASN VAL ALA ALA LEU PRO GLY SEQRES 8 C 519 ILE VAL HIS ARG SER ILE GLY LEU PRO ASP VAL HIS SER SEQRES 9 C 519 GLY TYR GLY PHE ALA ILE GLY ASN MET ALA ALA PHE ASP SEQRES 10 C 519 MET GLU ASN PRO ASP ALA VAL VAL SER PRO GLY GLY VAL SEQRES 11 C 519 GLY PHE ASP ILE ASN CYS GLY VAL ARG LEU LEU ARG THR SEQRES 12 C 519 ASN LEU ASP GLU GLY ASP VAL GLN PRO VAL LYS GLU GLN SEQRES 13 C 519 LEU ALA GLN SER LEU PHE ASP HIS ILE PRO VAL GLY VAL SEQRES 14 C 519 GLY SER LYS GLY VAL ILE PRO MET GLY ALA LYS ASP LEU SEQRES 15 C 519 GLU GLU ALA LEU GLU MET GLY VAL ASP TRP SER LEU ARG SEQRES 16 C 519 GLU GLY TYR ALA TRP ALA GLU ASP LYS GLU HIS CYS GLU SEQRES 17 C 519 GLU TYR GLY ARG MET LEU GLN ALA ASP PRO ASN LYS VAL SEQRES 18 C 519 SER SER LYS ALA LYS LYS ARG GLY LEU PRO GLN LEU GLY SEQRES 19 C 519 THR LEU GLY ALA GLY ASN HIS TYR ALA GLU ILE GLN VAL SEQRES 20 C 519 VAL ASP GLU ILE TYR ASN ASP TYR ALA ALA LYS LYS MET SEQRES 21 C 519 GLY ILE ASP HIS LYS GLY GLN VAL CYS VAL MET ILE HIS SEQRES 22 C 519 SER GLY SER ARG GLY LEU GLY HIS GLN VAL ALA THR ASP SEQRES 23 C 519 ALA LEU VAL ALA MET GLU LYS ALA MET LYS ARG ASP ARG SEQRES 24 C 519 ILE THR VAL ASN ASP ARG GLN LEU ALA CYS ALA ARG ILE SEQRES 25 C 519 THR SER GLU GLU GLY GLN ASP TYR LEU LYS GLY MET ALA SEQRES 26 C 519 ALA ALA GLY ASN TYR ALA TRP VAL ASN ARG SER SER MET SEQRES 27 C 519 THR PHE LEU THR ARG GLN ALA PHE SER LYS VAL PHE SER SEQRES 28 C 519 THR THR PRO ASP ASP LEU ASP MET HIS VAL ILE TYR ASP SEQRES 29 C 519 VAL SER HIS ASN ILE ALA LYS VAL GLU GLU HIS MET VAL SEQRES 30 C 519 ASP GLY ARG GLN LYS THR LEU LEU VAL HIS ARG LYS GLY SEQRES 31 C 519 SER THR ARG ALA PHE PRO PRO HIS HIS PRO LEU ILE PRO SEQRES 32 C 519 VAL ASP TYR GLN LEU THR GLY GLN PRO VAL LEU ILE GLY SEQRES 33 C 519 GLY THR MET GLY THR CYS SER TYR VAL LEU THR GLY THR SEQRES 34 C 519 GLU GLN GLY MET THR GLU THR PHE GLY THR THR CYS HIS SEQRES 35 C 519 GLY ALA GLY ARG ALA LEU SER ARG ALA LYS SER ARG ARG SEQRES 36 C 519 ASN LEU ASP PHE GLN ASP VAL LEU ASP LYS LEU ALA ASP SEQRES 37 C 519 MET GLY ILE ALA ILE ARG VAL ALA SER PRO LYS LEU VAL SEQRES 38 C 519 MET GLU GLU ALA PRO GLU SER TYR LYS ASN VAL THR ASP SEQRES 39 C 519 VAL VAL ASN THR CYS HIS ASP ALA GLY ILE SER LYS LYS SEQRES 40 C 519 ALA ILE LYS LEU ARG PRO ILE ALA VAL ILE LYS GLY SEQRES 1 D 296 MET GLU SER ASP ILE LEU ASP ILE LEU GLU GLN LEU GLY SEQRES 2 D 296 TYR ASP GLY PRO LEU ALA GLU GLU ALA CYS LEU LEU ALA SEQRES 3 D 296 GLU CYS GLY ARG GLY PHE SER SER SER GLU TYR VAL ASN SEQRES 4 D 296 LEU LEU THR TRP LEU THR LYS GLN LEU THR GLN PHE THR SEQRES 5 D 296 GLU THR HIS THR GLN ASP GLU ILE ILE THR ALA ASP PRO SEQRES 6 D 296 LEU ASP VAL SER ARG LEU LEU LYS ASP CYS CYS CYS PRO SEQRES 7 D 296 TYR GLU GLY LEU ALA SER ARG LEU ALA ASN GLY ASP VAL SEQRES 8 D 296 LYS ASP THR ARG ASP HIS LEU LYS ILE ILE LEU PHE VAL SEQRES 9 D 296 SER SER GLU LEU GLN SER ALA GLN LEU LEU LEU SER LYS SEQRES 10 D 296 THR LEU ARG ASP ALA GLU GLU ARG GLU MET ARG SER CYS SEQRES 11 D 296 SER PRO LEU GLN ASP LEU SER VAL ILE CYS HIS THR LEU SEQRES 12 D 296 THR LEU PRO ASP PRO ALA GLY ARG ASP PRO THR ASP THR SEQRES 13 D 296 PHE THR ASP ILE GLN THR GLN VAL ASN VAL LEU LEU GLU SEQRES 14 D 296 LYS LEU PRO GLU THR HIS ILE GLY ALA PRO ALA LEU GLN SEQRES 15 D 296 ARG SER ILE SER ALA GLU GLN TRP GLU GLU LEU GLU LYS SEQRES 16 D 296 ILE ASN SER THR LEU SER ALA GLU TYR GLU CYS ARG ARG SEQRES 17 D 296 ARG MET LEU ILE LYS ARG LEU ASP VAL THR VAL GLN SER SEQRES 18 D 296 PHE SER TRP SER ASP ARG ALA LYS VAL LYS ILE ASP GLN SEQRES 19 D 296 MET ALA ARG ALA TYR GLN PRO LYS ARG HIS SER LEU SER SEQRES 20 D 296 VAL ARG SER SER VAL SER LEU ALA HIS LEU LEU ALA ALA SEQRES 21 D 296 ARG ARG ASP ILE CYS ASN MET VAL LYS THR SER SER GLY SEQRES 22 D 296 SER SER ARG GLN ASN THR SER CYS ALA VAL ASN ARG ILE SEQRES 23 D 296 LEU MET GLY ARG VAL PRO ASP ARG GLY GLY SEQRES 1 E 242 MET PHE ARG ARG LYS LEU THR ALA LEU GLU TYR HIS ASN SEQRES 2 E 242 PRO THR GLY PHE ASP CYS LYS ASP GLU THR GLU PHE ARG SEQRES 3 E 242 ASN PHE ILE VAL TRP LEU GLU ASP GLN LYS ILE ARG HIS SEQRES 4 E 242 TYR LYS ILE GLU ASP ARG GLY ASN LEU ARG ASN ILE PRO SEQRES 5 E 242 SER SER ASP TRP PRO LYS TYR PHE GLU LYS TYR LEU GLN SEQRES 6 E 242 ASP VAL ASN CYS PRO PHE SER VAL GLN GLU ARG GLN GLU SEQRES 7 E 242 THR VAL ASP TRP LEU LEU GLY LEU ALA VAL ARG PHE GLU SEQRES 8 E 242 TYR GLY ASP ASN VAL GLU LYS TYR ARG ASN CYS LYS PRO SEQRES 9 E 242 VAL THR GLU THR ASN ASP VAL GLN LYS SER ALA ASP PRO SEQRES 10 E 242 LEU ILE ASN LEU ASP SER ASN ASN PRO ASP PHE LYS ALA SEQRES 11 E 242 GLY VAL LEU ALA LEU ALA ASN LEU LEU LYS ILE GLN ARG SEQRES 12 E 242 HIS ASP ASP TYR LEU VAL MET LEU LYS ALA ILE LYS ILE SEQRES 13 E 242 LEU VAL GLN GLU ARG LEU THR PRO ASP ALA ILE ALA LYS SEQRES 14 E 242 ALA SER GLN ALA LYS GLU GLY LEU PRO VAL THR LEU ASP SEQRES 15 E 242 LYS HIS ILE LEU GLY PHE ASP THR GLY ASP ALA THR LEU SEQRES 16 E 242 ASN GLU ALA ALA GLN ILE LEU ARG LEU LEU HIS ILE GLU SEQRES 17 E 242 GLU LEU ARG GLU LEU GLN THR LYS ILE ASN GLU ALA ILE SEQRES 18 E 242 VAL ALA VAL GLN ALA ILE ILE ALA ASP PRO LYS THR ASP SEQRES 19 E 242 HIS ARG LEU GLY LYS VAL GLY ARG SEQRES 1 F 83 MET ALA SER HIS ARG THR ASP ARG THR LYS ASN PRO THR SEQRES 2 F 83 SER ASN GLY ASP VAL SER LYS VAL ASP LEU LEU LEU HIS SEQRES 3 F 83 PRO GLU LEU LEU SER GLN GLU PHE ILE GLN LEU MET LEU SEQRES 4 F 83 GLN GLU ARG ASN ILE ALA VAL SER ASP PRO GLU ASP ARG SEQRES 5 F 83 ASP ARG LEU THR GLY LEU TYR LEU GLN HIS VAL ILE PRO SEQRES 6 F 83 LEU PRO GLN ARG GLU LEU PRO ARG SER ARG TRP GLY LYS SEQRES 7 F 83 ARG MET GLU LYS SER HELIX 1 AA1 PRO B 710 TYR B 731 1 22 HELIX 2 AA2 SER C 4 GLN C 10 1 7 HELIX 3 AA3 ASN C 39 ARG C 55 1 17 HELIX 4 AA4 PRO C 64 ALA C 73 1 10 HELIX 5 AA5 SER C 112 GLY C 117 1 6 HELIX 6 AA6 GLU C 133 GLN C 137 1 5 HELIX 7 AA7 VAL C 139 ILE C 151 1 13 HELIX 8 AA8 GLY C 164 MET C 174 1 11 HELIX 9 AA9 GLY C 175 GLU C 182 1 8 HELIX 10 AB1 TRP C 186 HIS C 192 1 7 HELIX 11 AB2 CYS C 193 ARG C 198 5 6 HELIX 12 AB3 ASP C 203 VAL C 207 5 5 HELIX 13 AB4 SER C 208 LEU C 216 1 9 HELIX 14 AB5 ASN C 239 GLY C 247 1 9 HELIX 15 AB6 SER C 262 ARG C 285 1 24 HELIX 16 AB7 SER C 300 SER C 337 1 38 HELIX 17 AB8 THR C 339 ASP C 344 1 6 HELIX 18 AB9 VAL C 390 LEU C 394 5 5 HELIX 19 AC1 THR C 415 THR C 422 1 8 HELIX 20 AC2 ASN C 477 ALA C 488 1 12 HELIX 21 AC3 GLU D 2 GLY D 13 1 12 HELIX 22 AC4 GLY D 16 ALA D 19 5 4 HELIX 23 AC5 GLU D 20 GLY D 31 1 12 HELIX 24 AC6 SER D 34 THR D 52 1 19 HELIX 25 AC7 ASP D 64 CYS D 75 1 12 HELIX 26 AC8 GLY D 81 GLY D 89 1 9 HELIX 27 AC9 ASP D 93 SER D 129 1 37 HELIX 28 AD1 SER D 131 LEU D 143 1 13 HELIX 29 AD2 ASP D 152 GLU D 169 1 18 HELIX 30 AD3 SER D 186 SER D 223 1 38 HELIX 31 AD4 TRP D 224 SER D 225 5 2 HELIX 32 AD5 ASP D 226 VAL D 230 5 5 HELIX 33 AD6 LYS D 231 HIS D 244 1 14 HELIX 34 AD7 SER D 253 ALA D 260 1 8 HELIX 35 AD8 PHE E 2 LEU E 9 1 8 HELIX 36 AD9 GLU E 22 LYS E 36 1 15 HELIX 37 AE1 ARG E 45 ASN E 50 1 6 HELIX 38 AE2 ASP E 55 VAL E 67 1 13 HELIX 39 AE3 GLU E 75 GLY E 93 1 19 HELIX 40 AE4 ASN E 95 ASN E 101 1 7 HELIX 41 AE5 ASN E 125 LEU E 139 1 15 HELIX 42 AE6 LEU E 148 LEU E 162 1 15 HELIX 43 AE7 THR E 163 SER E 171 1 9 HELIX 44 AE8 THR E 180 HIS E 184 5 5 HELIX 45 AE9 THR E 194 ILE E 228 1 35 HELIX 46 AF1 SER F 19 LEU F 25 1 7 HELIX 47 AF2 SER F 31 ARG F 42 1 12 HELIX 48 AF3 ASP F 51 VAL F 63 1 13 HELIX 49 AF4 SER F 74 LYS F 82 1 9 SHEET 1 AA1 2 LEU C 12 HIS C 16 0 SHEET 2 AA1 2 CYS C 19 ILE C 22 -1 O CYS C 19 N ILE C 15 SHEET 1 AA2 5 GLY C 34 PHE C 36 0 SHEET 2 AA2 5 SER C 82 HIS C 89 1 O SER C 82 N VAL C 35 SHEET 3 AA2 5 ILE C 96 ASP C 103 -1 O ILE C 96 N HIS C 89 SHEET 4 AA2 5 LEU C 370 ARG C 374 -1 O HIS C 373 N ALA C 100 SHEET 5 AA2 5 LYS C 357 GLU C 359 -1 N LYS C 357 O VAL C 372 SHEET 1 AA3 2 VAL C 110 VAL C 111 0 SHEET 2 AA3 2 ALA C 296 ARG C 297 -1 O ALA C 296 N VAL C 111 SHEET 1 AA4 7 VAL C 347 SER C 352 0 SHEET 2 AA4 7 GLY C 123 ASP C 132 -1 N LEU C 126 O ILE C 348 SHEET 3 AA4 7 GLN C 253 SER C 260 -1 O ILE C 258 N ARG C 125 SHEET 4 AA4 7 ILE C 231 ILE C 237 -1 N GLN C 232 O CYS C 255 SHEET 5 AA4 7 LYS C 492 ALA C 501 -1 O LYS C 496 N ASP C 235 SHEET 6 AA4 7 SER C 409 THR C 413 -1 N VAL C 411 O ALA C 494 SHEET 7 AA4 7 PRO C 398 ILE C 401 -1 N VAL C 399 O LEU C 412 SHEET 1 AA5 2 MET C 362 VAL C 363 0 SHEET 2 AA5 2 ARG C 366 GLN C 367 -1 O ARG C 366 N VAL C 363 SHEET 1 AA6 2 SER C 377 ARG C 379 0 SHEET 2 AA6 2 THR C 425 CYS C 427 -1 O THR C 426 N THR C 378 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 TER 216 PRO B 733 TER 3638 GLY C 505 TER 5577 ASN D 266 TER 7206 ILE E 228 TER 7733 LYS F 82 MASTER 389 0 0 49 20 0 0 6 7728 5 0 93 END