HEADER RNA BINDING PROTEIN 12-MAR-24 9ENB TITLE HUMAN PSEUDOURIDINE SYNTHASE 3 (PUS3 R116A MUTANT) AND TWO TRNA-GLN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA PSEUDOURIDINE(38/39) SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRNA PSEUDOURIDINE SYNTHASE 3,TRNA PSEUDOURIDYLATE SYNTHASE COMPND 5 3,TRNA-URIDINE ISOMERASE 3; COMPND 6 EC: 5.4.99.45; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: R116A SINGLE MUTATION; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: TRNA-GLN; COMPND 12 CHAIN: C, D; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PUS3, FKSG32; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS RNA MODIFICATION, PSEUDOURIDYLATION, TRNA, HOMODIMER, RNA BINDING KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.-Y.LIN,J.JEZOWSKI,S.GLATT REVDAT 2 24-JUL-24 9ENB 1 JRNL REVDAT 1 10-JUL-24 9ENB 0 JRNL AUTH T.Y.LIN,L.KLEEMANN,J.JEZOWSKI,D.DOBOSZ,M.RAWSKI,P.INDYKA, JRNL AUTH 2 G.WAZNY,R.MEHTA,A.CHRAMIEC-GLABIK,L.KOZIEJ,T.RANFF, JRNL AUTH 3 C.FUFEZAN,M.WAWRO,J.KOCHAN,J.BERETA,S.A.LEIDEL,S.GLATT JRNL TITL THE MOLECULAR BASIS OF TRNA SELECTIVITY BY HUMAN JRNL TITL 2 PSEUDOURIDINE SYNTHASE 3. JRNL REF MOL.CELL V. 84 2472 2024 JRNL REFN ISSN 1097-2765 JRNL PMID 38996458 JRNL DOI 10.1016/J.MOLCEL.2024.06.013 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, 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 : 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) : 2.660 REMARK 3 NUMBER OF PARTICLES : 569272 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 9ENB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292136974. 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 : HOMODIMER OF HUMAN PUS3 AND TWO REMARK 245 TRNA-GLN; PSEUDOURIDINE REMARK 245 SYNTHASE 3 (PUS3); TRNA-GLN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 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 : 8393 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) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 4000.00 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 TYR A 3 REMARK 465 ASN A 4 REMARK 465 ASP A 5 REMARK 465 THR A 6 REMARK 465 ASP A 7 REMARK 465 ARG A 8 REMARK 465 ASN A 9 REMARK 465 GLN A 10 REMARK 465 THR A 11 REMARK 465 GLU A 12 REMARK 465 LYS A 13 REMARK 465 LEU A 14 REMARK 465 LEU A 15 REMARK 465 LYS A 16 REMARK 465 ARG A 17 REMARK 465 VAL A 18 REMARK 465 ARG A 19 REMARK 465 GLU A 20 REMARK 465 LEU A 21 REMARK 465 GLU A 22 REMARK 465 GLN A 23 REMARK 465 GLU A 24 REMARK 465 VAL A 25 REMARK 465 GLN A 26 REMARK 465 ARG A 27 REMARK 465 LEU A 28 REMARK 465 LYS A 29 REMARK 465 LYS A 30 REMARK 465 GLU A 31 REMARK 465 GLN A 32 REMARK 465 ALA A 33 REMARK 465 LYS A 34 REMARK 465 ASN A 35 REMARK 465 LYS A 36 REMARK 465 GLU A 37 REMARK 465 ASP A 38 REMARK 465 SER A 39 REMARK 465 ASN A 40 REMARK 465 ILE A 41 REMARK 465 ARG A 42 REMARK 465 GLU A 43 REMARK 465 ASN A 44 REMARK 465 SER A 45 REMARK 465 ALA A 46 REMARK 465 GLY A 47 REMARK 465 ALA A 48 REMARK 465 GLY A 49 REMARK 465 LYS A 50 REMARK 465 THR A 51 REMARK 465 ARG A 138 REMARK 465 GLY A 139 REMARK 465 ARG A 140 REMARK 465 ASP A 141 REMARK 465 SER A 142 REMARK 465 GLU A 143 REMARK 465 ASP A 144 REMARK 465 PHE A 145 REMARK 465 ASN A 146 REMARK 465 VAL A 147 REMARK 465 LYS A 148 REMARK 465 GLU A 149 REMARK 465 GLU A 150 REMARK 465 ALA A 151 REMARK 465 ASN A 152 REMARK 465 ALA A 153 REMARK 465 ALA A 154 REMARK 465 ALA A 155 REMARK 465 ASP A 370 REMARK 465 THR A 371 REMARK 465 VAL A 372 REMARK 465 PRO A 373 REMARK 465 VAL A 374 REMARK 465 PRO A 375 REMARK 465 CYS A 376 REMARK 465 GLY A 377 REMARK 465 ILE A 378 REMARK 465 GLY A 379 REMARK 465 PRO A 380 REMARK 465 LYS A 381 REMARK 465 MET A 382 REMARK 465 ASP A 383 REMARK 465 GLY A 384 REMARK 465 MET A 385 REMARK 465 THR A 386 REMARK 465 GLU A 387 REMARK 465 TRP A 388 REMARK 465 GLY A 389 REMARK 465 ASN A 390 REMARK 465 VAL A 391 REMARK 465 LYS A 392 REMARK 465 PRO A 393 REMARK 465 SER A 394 REMARK 465 VAL A 395 REMARK 465 GLU A 404 REMARK 465 GLY A 405 REMARK 465 VAL A 406 REMARK 465 LYS A 407 REMARK 465 MET A 408 REMARK 465 ARG A 409 REMARK 465 THR A 410 REMARK 465 GLN A 421 REMARK 465 GLY A 422 REMARK 465 LEU A 423 REMARK 465 GLU A 424 REMARK 465 SER A 425 REMARK 465 ARG A 426 REMARK 465 ILE A 427 REMARK 465 GLN A 428 REMARK 465 HIS A 429 REMARK 465 PHE A 430 REMARK 465 VAL A 431 REMARK 465 ARG A 432 REMARK 465 ARG A 433 REMARK 465 GLY A 434 REMARK 465 ARG A 435 REMARK 465 ILE A 436 REMARK 465 GLU A 437 REMARK 465 HIS A 438 REMARK 465 PRO A 439 REMARK 465 HIS A 440 REMARK 465 LEU A 441 REMARK 465 PHE A 442 REMARK 465 HIS A 443 REMARK 465 GLU A 444 REMARK 465 GLU A 445 REMARK 465 GLU A 446 REMARK 465 THR A 447 REMARK 465 LYS A 448 REMARK 465 ALA A 449 REMARK 465 LYS A 450 REMARK 465 ARG A 451 REMARK 465 ASP A 452 REMARK 465 CYS A 453 REMARK 465 ASN A 454 REMARK 465 ASP A 455 REMARK 465 THR A 456 REMARK 465 LEU A 457 REMARK 465 GLU A 458 REMARK 465 GLU A 459 REMARK 465 GLU A 460 REMARK 465 ASN A 461 REMARK 465 THR A 462 REMARK 465 ASN A 463 REMARK 465 LEU A 464 REMARK 465 GLU A 465 REMARK 465 THR A 466 REMARK 465 PRO A 467 REMARK 465 THR A 468 REMARK 465 LYS A 469 REMARK 465 ARG A 470 REMARK 465 VAL A 471 REMARK 465 CYS A 472 REMARK 465 VAL A 473 REMARK 465 ASP A 474 REMARK 465 THR A 475 REMARK 465 GLU A 476 REMARK 465 ILE A 477 REMARK 465 LYS A 478 REMARK 465 SER A 479 REMARK 465 ILE A 480 REMARK 465 ILE A 481 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 TYR B 3 REMARK 465 ASN B 4 REMARK 465 ASP B 5 REMARK 465 THR B 6 REMARK 465 ASP B 7 REMARK 465 ARG B 8 REMARK 465 ASN B 9 REMARK 465 GLN B 10 REMARK 465 THR B 11 REMARK 465 GLU B 12 REMARK 465 LYS B 13 REMARK 465 LEU B 14 REMARK 465 LEU B 15 REMARK 465 LYS B 16 REMARK 465 ARG B 17 REMARK 465 VAL B 18 REMARK 465 ARG B 19 REMARK 465 GLU B 20 REMARK 465 LEU B 21 REMARK 465 GLU B 22 REMARK 465 GLN B 23 REMARK 465 GLU B 24 REMARK 465 VAL B 25 REMARK 465 GLN B 26 REMARK 465 ARG B 27 REMARK 465 LEU B 28 REMARK 465 LYS B 29 REMARK 465 LYS B 30 REMARK 465 GLU B 31 REMARK 465 GLN B 32 REMARK 465 ALA B 33 REMARK 465 LYS B 34 REMARK 465 ASN B 35 REMARK 465 LYS B 36 REMARK 465 GLU B 37 REMARK 465 ASP B 38 REMARK 465 SER B 39 REMARK 465 ASN B 40 REMARK 465 ILE B 41 REMARK 465 ARG B 42 REMARK 465 GLU B 43 REMARK 465 ASN B 44 REMARK 465 SER B 45 REMARK 465 ALA B 46 REMARK 465 GLY B 47 REMARK 465 ALA B 48 REMARK 465 GLY B 49 REMARK 465 LYS B 50 REMARK 465 THR B 51 REMARK 465 ARG B 138 REMARK 465 GLY B 139 REMARK 465 ARG B 140 REMARK 465 ASP B 141 REMARK 465 SER B 142 REMARK 465 GLU B 143 REMARK 465 ASP B 144 REMARK 465 PHE B 145 REMARK 465 ASN B 146 REMARK 465 VAL B 147 REMARK 465 LYS B 148 REMARK 465 GLU B 149 REMARK 465 GLU B 150 REMARK 465 ALA B 151 REMARK 465 ASN B 152 REMARK 465 ALA B 153 REMARK 465 ALA B 154 REMARK 465 ALA B 155 REMARK 465 ASP B 370 REMARK 465 THR B 371 REMARK 465 VAL B 372 REMARK 465 PRO B 373 REMARK 465 VAL B 374 REMARK 465 PRO B 375 REMARK 465 CYS B 376 REMARK 465 GLY B 377 REMARK 465 ILE B 378 REMARK 465 GLY B 379 REMARK 465 PRO B 380 REMARK 465 LYS B 381 REMARK 465 MET B 382 REMARK 465 ASP B 383 REMARK 465 GLY B 384 REMARK 465 MET B 385 REMARK 465 THR B 386 REMARK 465 GLU B 387 REMARK 465 TRP B 388 REMARK 465 GLY B 389 REMARK 465 ASN B 390 REMARK 465 VAL B 391 REMARK 465 LYS B 392 REMARK 465 PRO B 393 REMARK 465 SER B 394 REMARK 465 VAL B 395 REMARK 465 GLU B 404 REMARK 465 GLY B 405 REMARK 465 VAL B 406 REMARK 465 LYS B 407 REMARK 465 MET B 408 REMARK 465 ARG B 409 REMARK 465 THR B 410 REMARK 465 GLN B 421 REMARK 465 GLY B 422 REMARK 465 LEU B 423 REMARK 465 GLU B 424 REMARK 465 SER B 425 REMARK 465 ARG B 426 REMARK 465 ILE B 427 REMARK 465 GLN B 428 REMARK 465 HIS B 429 REMARK 465 PHE B 430 REMARK 465 VAL B 431 REMARK 465 ARG B 432 REMARK 465 ARG B 433 REMARK 465 GLY B 434 REMARK 465 ARG B 435 REMARK 465 ILE B 436 REMARK 465 GLU B 437 REMARK 465 HIS B 438 REMARK 465 PRO B 439 REMARK 465 HIS B 440 REMARK 465 LEU B 441 REMARK 465 PHE B 442 REMARK 465 HIS B 443 REMARK 465 GLU B 444 REMARK 465 GLU B 445 REMARK 465 GLU B 446 REMARK 465 THR B 447 REMARK 465 LYS B 448 REMARK 465 ALA B 449 REMARK 465 LYS B 450 REMARK 465 ARG B 451 REMARK 465 ASP B 452 REMARK 465 CYS B 453 REMARK 465 ASN B 454 REMARK 465 ASP B 455 REMARK 465 THR B 456 REMARK 465 LEU B 457 REMARK 465 GLU B 458 REMARK 465 GLU B 459 REMARK 465 GLU B 460 REMARK 465 ASN B 461 REMARK 465 THR B 462 REMARK 465 ASN B 463 REMARK 465 LEU B 464 REMARK 465 GLU B 465 REMARK 465 THR B 466 REMARK 465 PRO B 467 REMARK 465 THR B 468 REMARK 465 LYS B 469 REMARK 465 ARG B 470 REMARK 465 VAL B 471 REMARK 465 CYS B 472 REMARK 465 VAL B 473 REMARK 465 ASP B 474 REMARK 465 THR B 475 REMARK 465 GLU B 476 REMARK 465 ILE B 477 REMARK 465 LYS B 478 REMARK 465 SER B 479 REMARK 465 ILE B 480 REMARK 465 ILE B 481 REMARK 465 C C 73 REMARK 465 C C 74 REMARK 465 A C 75 REMARK 465 C D 73 REMARK 465 C D 74 REMARK 465 A D 75 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 ARG A 53 19.81 58.61 REMARK 500 ASP A 118 -177.64 -68.02 REMARK 500 ALA A 202 -62.29 -92.84 REMARK 500 GLN A 214 45.98 -82.64 REMARK 500 GLU A 255 -162.87 -77.68 REMARK 500 GLN A 259 -6.80 74.20 REMARK 500 ASN A 331 59.19 39.00 REMARK 500 ALA A 401 34.31 -99.11 REMARK 500 ARG B 53 19.93 57.90 REMARK 500 ASN B 87 57.98 -93.60 REMARK 500 PRO B 182 38.86 -78.70 REMARK 500 ALA B 202 -63.44 -92.23 REMARK 500 PHE B 222 34.52 -99.09 REMARK 500 PRO B 253 46.21 -84.98 REMARK 500 PRO B 261 2.59 -69.11 REMARK 500 PRO B 296 44.99 -76.59 REMARK 500 ASN B 331 59.14 38.93 REMARK 500 LYS B 419 57.90 -93.15 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 MG C 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U C 8 OP1 REMARK 620 2 G C 9 OP2 94.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 58 OP1 REMARK 620 2 U C 59 O4 85.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U D 8 OP1 REMARK 620 2 G D 9 OP2 94.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A D 58 OP1 REMARK 620 2 U D 59 O4 85.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16917 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-16926 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-19830 RELATED DB: EMDB REMARK 900 HUMAN PSEUDOURIDINE SYNTHASE 3 (PUS3 R116A MUTANT) AND TWO TRNA-GLN DBREF 9ENB A 1 481 UNP Q9BZE2 PUS3_HUMAN 1 481 DBREF 9ENB B 1 481 UNP Q9BZE2 PUS3_HUMAN 1 481 DBREF 9ENB C 1 75 PDB 9ENB 9ENB 1 75 DBREF 9ENB D 1 75 PDB 9ENB 9ENB 1 75 SEQADV 9ENB ALA A 116 UNP Q9BZE2 ARG 116 ENGINEERED MUTATION SEQADV 9ENB ALA B 116 UNP Q9BZE2 ARG 116 ENGINEERED MUTATION SEQRES 1 A 481 MET ALA TYR ASN ASP THR ASP ARG ASN GLN THR GLU LYS SEQRES 2 A 481 LEU LEU LYS ARG VAL ARG GLU LEU GLU GLN GLU VAL GLN SEQRES 3 A 481 ARG LEU LYS LYS GLU GLN ALA LYS ASN LYS GLU ASP SER SEQRES 4 A 481 ASN ILE ARG GLU ASN SER ALA GLY ALA GLY LYS THR LYS SEQRES 5 A 481 ARG ALA PHE ASP PHE SER ALA HIS GLY ARG ARG HIS VAL SEQRES 6 A 481 ALA LEU ARG ILE ALA TYR MET GLY TRP GLY TYR GLN GLY SEQRES 7 A 481 PHE ALA SER GLN GLU ASN THR ASN ASN THR ILE GLU GLU SEQRES 8 A 481 LYS LEU PHE GLU ALA LEU THR LYS THR ARG LEU VAL GLU SEQRES 9 A 481 SER ARG GLN THR SER ASN TYR HIS ARG CYS GLY ALA THR SEQRES 10 A 481 ASP LYS GLY VAL SER ALA PHE GLY GLN VAL ILE SER LEU SEQRES 11 A 481 ASP LEU ARG SER GLN PHE PRO ARG GLY ARG ASP SER GLU SEQRES 12 A 481 ASP PHE ASN VAL LYS GLU GLU ALA ASN ALA ALA ALA GLU SEQRES 13 A 481 GLU ILE ARG TYR THR HIS ILE LEU ASN ARG VAL LEU PRO SEQRES 14 A 481 PRO ASP ILE ARG ILE LEU ALA TRP ALA PRO VAL GLU PRO SEQRES 15 A 481 SER PHE SER ALA ARG PHE SER CYS LEU GLU ARG THR TYR SEQRES 16 A 481 ARG TYR PHE PHE PRO ARG ALA ASP LEU ASP ILE VAL THR SEQRES 17 A 481 MET ASP TYR ALA ALA GLN LYS TYR VAL GLY THR HIS ASP SEQRES 18 A 481 PHE ARG ASN LEU CYS LYS MET ASP VAL ALA ASN GLY VAL SEQRES 19 A 481 ILE ASN PHE GLN ARG THR ILE LEU SER ALA GLN VAL GLN SEQRES 20 A 481 LEU VAL GLY GLN SER PRO GLY GLU GLY ARG TRP GLN GLU SEQRES 21 A 481 PRO PHE GLN LEU CYS GLN PHE GLU VAL THR GLY GLN ALA SEQRES 22 A 481 PHE LEU TYR HIS GLN VAL ARG CYS MET MET ALA ILE LEU SEQRES 23 A 481 PHE LEU ILE GLY GLN GLY MET GLU LYS PRO GLU ILE ILE SEQRES 24 A 481 ASP GLU LEU LEU ASN ILE GLU LYS ASN PRO GLN LYS PRO SEQRES 25 A 481 GLN TYR SER MET ALA VAL GLU PHE PRO LEU VAL LEU TYR SEQRES 26 A 481 ASP CYS LYS PHE GLU ASN VAL LYS TRP ILE TYR ASP GLN SEQRES 27 A 481 GLU ALA GLN GLU PHE ASN ILE THR HIS LEU GLN GLN LEU SEQRES 28 A 481 TRP ALA ASN HIS ALA VAL LYS THR HIS MET LEU TYR SER SEQRES 29 A 481 MET LEU GLN GLY LEU ASP THR VAL PRO VAL PRO CYS GLY SEQRES 30 A 481 ILE GLY PRO LYS MET ASP GLY MET THR GLU TRP GLY ASN SEQRES 31 A 481 VAL LYS PRO SER VAL ILE LYS GLN THR SER ALA PHE VAL SEQRES 32 A 481 GLU GLY VAL LYS MET ARG THR TYR LYS PRO LEU MET ASP SEQRES 33 A 481 ARG PRO LYS CYS GLN GLY LEU GLU SER ARG ILE GLN HIS SEQRES 34 A 481 PHE VAL ARG ARG GLY ARG ILE GLU HIS PRO HIS LEU PHE SEQRES 35 A 481 HIS GLU GLU GLU THR LYS ALA LYS ARG ASP CYS ASN ASP SEQRES 36 A 481 THR LEU GLU GLU GLU ASN THR ASN LEU GLU THR PRO THR SEQRES 37 A 481 LYS ARG VAL CYS VAL ASP THR GLU ILE LYS SER ILE ILE SEQRES 1 B 481 MET ALA TYR ASN ASP THR ASP ARG ASN GLN THR GLU LYS SEQRES 2 B 481 LEU LEU LYS ARG VAL ARG GLU LEU GLU GLN GLU VAL GLN SEQRES 3 B 481 ARG LEU LYS LYS GLU GLN ALA LYS ASN LYS GLU ASP SER SEQRES 4 B 481 ASN ILE ARG GLU ASN SER ALA GLY ALA GLY LYS THR LYS SEQRES 5 B 481 ARG ALA PHE ASP PHE SER ALA HIS GLY ARG ARG HIS VAL SEQRES 6 B 481 ALA LEU ARG ILE ALA TYR MET GLY TRP GLY TYR GLN GLY SEQRES 7 B 481 PHE ALA SER GLN GLU ASN THR ASN ASN THR ILE GLU GLU SEQRES 8 B 481 LYS LEU PHE GLU ALA LEU THR LYS THR ARG LEU VAL GLU SEQRES 9 B 481 SER ARG GLN THR SER ASN TYR HIS ARG CYS GLY ALA THR SEQRES 10 B 481 ASP LYS GLY VAL SER ALA PHE GLY GLN VAL ILE SER LEU SEQRES 11 B 481 ASP LEU ARG SER GLN PHE PRO ARG GLY ARG ASP SER GLU SEQRES 12 B 481 ASP PHE ASN VAL LYS GLU GLU ALA ASN ALA ALA ALA GLU SEQRES 13 B 481 GLU ILE ARG TYR THR HIS ILE LEU ASN ARG VAL LEU PRO SEQRES 14 B 481 PRO ASP ILE ARG ILE LEU ALA TRP ALA PRO VAL GLU PRO SEQRES 15 B 481 SER PHE SER ALA ARG PHE SER CYS LEU GLU ARG THR TYR SEQRES 16 B 481 ARG TYR PHE PHE PRO ARG ALA ASP LEU ASP ILE VAL THR SEQRES 17 B 481 MET ASP TYR ALA ALA GLN LYS TYR VAL GLY THR HIS ASP SEQRES 18 B 481 PHE ARG ASN LEU CYS LYS MET ASP VAL ALA ASN GLY VAL SEQRES 19 B 481 ILE ASN PHE GLN ARG THR ILE LEU SER ALA GLN VAL GLN SEQRES 20 B 481 LEU VAL GLY GLN SER PRO GLY GLU GLY ARG TRP GLN GLU SEQRES 21 B 481 PRO PHE GLN LEU CYS GLN PHE GLU VAL THR GLY GLN ALA SEQRES 22 B 481 PHE LEU TYR HIS GLN VAL ARG CYS MET MET ALA ILE LEU SEQRES 23 B 481 PHE LEU ILE GLY GLN GLY MET GLU LYS PRO GLU ILE ILE SEQRES 24 B 481 ASP GLU LEU LEU ASN ILE GLU LYS ASN PRO GLN LYS PRO SEQRES 25 B 481 GLN TYR SER MET ALA VAL GLU PHE PRO LEU VAL LEU TYR SEQRES 26 B 481 ASP CYS LYS PHE GLU ASN VAL LYS TRP ILE TYR ASP GLN SEQRES 27 B 481 GLU ALA GLN GLU PHE ASN ILE THR HIS LEU GLN GLN LEU SEQRES 28 B 481 TRP ALA ASN HIS ALA VAL LYS THR HIS MET LEU TYR SER SEQRES 29 B 481 MET LEU GLN GLY LEU ASP THR VAL PRO VAL PRO CYS GLY SEQRES 30 B 481 ILE GLY PRO LYS MET ASP GLY MET THR GLU TRP GLY ASN SEQRES 31 B 481 VAL LYS PRO SER VAL ILE LYS GLN THR SER ALA PHE VAL SEQRES 32 B 481 GLU GLY VAL LYS MET ARG THR TYR LYS PRO LEU MET ASP SEQRES 33 B 481 ARG PRO LYS CYS GLN GLY LEU GLU SER ARG ILE GLN HIS SEQRES 34 B 481 PHE VAL ARG ARG GLY ARG ILE GLU HIS PRO HIS LEU PHE SEQRES 35 B 481 HIS GLU GLU GLU THR LYS ALA LYS ARG ASP CYS ASN ASP SEQRES 36 B 481 THR LEU GLU GLU GLU ASN THR ASN LEU GLU THR PRO THR SEQRES 37 B 481 LYS ARG VAL CYS VAL ASP THR GLU ILE LYS SER ILE ILE SEQRES 1 C 75 G G C C C C A U G G U G U SEQRES 2 C 75 A A U G G U U A G C A C U SEQRES 3 C 75 C U G G A C U U U G A A U SEQRES 4 C 75 C C A G C G A U C C G A G SEQRES 5 C 75 U U C A A A U C U C G G U SEQRES 6 C 75 G G G A C C U C C A SEQRES 1 D 75 G G C C C C A U G G U G U SEQRES 2 D 75 A A U G G U U A G C A C U SEQRES 3 D 75 C U G G A C U U U G A A U SEQRES 4 D 75 C C A G C G A U C C G A G SEQRES 5 D 75 U U C A A A U C U C G G U SEQRES 6 D 75 G G G A C C U C C A HET MG C 101 1 HET MG C 102 1 HET MG C 103 1 HET MG D 101 1 HET MG D 102 1 HET MG D 103 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 6(MG 2+) HELIX 1 AA1 ASP A 56 HIS A 60 5 5 HELIX 2 AA2 MET A 72 TYR A 76 5 5 HELIX 3 AA3 THR A 88 THR A 100 1 13 HELIX 4 AA4 SER A 105 SER A 109 5 5 HELIX 5 AA5 ARG A 159 LEU A 168 1 10 HELIX 6 AA6 ASP A 205 GLN A 214 1 10 HELIX 7 AA7 ARG A 223 CYS A 226 5 4 HELIX 8 AA8 ASP A 229 GLY A 233 5 5 HELIX 9 AA9 HIS A 277 GLN A 291 1 15 HELIX 10 AB1 GLU A 297 LEU A 303 1 7 HELIX 11 AB2 ASP A 337 LEU A 369 1 33 HELIX 12 AB3 ASP B 56 HIS B 60 5 5 HELIX 13 AB4 MET B 72 TYR B 76 5 5 HELIX 14 AB5 THR B 88 THR B 100 1 13 HELIX 15 AB6 SER B 105 SER B 109 5 5 HELIX 16 AB7 ARG B 159 LEU B 168 1 10 HELIX 17 AB8 ASP B 205 GLN B 214 1 10 HELIX 18 AB9 ARG B 223 CYS B 226 5 4 HELIX 19 AC1 ASP B 229 GLY B 233 5 5 HELIX 20 AC2 GLN B 259 PHE B 262 5 4 HELIX 21 AC3 HIS B 277 GLN B 291 1 15 HELIX 22 AC4 GLU B 297 LEU B 303 1 7 HELIX 23 AC5 ASP B 337 LEU B 369 1 33 HELIX 24 AC6 PRO B 413 ARG B 417 5 5 SHEET 1 AA1 4 HIS A 112 ARG A 113 0 SHEET 2 AA1 4 SER A 122 SER A 134 -1 O SER A 129 N HIS A 112 SHEET 3 AA1 4 GLY A 61 TYR A 71 -1 N LEU A 67 O ILE A 128 SHEET 4 AA1 4 ARG A 173 PRO A 179 -1 O LEU A 175 N ARG A 68 SHEET 1 AA2 7 HIS A 112 ARG A 113 0 SHEET 2 AA2 7 SER A 122 SER A 134 -1 O SER A 129 N HIS A 112 SHEET 3 AA2 7 LEU A 322 LYS A 328 1 O LEU A 324 N PHE A 124 SHEET 4 AA2 7 GLU A 192 PRO A 200 -1 N THR A 194 O TYR A 325 SHEET 5 AA2 7 LEU A 264 GLY A 271 -1 O CYS A 265 N PHE A 199 SHEET 6 AA2 7 GLN A 238 VAL A 249 -1 N LEU A 242 O THR A 270 SHEET 7 AA2 7 GLY A 218 ASP A 221 -1 N GLY A 218 O ILE A 241 SHEET 1 AA3 4 HIS B 112 ARG B 113 0 SHEET 2 AA3 4 SER B 122 SER B 134 -1 O SER B 129 N HIS B 112 SHEET 3 AA3 4 GLY B 61 TYR B 71 -1 N VAL B 65 O LEU B 130 SHEET 4 AA3 4 ARG B 173 PRO B 179 -1 O LEU B 175 N ARG B 68 SHEET 1 AA4 7 HIS B 112 ARG B 113 0 SHEET 2 AA4 7 SER B 122 SER B 134 -1 O SER B 129 N HIS B 112 SHEET 3 AA4 7 LEU B 322 LYS B 328 1 O LEU B 324 N PHE B 124 SHEET 4 AA4 7 GLU B 192 PRO B 200 -1 N THR B 194 O TYR B 325 SHEET 5 AA4 7 LEU B 264 GLY B 271 -1 O CYS B 265 N PHE B 199 SHEET 6 AA4 7 GLN B 238 VAL B 249 -1 N LEU B 242 O THR B 270 SHEET 7 AA4 7 GLY B 218 ASP B 221 -1 N GLY B 218 O ILE B 241 SSBOND 1 CYS A 114 CYS A 327 1555 1555 2.04 SSBOND 2 CYS B 114 CYS B 327 1555 1555 2.04 LINK OP1 U C 8 MG MG C 102 1555 1555 2.56 LINK OP2 G C 9 MG MG C 102 1555 1555 2.16 LINK OP2 G C 10 MG MG C 101 1555 1555 2.76 LINK OP1 A C 58 MG MG C 103 1555 1555 2.54 LINK O4 U C 59 MG MG C 103 1555 1555 2.94 LINK OP1 U D 8 MG MG D 102 1555 1555 2.55 LINK OP2 G D 9 MG MG D 102 1555 1555 2.15 LINK OP2 G D 10 MG MG D 103 1555 1555 2.76 LINK OP1 A D 58 MG MG D 101 1555 1555 2.54 LINK O4 U D 59 MG MG D 101 1555 1555 2.94 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