HEADER TRANSFERASE 17-AUG-22 8E3S TITLE CRYOEM STRUCTURE OF YEAST ARGINYLTRANSFERASE 1 (ATE1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGINYL-TRNA--PROTEIN TRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ARGINYLTRANSFERASE 1,R-TRANSFERASE 1,ARGININE-TRNA--PROTEIN COMPND 5 TRANSFERASE 1; COMPND 6 EC: 2.3.2.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: ATE1, YGL017W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARGINYLTRANSFERASE, POST-TRANSLATIONAL MODIFICATION, ENZYME, KEYWDS 2 TRANSFERASE EXPDTA ELECTRON MICROSCOPY AUTHOR W.HUANG,Y.ZHANG,D.J.TAYLOR REVDAT 2 01-MAY-24 8E3S 1 JRNL REVDAT 1 26-APR-23 8E3S 0 JRNL AUTH T.ABEYWANSHA,W.HUANG,X.YE,A.NAWROCKI,X.LAN,E.JANKOWSKY, JRNL AUTH 2 D.J.TAYLOR,Y.ZHANG JRNL TITL THE STRUCTURAL BASIS OF TRNA RECOGNITION BY JRNL TITL 2 ARGINYL-TRNA-PROTEIN TRANSFERASE. JRNL REF NAT COMMUN V. 14 2232 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37076488 JRNL DOI 10.1038/S41467-023-38004-8 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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 : 523915 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 8E3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267800. 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 : APO FORM OF YEAST REMARK 245 ARGINYLTRANSFERASE 1 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 : 7.10 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 5000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 25000.00 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) : 4000.00 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 44 O TYR A 411 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 2 -30.33 -130.25 REMARK 500 ASP A 3 27.09 -140.61 REMARK 500 LEU A 97 117.03 -163.71 REMARK 500 ARG A 452 13.73 -142.55 REMARK 500 ILE A 467 -60.34 -92.46 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 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 CYS A 23 SG 84.9 REMARK 620 3 CYS A 94 SG 148.2 89.5 REMARK 620 4 CYS A 95 SG 92.6 91.3 118.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27871 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF YEAST ARGINYLTRANSFERASE 1 (ATE1) DBREF 8E3S A 1 503 UNP P16639 ATE1_YEAST 1 503 SEQRES 1 A 503 MET SER ASP ARG PHE VAL ILE TRP ALA PRO SER MET HIS SEQRES 2 A 503 ASN GLU PRO ALA ALA LYS CYS GLY TYR CYS HIS GLY ASN SEQRES 3 A 503 LYS GLY GLY ASN MET ASP GLN LEU PHE ALA LEU ASP SER SEQRES 4 A 503 TRP ALA HIS ARG TYR MET ASN LYS MET ASP VAL VAL LYS SEQRES 5 A 503 ILE GLU ASN CYS THR ILE GLY SER PHE VAL GLU HIS MET SEQRES 6 A 503 ASP VAL ALA THR TYR ASP ARG MET CYS ASN MET GLY PHE SEQRES 7 A 503 ARG ARG SER GLY LYS PHE LEU TYR LYS VAL ASP PRO LEU SEQRES 8 A 503 ARG ASN CYS CYS ARG LEU TYR THR ILE ARG THR ALA PRO SEQRES 9 A 503 GLN GLU LEU ASN MET THR LYS GLU LEU LYS LYS CYS ILE SEQRES 10 A 503 SER ARG PHE ALA THR ARG ILE THR SER GLU ASP TYR CYS SEQRES 11 A 503 PRO ALA ALA VAL ALA SER SER ASP PHE VAL GLY LYS ILE SEQRES 12 A 503 VAL ASN ALA GLU MET ASN SER LYS THR PHE TYR THR ARG SEQRES 13 A 503 PHE GLU PRO ALA LEU TYR SER GLU GLU LYS TYR HIS LEU SEQRES 14 A 503 PHE VAL LYS TYR GLN GLU LYS VAL HIS GLN ASP TYR ASN SEQRES 15 A 503 ASN SER PRO LYS SER PHE LYS ARG PHE LEU CYS ASP THR SEQRES 16 A 503 PRO PHE GLY PRO GLU ALA VAL LEU GLY THR GLN GLU SER SEQRES 17 A 503 TRP GLU GLN LEU ASN ASN TRP GLN ARG MET LYS PRO GLY SEQRES 18 A 503 GLU LYS LEU LYS HIS MET GLY PRO VAL HIS GLU CYS TYR SEQRES 19 A 503 TYR TYR GLU GLY LYS LEU ILE ALA ILE THR VAL SER ASP SEQRES 20 A 503 ILE LEU PRO SER GLY ILE SER SER VAL TYR PHE ILE TRP SEQRES 21 A 503 ASP PRO ASP TYR SER LYS TRP SER LEU GLY LYS LEU SER SEQRES 22 A 503 ALA LEU ARG ASP LEU ALA ILE ILE GLN ARG THR ASN LEU SEQRES 23 A 503 GLN TYR TYR TYR LEU GLY TYR TYR ILE GLU ASP CYS PRO SEQRES 24 A 503 LYS MET ASN TYR LYS ALA ASN TYR GLY ALA GLU VAL LEU SEQRES 25 A 503 ASP VAL CYS HIS SER LYS TYR ILE PRO LEU LYS PRO ILE SEQRES 26 A 503 GLN ASP MET ILE SER ARG GLY LYS LEU PHE VAL ILE GLY SEQRES 27 A 503 GLU GLU GLU THR LYS VAL THR LYS GLU LEU TYR LEU VAL SEQRES 28 A 503 ASP SER GLU THR GLY ARG GLY GLU GLY PHE PRO THR ASP SEQRES 29 A 503 ASN VAL VAL LYS TYR LYS ASN ILE ALA GLU GLU ILE TYR SEQRES 30 A 503 GLY VAL GLY GLY CYS ALA PHE LYS SER ALA ASN GLU SER SEQRES 31 A 503 ALA LEU GLU LEU LYS GLU LEU TYR GLY ILE PRO TYR GLU SEQRES 32 A 503 GLU GLU ASP LEU ASP THR ILE TYR HIS LEU LYS GLU HIS SEQRES 33 A 503 ASN GLY HIS ALA PRO ASN GLY ILE PRO ASN VAL VAL PRO SEQRES 34 A 503 GLY LEU LEU PRO LEU TRP GLU LEU LEU ASP ILE MET GLN SEQRES 35 A 503 SER GLY LYS ILE THR ASP LEU GLU GLY ARG LEU PHE LEU SEQRES 36 A 503 PHE GLU ILE GLU THR GLU GLY ILE ARG PRO LEU ILE ASN SEQRES 37 A 503 PHE TYR SER GLU PRO PRO ASN VAL LYS LYS ARG ILE CYS SEQRES 38 A 503 ASP VAL ILE ARG LEU PHE GLY PHE GLU THR CYS MET LYS SEQRES 39 A 503 ALA VAL ILE LEU TYR SER GLU GLN MET HET ZN A 601 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 AA1 PRO A 16 CYS A 20 5 5 HELIX 2 AA2 ASN A 30 PHE A 35 1 6 HELIX 3 AA3 LEU A 37 MET A 45 1 9 HELIX 4 AA4 ASP A 66 GLY A 77 1 12 HELIX 5 AA5 ALA A 103 LEU A 107 5 5 HELIX 6 AA6 THR A 110 THR A 125 1 16 HELIX 7 AA7 ASP A 138 ASN A 149 1 12 HELIX 8 AA8 SER A 163 HIS A 178 1 16 HELIX 9 AA9 SER A 184 CYS A 193 1 10 HELIX 10 AB1 GLY A 198 GLY A 204 1 7 HELIX 11 AB2 THR A 205 ASN A 214 1 10 HELIX 12 AB3 TRP A 215 MET A 218 5 4 HELIX 13 AB4 PRO A 262 SER A 265 5 4 HELIX 14 AB5 SER A 268 THR A 284 1 17 HELIX 15 AB6 MET A 301 ASN A 306 5 6 HELIX 16 AB7 ILE A 325 SER A 330 1 6 HELIX 17 AB8 SER A 353 ARG A 357 5 5 HELIX 18 AB9 ILE A 372 GLY A 378 1 7 HELIX 19 AC1 CYS A 382 TYR A 398 1 17 HELIX 20 AC2 LEU A 413 GLY A 418 5 6 HELIX 21 AC3 PRO A 433 SER A 443 1 11 HELIX 22 AC4 GLY A 444 LEU A 449 5 6 HELIX 23 AC5 PRO A 473 GLY A 488 1 16 HELIX 24 AC6 GLY A 488 LYS A 494 1 7 SHEET 1 AA1 4 SER A 11 HIS A 13 0 SHEET 2 AA1 4 THR A 57 HIS A 64 -1 O GLY A 59 N SER A 11 SHEET 3 AA1 4 PHE A 84 LYS A 87 -1 O LYS A 87 N ILE A 58 SHEET 4 AA1 4 ARG A 79 SER A 81 -1 N SER A 81 O PHE A 84 SHEET 1 AA2 6 SER A 11 HIS A 13 0 SHEET 2 AA2 6 THR A 57 HIS A 64 -1 O GLY A 59 N SER A 11 SHEET 3 AA2 6 PHE A 5 TRP A 8 -1 N VAL A 6 O HIS A 64 SHEET 4 AA2 6 ALA A 495 TYR A 499 1 O VAL A 496 N PHE A 5 SHEET 5 AA2 6 PHE A 454 GLU A 457 1 N PHE A 456 O ILE A 497 SHEET 6 AA2 6 GLY A 462 PRO A 465 -1 O ARG A 464 N LEU A 455 SHEET 1 AA3 4 TYR A 289 TYR A 294 0 SHEET 2 AA3 4 TYR A 98 THR A 102 -1 N TYR A 98 O TYR A 294 SHEET 3 AA3 4 GLU A 310 ASP A 313 -1 O LEU A 312 N THR A 99 SHEET 4 AA3 4 LYS A 318 PRO A 321 -1 O LYS A 318 N ASP A 313 SHEET 1 AA4 4 PHE A 153 GLU A 158 0 SHEET 2 AA4 4 GLY A 228 TYR A 236 -1 O HIS A 231 N GLU A 158 SHEET 3 AA4 4 LYS A 239 LEU A 249 -1 O THR A 244 N GLU A 232 SHEET 4 AA4 4 GLY A 252 TRP A 260 -1 O GLY A 252 N LEU A 249 SHEET 1 AA5 2 ILE A 337 GLY A 338 0 SHEET 2 AA5 2 LYS A 370 ASN A 371 -1 O LYS A 370 N GLY A 338 LINK SG CYS A 20 ZN ZN A 601 1555 1555 2.35 LINK SG CYS A 23 ZN ZN A 601 1555 1555 2.28 LINK SG CYS A 94 ZN ZN A 601 1555 1555 2.35 LINK SG CYS A 95 ZN ZN A 601 1555 1555 2.28 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