HEADER TRANSFERASE/RNA 19-MAR-25 9U48 TITLE CRYO-EM STRUCTURE OF SPMETTL16 IN COMPLEX WITH U6 SNRNA AND SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: U6 SMALL NUCLEAR RNA (ADENINE-(43)-N(6))-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.346; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES MET A -22 TO SER A 0 ARE EXPRESSION TAGS. MET COMPND 7 A 1 TO PHE A 23 ARE PART OF THE PROTEIN SEQUENCE, BASED ON COMPND 8 PUBLICATION (DOI: 10.1038/S41467-021-23457-6).; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: U6 SMALL NUCLEAR RNA; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 STRAIN: ED668; SOURCE 6 GENE: SPAC27D7.08C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA2; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 13 ORGANISM_COMMON: FISSION YEAST; SOURCE 14 ORGANISM_TAXID: 4896 KEYWDS M6A METHYLTRANSFERASE, U6 SNRNA, PROTEIN-RNA COMPLEX, SPLICING, KEYWDS 2 TRANSFERASE, TRANSFERASE-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR J.JU,K.TOMITA REVDAT 2 24-SEP-25 9U48 1 JRNL REVDAT 1 06-AUG-25 9U48 0 JRNL AUTH J.JU,K.TOMITA JRNL TITL STRUCTURES AND MECHANISMS OF U6 SNRNA M 6 A MODIFICATION BY JRNL TITL 2 METTL16. JRNL REF NAT COMMUN V. 16 7708 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40841561 JRNL DOI 10.1038/S41467-025-63021-0 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, PHENIX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 425927 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 9U48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-25. REMARK 100 THE DEPOSITION ID IS D_1300057454. 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 : SCHIZOSACCHAROMYCES POMBE N6 REMARK 245 -METHYLADENOSINE REMARK 245 METHYLTRANSFERASE METTL16 IN REMARK 245 COMPLEX WITH U6 SNRNA AND SAM 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 : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 8497 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) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 5000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 LYS A 4 REMARK 465 THR A 5 REMARK 465 ASP A 6 REMARK 465 ILE A 7 REMARK 465 ILE A 8 REMARK 465 ASN A 9 REMARK 465 PHE A 10 REMARK 465 ASP A 11 REMARK 465 SER A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 ARG A 15 REMARK 465 ASP A 16 REMARK 465 TYR A 17 REMARK 465 PRO A 18 REMARK 465 ASP A 19 REMARK 465 LEU A 20 REMARK 465 ARG A 21 REMARK 465 SER A 22 REMARK 465 PHE A 23 REMARK 465 VAL A 24 REMARK 465 LYS A 25 REMARK 465 ASN A 26 REMARK 465 GLY A 27 REMARK 465 ARG A 28 REMARK 465 ILE A 29 REMARK 465 ASP A 30 REMARK 465 PHE A 31 REMARK 465 TRP A 32 REMARK 465 ASN A 33 REMARK 465 GLU A 34 REMARK 465 ASP A 35 REMARK 465 ALA A 36 REMARK 465 ILE A 37 REMARK 465 ARG A 38 REMARK 465 THR A 39 REMARK 465 LEU A 40 REMARK 465 GLY A 41 REMARK 465 LYS A 42 REMARK 465 ALA A 43 REMARK 465 ILE A 44 REMARK 465 LEU A 45 REMARK 465 ASP A 46 REMARK 465 ARG A 47 REMARK 465 ASP A 48 REMARK 465 TYR A 49 REMARK 465 SER A 50 REMARK 465 LEU A 51 REMARK 465 ARG A 52 REMARK 465 VAL A 53 REMARK 465 GLU A 54 REMARK 465 PHE A 55 REMARK 465 SER A 187 REMARK 465 GLY A 188 REMARK 465 VAL A 189 REMARK 465 CYS A 190 REMARK 465 THR A 191 REMARK 465 GLY A 192 REMARK 465 VAL A 193 REMARK 465 TYR A 194 REMARK 465 G B 1 REMARK 465 A B 2 REMARK 465 U B 3 REMARK 465 C B 4 REMARK 465 U B 5 REMARK 465 U B 6 REMARK 465 C B 7 REMARK 465 G B 8 REMARK 465 G B 9 REMARK 465 A B 10 REMARK 465 U B 11 REMARK 465 C B 12 REMARK 465 A B 13 REMARK 465 C B 14 REMARK 465 U B 15 REMARK 465 U B 16 REMARK 465 U B 17 REMARK 465 G B 18 REMARK 465 G B 19 REMARK 465 U B 20 REMARK 465 C B 21 REMARK 465 A B 22 REMARK 465 A B 23 REMARK 465 A B 24 REMARK 465 U B 25 REMARK 465 U B 26 REMARK 465 G B 27 REMARK 465 A B 28 REMARK 465 A B 29 REMARK 465 A B 30 REMARK 465 C B 31 REMARK 465 G B 32 REMARK 465 A B 33 REMARK 465 U B 34 REMARK 465 A B 84 REMARK 465 G B 85 REMARK 465 A B 86 REMARK 465 G B 87 REMARK 465 A B 88 REMARK 465 A B 89 REMARK 465 A B 90 REMARK 465 A B 91 REMARK 465 C B 92 REMARK 465 C B 93 REMARK 465 C B 94 REMARK 465 A B 95 REMARK 465 U B 96 REMARK 465 U B 97 REMARK 465 U B 98 REMARK 465 U B 99 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 LEU A 60 17.89 51.23 REMARK 500 MET A 159 -169.10 -79.89 REMARK 500 ASN A 168 80.60 -153.17 REMARK 500 GLN A 183 66.52 -102.79 REMARK 500 LEU A 284 37.23 -99.38 REMARK 500 SER A 334 139.87 -172.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9M86 RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: EMD-63834 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SPMETTL16 IN COMPLEX WITH U6 SNRNA AND SAM DBREF 9U48 A -22 23 PDB 9U48 9U48 -22 23 DBREF 9U48 A 24 398 UNP O42662 MTL16_SCHPO 11 385 DBREF1 9U48 B 2 99 GB 3JB9_N DBREF2 9U48 B 929984519 2 99 SEQADV 9U48 G B 1 GB 929984519 EXPRESSION TAG SEQRES 1 A 421 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 421 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR ASP SEQRES 3 A 421 LYS THR ASP ILE ILE ASN PHE ASP SER LEU ALA ARG ASP SEQRES 4 A 421 TYR PRO ASP LEU ARG SER PHE VAL LYS ASN GLY ARG ILE SEQRES 5 A 421 ASP PHE TRP ASN GLU ASP ALA ILE ARG THR LEU GLY LYS SEQRES 6 A 421 ALA ILE LEU ASP ARG ASP TYR SER LEU ARG VAL GLU PHE SEQRES 7 A 421 PRO GLU ASN ARG LEU CYS PRO MET VAL PRO ASN ARG ALA SEQRES 8 A 421 THR TYR ILE ARG TYR ILE HIS ASP LEU LEU SER SER THR SEQRES 9 A 421 SER GLY GLN LYS ASP LYS LYS ARG ILE ILE GLY LEU ASP SEQRES 10 A 421 ILE GLY THR GLY ALA SER CYS ILE TYR PRO LEU LEU GLY SEQRES 11 A 421 CYS ARG MET TYR SER TYR ASP PHE VAL GLY THR GLU ILE SEQRES 12 A 421 ASP LYS PHE SER PHE GLU THR ALA LYS SER ASN ILE LEU SEQRES 13 A 421 GLN ASN ASN MET GLU SER GLN ILE LYS ILE VAL LEU ARG SEQRES 14 A 421 SER LYS GLN ASP CYS LEU LEU PRO ASP THR GLU GLY MET SEQRES 15 A 421 GLU GLU PHE THR PHE VAL MET CYS ASN PRO PRO PHE TYR SEQRES 16 A 421 GLU HIS GLU GLU ASP PHE ILE ASN PHE LYS GLN ASN PRO SEQRES 17 A 421 PRO SER GLY VAL CYS THR GLY VAL TYR HIS GLU MET VAL SEQRES 18 A 421 THR GLU GLY GLY GLU VAL GLY PHE ALA ASN LYS ILE LEU SEQRES 19 A 421 THR GLU SER LYS LYS ARG LYS GLY ILE GLN TRP TYR THR SEQRES 20 A 421 CYS MET PHE GLY LYS LYS SER SER VAL PRO ALA VAL VAL SEQRES 21 A 421 ASP LYS LEU ARG GLU GLN ASN ILE SER ASN TYR GLY ILE SEQRES 22 A 421 TYR GLU LEU ALA LEU GLY LYS THR LYS ARG TRP ILE ILE SEQRES 23 A 421 CYS TRP SER PHE GLN ALA MET ARG PRO HIS ASN GLU LEU SEQRES 24 A 421 ILE ARG PRO SER SER THR SER LEU SER LYS TYR PHE PRO SEQRES 25 A 421 HIS LYS VAL LEU GLN ASN TRP THR LEU ASP PRO GLU LEU SEQRES 26 A 421 CYS ALA GLN ILE ASP ASP ILE LEU GLN LYS PHE LEU ASP SEQRES 27 A 421 ASP ASN LYS ILE PRO TRP SER LYS LYS GLY SER VAL LEU SEQRES 28 A 421 GLU ILE SER THR LYS SER ILE THR TRP SER ARG LYS ALA SEQRES 29 A 421 ARG ARG ILE SER LYS SER GLN THR SER VAL SER SER LEU SEQRES 30 A 421 GLU GLY GLN MET LYS CYS GLU LEU ASN VAL ILE ASP ASN SEQRES 31 A 421 GLN LEU GLN CYS LYS TRP ILE GLU GLY TYR ASP TYR ASN SEQRES 32 A 421 VAL TYR GLU SER PHE CYS SER ALA LEU ALA ARG ALA LEU SEQRES 33 A 421 ARG ASP ASN LYS LYS SEQRES 1 B 99 G A U C U U C G G A U C A SEQRES 2 B 99 C U U U G G U C A A A U U SEQRES 3 B 99 G A A A C G A U A C A G A SEQRES 4 B 99 G A A G A U U A G C A U G SEQRES 5 B 99 G C C C C U G C A C A A G SEQRES 6 B 99 G A U G A C A C U G C G A SEQRES 7 B 99 C A U U G A G A G A A A A SEQRES 8 B 99 C C C A U U U U HET SAM A 401 27 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 3 SAM C15 H22 N6 O5 S HELIX 1 1 PRO A 65 SER A 79 1 15 HELIX 2 2 ILE A 102 TYR A 111 1 10 HELIX 3 3 PHE A 123 ASN A 135 1 13 HELIX 4 4 GLU A 175 PHE A 181 1 7 HELIX 5 5 GLY A 202 LYS A 215 1 14 HELIX 6 6 LYS A 230 GLN A 243 1 14 HELIX 7 7 ASN A 274 ILE A 277 1 4 HELIX 8 8 SER A 285 TYR A 287 1 3 HELIX 9 9 PRO A 300 ASN A 317 1 18 HELIX 10 10 ARG A 339 LYS A 346 1 8 HELIX 11 11 TYR A 379 LYS A 397 1 19 SHEET 1 1 1 ILE A 91 ILE A 95 0 SHEET 1 2 1 ASP A 114 GLU A 119 0 SHEET 1 3 1 ILE A 141 LEU A 145 0 SHEET 1 4 1 PHE A 164 CYS A 167 0 SHEET 1 5 1 TRP A 222 PHE A 227 0 SHEET 1 6 1 ASN A 247 LEU A 255 0 SHEET 1 7 1 THR A 258 SER A 266 0 SHEET 1 8 1 LEU A 293 THR A 297 0 SHEET 1 9 1 TRP A 321 LYS A 323 0 SHEET 1 10 1 LEU A 328 THR A 332 0 SHEET 1 11 1 MET A 358 ILE A 365 0 SHEET 1 12 1 GLN A 368 GLY A 376 0 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 3766 3767 CONECT 3767 3766 3768 3771 CONECT 3768 3767 3769 3770 CONECT 3769 3768 CONECT 3770 3768 CONECT 3771 3767 3772 CONECT 3772 3771 3773 CONECT 3773 3772 3774 3775 CONECT 3774 3773 CONECT 3775 3773 3776 CONECT 3776 3775 3777 3778 CONECT 3777 3776 3782 CONECT 3778 3776 3779 3780 CONECT 3779 3778 CONECT 3780 3778 3781 3782 CONECT 3781 3780 CONECT 3782 3777 3780 3783 CONECT 3783 3782 3784 3792 CONECT 3784 3783 3785 CONECT 3785 3784 3786 CONECT 3786 3785 3787 3792 CONECT 3787 3786 3788 3789 CONECT 3788 3787 CONECT 3789 3787 3790 CONECT 3790 3789 3791 CONECT 3791 3790 3792 CONECT 3792 3783 3786 3791 MASTER 271 0 1 11 12 0 0 6 3790 2 27 41 END