HEADER RNA BINDING PROTEIN 13-DEC-17 5YZ9 TITLE ZINC FINGER DOMAIN OF METTL3-METTL14 N6-METHYLADENOSINE TITLE 2 METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N6-ADENOSINE-METHYLTRANSFERASE CATALYTIC SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METHYLTRANSFERASE-LIKE PROTEIN 3,HMETTL3,N6-ADENOSINE- COMPND 5 METHYLTRANSFERASE 70 KDA SUBUNIT,MT-A70; COMPND 6 EC: 2.1.1.62; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: METTL3, MTA70; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA BINDING, ZINC FINGER, N6-METHYLADENOSINE METHYLTRANSFERASE, RNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 25 AUTHOR X.DONG,C.TANG,Z.GONG,P.YIN,J.B.HUANG REVDAT 3 01-MAY-24 5YZ9 1 REMARK REVDAT 2 27-MAR-19 5YZ9 1 JRNL REVDAT 1 28-MAR-18 5YZ9 0 JRNL AUTH J.HUANG,X.DONG,Z.GONG,L.Y.QIN,S.YANG,Y.L.ZHU,X.WANG,D.ZHANG, JRNL AUTH 2 T.ZOU,P.YIN,C.TANG JRNL TITL SOLUTION STRUCTURE OF THE RNA RECOGNITION DOMAIN OF JRNL TITL 2 METTL3-METTL14 N6-METHYLADENOSINE METHYLTRANSFERASE. JRNL REF PROTEIN CELL V. 10 272 2019 JRNL REFN ESSN 1674-8018 JRNL PMID 29542011 JRNL DOI 10.1007/S13238-018-0518-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006137. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 760 MMHG REMARK 210 SAMPLE CONTENTS : 20 MM PBS, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D H(CCO) REMARK 210 NH; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, CCPNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 960 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 265 REMARK 265 EXPERIMENTAL DETAILS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-25 REMARK 465 RES C SSSEQI REMARK 465 ALA A 256 REMARK 465 HIS A 257 REMARK 465 MET A 258 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 CYS A 276 -117.68 -95.29 REMARK 500 1 TYR A 278 -73.91 -99.62 REMARK 500 1 LYS A 281 -72.83 -75.64 REMARK 500 1 ASP A 289 52.85 -117.69 REMARK 500 1 PRO A 293 -115.48 -37.67 REMARK 500 1 CYS A 294 178.05 47.13 REMARK 500 1 LYS A 296 -10.90 59.42 REMARK 500 1 PHE A 299 125.68 -27.62 REMARK 500 1 HIS A 306 100.61 -59.41 REMARK 500 1 GLU A 309 -7.41 -58.00 REMARK 500 1 ASP A 313 -45.69 -173.97 REMARK 500 1 CYS A 314 -72.17 56.82 REMARK 500 1 LEU A 317 -18.12 -40.72 REMARK 500 1 ASN A 318 -69.21 -157.28 REMARK 500 1 PHE A 321 -119.58 57.03 REMARK 500 1 ASP A 324 -17.49 -42.24 REMARK 500 1 THR A 325 -93.20 -86.89 REMARK 500 1 LYS A 327 -135.16 -65.77 REMARK 500 1 HIS A 330 134.32 177.81 REMARK 500 1 SER A 336 165.04 -48.27 REMARK 500 1 GLU A 340 113.65 58.79 REMARK 500 1 SER A 350 48.93 -170.14 REMARK 500 2 CYS A 276 -115.60 -91.19 REMARK 500 2 TYR A 278 -73.60 -99.54 REMARK 500 2 LYS A 281 -71.99 -80.36 REMARK 500 2 ASP A 291 30.59 -90.08 REMARK 500 2 PRO A 293 -110.55 -37.90 REMARK 500 2 CYS A 294 178.55 47.49 REMARK 500 2 LYS A 296 -25.18 66.60 REMARK 500 2 PHE A 299 130.07 -28.59 REMARK 500 2 HIS A 306 98.58 -60.90 REMARK 500 2 SER A 315 50.50 -157.26 REMARK 500 2 PHE A 316 -18.13 -41.53 REMARK 500 2 ASN A 318 -73.30 -153.56 REMARK 500 2 PHE A 321 -116.98 55.61 REMARK 500 2 ASP A 324 -15.13 -42.80 REMARK 500 2 THR A 325 -93.38 -90.04 REMARK 500 2 LYS A 327 -134.34 -69.37 REMARK 500 2 HIS A 330 144.99 175.97 REMARK 500 2 ASP A 338 -45.60 -166.97 REMARK 500 2 GLU A 340 69.25 -68.46 REMARK 500 2 PRO A 342 169.35 -39.60 REMARK 500 2 SER A 350 10.53 -168.32 REMARK 500 3 CYS A 276 -113.49 -90.86 REMARK 500 3 TYR A 278 -74.39 -100.94 REMARK 500 3 LYS A 281 -72.25 -79.69 REMARK 500 3 PRO A 293 -111.73 -37.41 REMARK 500 3 CYS A 294 177.78 49.03 REMARK 500 3 LYS A 296 -31.82 65.72 REMARK 500 3 HIS A 298 160.43 -46.96 REMARK 500 REMARK 500 THIS ENTRY HAS 566 RAMACHANDRAN OUTLIERS. 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 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 276 SG REMARK 620 2 CYS A 284 SG 116.0 REMARK 620 3 CYS A 294 SG 116.1 116.1 REMARK 620 4 HIS A 298 NE2 101.6 101.5 101.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 314 SG REMARK 620 2 CYS A 320 SG 116.1 REMARK 620 3 CYS A 326 SG 116.0 116.1 REMARK 620 4 HIS A 330 NE2 101.6 101.6 101.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 802 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36143 RELATED DB: BMRB REMARK 900 ZINC FINGER DOMAIN OF METTL3-METTL14 N6-METHYLADENOSINE REMARK 900 METHYLTRANSFERASE DBREF 5YZ9 A 259 357 UNP Q86U44 MTA70_HUMAN 259 357 SEQADV 5YZ9 ALA A 256 UNP Q86U44 EXPRESSION TAG SEQADV 5YZ9 HIS A 257 UNP Q86U44 EXPRESSION TAG SEQADV 5YZ9 MET A 258 UNP Q86U44 EXPRESSION TAG SEQADV 5YZ9 SER A 336 UNP Q86U44 CYS 336 ENGINEERED MUTATION SEQRES 1 A 102 ALA HIS MET SER ILE VAL GLU LYS PHE ARG SER ARG GLY SEQRES 2 A 102 ARG ALA GLN VAL GLN GLU PHE CYS ASP TYR GLY THR LYS SEQRES 3 A 102 GLU GLU CYS MET LYS ALA SER ASP ALA ASP ARG PRO CYS SEQRES 4 A 102 ARG LYS LEU HIS PHE ARG ARG ILE ILE ASN LYS HIS THR SEQRES 5 A 102 ASP GLU SER LEU GLY ASP CYS SER PHE LEU ASN THR CYS SEQRES 6 A 102 PHE HIS MET ASP THR CYS LYS TYR VAL HIS TYR GLU ILE SEQRES 7 A 102 ASP ALA SER MET ASP SER GLU ALA PRO GLY SER LYS ASP SEQRES 8 A 102 HIS THR PRO SER GLN GLU LEU ALA LEU THR GLN HET ZN A 801 1 HET ZN A 802 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 ILE A 260 GLY A 268 1 9 HELIX 2 AA2 ARG A 269 PHE A 275 5 7 HELIX 3 AA3 LYS A 281 ASP A 289 1 9 SHEET 1 AA1 2 ARG A 300 ILE A 302 0 SHEET 2 AA1 2 GLU A 332 ASP A 334 -1 O GLU A 332 N ILE A 302 LINK SG CYS A 276 ZN ZN A 801 1555 1555 2.35 LINK SG CYS A 284 ZN ZN A 801 1555 1555 2.35 LINK SG CYS A 294 ZN ZN A 801 1555 1555 2.35 LINK NE2 HIS A 298 ZN ZN A 801 1555 1555 2.15 LINK SG CYS A 314 ZN ZN A 802 1555 1555 2.35 LINK SG CYS A 320 ZN ZN A 802 1555 1555 2.35 LINK SG CYS A 326 ZN ZN A 802 1555 1555 2.35 LINK NE2 HIS A 330 ZN ZN A 802 1555 1555 2.15 SITE 1 AC1 4 CYS A 276 CYS A 284 CYS A 294 HIS A 298 SITE 1 AC2 4 CYS A 314 CYS A 320 CYS A 326 HIS A 330 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 MODEL 1