HEADER RNA BINDING PROTEIN 07-JUL-20 6ZOT TITLE CRYSTAL STRUCTURE OF YTHDF3 YTH DOMAIN IN COMPLEX WITH M6A RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING FAMILY PROTEIN 3; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA; COMPND 7 CHAIN: C; COMPND 8 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: YTHDF3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS YTHDF3, M6A, COMPLEX, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.BEDI,A.CAFLISCH REVDAT 4 31-JAN-24 6ZOT 1 REMARK REVDAT 3 13-JAN-21 6ZOT 1 JRNL REVDAT 2 04-NOV-20 6ZOT 1 JRNL REVDAT 1 28-OCT-20 6ZOT 0 JRNL AUTH Y.LI,R.K.BEDI,E.V.MOROZ-OMORI,A.CAFLISCH JRNL TITL STRUCTURAL AND DYNAMIC INSIGHTS INTO REDUNDANT FUNCTION OF JRNL TITL 2 YTHDF PROTEINS. JRNL REF J.CHEM.INF.MODEL. V. 60 5932 2020 JRNL REFN ESSN 1549-960X JRNL PMID 33073985 JRNL DOI 10.1021/ACS.JCIM.0C01029 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.0600 - 4.2800 1.00 2693 143 0.1977 0.2532 REMARK 3 2 4.2800 - 3.4000 1.00 2551 134 0.1904 0.2234 REMARK 3 3 3.4000 - 2.9700 1.00 2506 132 0.2325 0.2981 REMARK 3 4 2.9700 - 2.7000 0.99 2507 132 0.2980 0.4200 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 2795 REMARK 3 ANGLE : 1.445 3805 REMARK 3 CHIRALITY : 0.093 408 REMARK 3 PLANARITY : 0.009 480 REMARK 3 DIHEDRAL : 18.810 388 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZOT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10844 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.95 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4RCI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M TRIS PH8, 0.2M REMARK 280 NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.37500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.37500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.37500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.37500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.37500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.37500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.37500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 649 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 650 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 101 LIES ON A SPECIAL POSITION. 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 B 373 REMARK 465 GLY B 374 REMARK 465 HIS B 375 REMARK 465 HIS B 376 REMARK 465 HIS B 377 REMARK 465 HIS B 378 REMARK 465 HIS B 379 REMARK 465 HIS B 380 REMARK 465 SER B 381 REMARK 465 SER B 382 REMARK 465 GLY B 383 REMARK 465 ARG B 384 REMARK 465 GLU B 385 REMARK 465 ASN B 386 REMARK 465 LEU B 387 REMARK 465 TYR B 388 REMARK 465 PHE B 389 REMARK 465 GLN B 390 REMARK 465 GLY B 391 REMARK 465 MET A 373 REMARK 465 GLY A 374 REMARK 465 HIS A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 SER A 381 REMARK 465 SER A 382 REMARK 465 GLY A 383 REMARK 465 ARG A 384 REMARK 465 GLU A 385 REMARK 465 ASN A 386 REMARK 465 LEU A 387 REMARK 465 TYR A 388 REMARK 465 PHE A 389 REMARK 465 GLN A 390 REMARK 465 GLY A 391 REMARK 465 HIS A 392 REMARK 465 PRO A 393 REMARK 465 VAL A 394 REMARK 465 LEU A 395 REMARK 465 GLU A 396 REMARK 465 LYS A 397 REMARK 465 LEU A 398 REMARK 465 LYS A 399 REMARK 465 ALA A 400 REMARK 465 ILE A 401 REMARK 465 ASN A 402 REMARK 465 TYR A 488 REMARK 465 ALA A 489 REMARK 465 GLY A 490 REMARK 465 VAL A 491 REMARK 465 TRP A 492 REMARK 465 SER A 493 REMARK 465 GLN A 494 REMARK 465 ASP A 495 REMARK 465 LYS A 496 REMARK 465 TRP A 497 REMARK 465 PHE A 563 REMARK 465 ALA A 564 REMARK 465 HIS A 565 REMARK 465 TYR A 566 REMARK 465 GLU A 567 REMARK 465 LYS A 568 REMARK 465 ARG A 569 REMARK 465 GLN A 570 REMARK 465 GLU A 571 REMARK 465 G C 1 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 LYS B 397 CD CE NZ REMARK 470 ILE B 401 CG1 CG2 CD1 REMARK 470 LYS B 407 CG CD CE NZ REMARK 470 ASP B 410 CG OD1 OD2 REMARK 470 LYS B 414 CG CD CE NZ REMARK 470 LYS B 446 CG CD CE NZ REMARK 470 LYS B 458 CG CD CE NZ REMARK 470 LYS B 504 CD CE NZ REMARK 470 LEU B 516 CG CD1 CD2 REMARK 470 ARG B 517 CD NE CZ NH1 NH2 REMARK 470 LYS B 548 CG CD CE NZ REMARK 470 LYS B 554 CD CE NZ REMARK 470 LYS A 407 CE NZ REMARK 470 ASP A 408 CG OD1 OD2 REMARK 470 LYS A 414 CG CD CE NZ REMARK 470 TYR A 424 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 LYS A 504 CD CE NZ REMARK 470 LYS A 548 CG CD CE NZ REMARK 470 ASP A 562 CG OD1 OD2 REMARK 470 G C 2 P OP1 OP2 O5' 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 O HIS A 472 O HOH A 601 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 650 O HOH B 650 8555 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE B 409 CB - CA - C ANGL. DEV. = -15.6 DEGREES REMARK 500 PHE B 409 N - CA - CB ANGL. DEV. = 12.1 DEGREES REMARK 500 PHE B 409 CB - CG - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG B 417 CG - CD - NE ANGL. DEV. = 19.0 DEGREES REMARK 500 ARG B 417 NE - CZ - NH1 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG B 417 NE - CZ - NH2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG B 447 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG B 447 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 447 NE - CZ - NH2 ANGL. DEV. = -9.3 DEGREES REMARK 500 G C 2 O4' - C1' - N9 ANGL. DEV. = 11.6 DEGREES REMARK 500 C C 4 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES REMARK 500 C C 4 N3 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 C C 4 C5 - C4 - N4 ANGL. DEV. = -5.1 DEGREES REMARK 500 C C 4 C6 - N1 - C1' ANGL. DEV. = -9.3 DEGREES REMARK 500 U C 5 N3 - C4 - O4 ANGL. DEV. = 5.3 DEGREES REMARK 500 U C 5 C5 - C4 - O4 ANGL. DEV. = -5.3 DEGREES 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 TRP B 411 2.08 -63.20 REMARK 500 ASN B 412 -92.39 56.49 REMARK 500 LEU B 413 -139.20 41.18 REMARK 500 LYS B 414 22.13 44.75 REMARK 500 ASN B 415 15.16 -176.10 REMARK 500 ASN B 456 -92.49 56.87 REMARK 500 ALA B 489 -52.64 64.69 REMARK 500 LYS B 500 140.06 -176.11 REMARK 500 ILE B 506 -70.67 -111.10 REMARK 500 ASN B 524 -126.44 -92.92 REMARK 500 ASP B 525 58.00 -119.40 REMARK 500 LEU B 540 -62.63 -29.84 REMARK 500 LYS A 414 -56.55 -28.85 REMARK 500 ASN A 456 44.61 38.82 REMARK 500 GLU A 522 5.36 -69.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE B 409 0.08 SIDE CHAIN REMARK 500 ARG B 447 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 651 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH B 652 DISTANCE = 10.01 ANGSTROMS REMARK 525 HOH A 647 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 648 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A 649 DISTANCE = 9.57 ANGSTROMS REMARK 525 HOH A 650 DISTANCE = 11.28 ANGSTROMS DBREF 6ZOT B 392 571 UNP Q7Z739 YTHD3_HUMAN 392 571 DBREF 6ZOT A 392 571 UNP Q7Z739 YTHD3_HUMAN 392 571 DBREF 6ZOT C 1 5 PDB 6ZOT 6ZOT 1 5 SEQADV 6ZOT MET B 373 UNP Q7Z739 INITIATING METHIONINE SEQADV 6ZOT GLY B 374 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS B 375 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS B 376 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS B 377 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS B 378 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS B 379 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS B 380 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT SER B 381 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT SER B 382 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLY B 383 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT ARG B 384 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLU B 385 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT ASN B 386 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT LEU B 387 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT TYR B 388 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT PHE B 389 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLN B 390 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLY B 391 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT MET A 373 UNP Q7Z739 INITIATING METHIONINE SEQADV 6ZOT GLY A 374 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS A 375 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS A 376 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS A 377 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS A 378 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS A 379 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT HIS A 380 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT SER A 381 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT SER A 382 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLY A 383 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT ARG A 384 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLU A 385 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT ASN A 386 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT LEU A 387 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT TYR A 388 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT PHE A 389 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLN A 390 UNP Q7Z739 EXPRESSION TAG SEQADV 6ZOT GLY A 391 UNP Q7Z739 EXPRESSION TAG SEQRES 1 B 199 MET GLY HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU SEQRES 2 B 199 ASN LEU TYR PHE GLN GLY HIS PRO VAL LEU GLU LYS LEU SEQRES 3 B 199 LYS ALA ILE ASN ASN TYR ASN PRO LYS ASP PHE ASP TRP SEQRES 4 B 199 ASN LEU LYS ASN GLY ARG VAL PHE ILE ILE LYS SER TYR SEQRES 5 B 199 SER GLU ASP ASP ILE HIS ARG SER ILE LYS TYR SER ILE SEQRES 6 B 199 TRP CYS SER THR GLU HIS GLY ASN LYS ARG LEU ASP ALA SEQRES 7 B 199 ALA TYR ARG SER LEU ASN GLY LYS GLY PRO LEU TYR LEU SEQRES 8 B 199 LEU PHE SER VAL ASN GLY SER GLY HIS PHE CYS GLY VAL SEQRES 9 B 199 ALA GLU MET LYS SER VAL VAL ASP TYR ASN ALA TYR ALA SEQRES 10 B 199 GLY VAL TRP SER GLN ASP LYS TRP LYS GLY LYS PHE GLU SEQRES 11 B 199 VAL LYS TRP ILE PHE VAL LYS ASP VAL PRO ASN ASN GLN SEQRES 12 B 199 LEU ARG HIS ILE ARG LEU GLU ASN ASN ASP ASN LYS PRO SEQRES 13 B 199 VAL THR ASN SER ARG ASP THR GLN GLU VAL PRO LEU GLU SEQRES 14 B 199 LYS ALA LYS GLN VAL LEU LYS ILE ILE ALA THR PHE LYS SEQRES 15 B 199 HIS THR THR SER ILE PHE ASP ASP PHE ALA HIS TYR GLU SEQRES 16 B 199 LYS ARG GLN GLU SEQRES 1 A 199 MET GLY HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU SEQRES 2 A 199 ASN LEU TYR PHE GLN GLY HIS PRO VAL LEU GLU LYS LEU SEQRES 3 A 199 LYS ALA ILE ASN ASN TYR ASN PRO LYS ASP PHE ASP TRP SEQRES 4 A 199 ASN LEU LYS ASN GLY ARG VAL PHE ILE ILE LYS SER TYR SEQRES 5 A 199 SER GLU ASP ASP ILE HIS ARG SER ILE LYS TYR SER ILE SEQRES 6 A 199 TRP CYS SER THR GLU HIS GLY ASN LYS ARG LEU ASP ALA SEQRES 7 A 199 ALA TYR ARG SER LEU ASN GLY LYS GLY PRO LEU TYR LEU SEQRES 8 A 199 LEU PHE SER VAL ASN GLY SER GLY HIS PHE CYS GLY VAL SEQRES 9 A 199 ALA GLU MET LYS SER VAL VAL ASP TYR ASN ALA TYR ALA SEQRES 10 A 199 GLY VAL TRP SER GLN ASP LYS TRP LYS GLY LYS PHE GLU SEQRES 11 A 199 VAL LYS TRP ILE PHE VAL LYS ASP VAL PRO ASN ASN GLN SEQRES 12 A 199 LEU ARG HIS ILE ARG LEU GLU ASN ASN ASP ASN LYS PRO SEQRES 13 A 199 VAL THR ASN SER ARG ASP THR GLN GLU VAL PRO LEU GLU SEQRES 14 A 199 LYS ALA LYS GLN VAL LEU LYS ILE ILE ALA THR PHE LYS SEQRES 15 A 199 HIS THR THR SER ILE PHE ASP ASP PHE ALA HIS TYR GLU SEQRES 16 A 199 LYS ARG GLN GLU SEQRES 1 C 5 G G 6MZ C U HET 6MZ C 3 23 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE FORMUL 3 6MZ C11 H16 N5 O7 P FORMUL 4 HOH *105(H2 O) HELIX 1 AA1 HIS B 392 ASN B 402 1 11 HELIX 2 AA2 SER B 425 SER B 436 1 12 HELIX 3 AA3 THR B 441 ASN B 456 1 16 HELIX 4 AA4 ASN B 514 LEU B 516 5 3 HELIX 5 AA5 PRO B 528 SER B 532 5 5 HELIX 6 AA6 PRO B 539 PHE B 553 1 15 HELIX 7 AA7 SER B 558 ASP B 561 5 4 HELIX 8 AA8 ASP B 562 ARG B 569 1 8 HELIX 9 AA9 ASN A 412 GLY A 416 5 5 HELIX 10 AB1 SER A 425 SER A 436 1 12 HELIX 11 AB2 THR A 441 ASN A 456 1 16 HELIX 12 AB3 ASN A 514 LEU A 516 5 3 HELIX 13 AB4 PRO A 528 SER A 532 5 5 HELIX 14 AB5 PRO A 539 PHE A 553 1 15 HELIX 15 AB6 SER A 558 ASP A 562 5 5 SHEET 1 AA1 6 ILE B 437 TRP B 438 0 SHEET 2 AA1 6 PHE B 501 PRO B 512 -1 O PHE B 501 N TRP B 438 SHEET 3 AA1 6 HIS B 472 MET B 479 -1 N PHE B 473 O VAL B 511 SHEET 4 AA1 6 LEU B 461 VAL B 467 -1 N LEU B 463 O ALA B 477 SHEET 5 AA1 6 ARG B 417 SER B 423 1 N PHE B 419 O TYR B 462 SHEET 6 AA1 6 GLU B 537 VAL B 538 -1 O VAL B 538 N VAL B 418 SHEET 1 AA2 6 ILE A 437 TRP A 438 0 SHEET 2 AA2 6 PHE A 501 PRO A 512 -1 O PHE A 501 N TRP A 438 SHEET 3 AA2 6 HIS A 472 MET A 479 -1 N PHE A 473 O VAL A 511 SHEET 4 AA2 6 LEU A 461 VAL A 467 -1 N PHE A 465 O CYS A 474 SHEET 5 AA2 6 ARG A 417 SER A 423 1 N ILE A 421 O LEU A 464 SHEET 6 AA2 6 GLN A 536 VAL A 538 -1 O GLN A 536 N ILE A 420 LINK O3' G C 2 P 6MZ C 3 1555 1555 1.62 LINK O3' 6MZ C 3 P C C 4 1555 1555 1.59 CRYST1 100.750 100.750 72.880 90.00 90.00 90.00 P 4 21 2 16 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 0.009926 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013721 0.00000