HEADER RNA BINDING PROTEIN 19-SEP-14 4RDN TITLE STRUCTURE OF YTH-YTHDF2 IN COMPLEX WITH M6A COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING FAMILY PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 408-552; COMPND 5 SYNONYM: CLL-ASSOCIATED ANTIGEN KW-14, HIGH-GLUCOSE-REGULATED PROTEIN COMPND 6 8, RENAL CARCINOMA ANTIGEN NY-REN-2; COMPND 7 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: YTHDF2, HGRG8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS M6A METHYLATED RNA BINDING, ATYPICAL BETA-PROPELLER, RNA BINDING, M6A KEYWDS 2 METHYLATED RNA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.D.LI,D.B.ZHAO,J.H.WU,Y.Y.SHI REVDAT 2 28-FEB-24 4RDN 1 REMARK SEQADV REVDAT 1 24-DEC-14 4RDN 0 JRNL AUTH F.LI,D.ZHAO,J.WU,Y.SHI JRNL TITL STRUCTURE OF THE YTH DOMAIN OF HUMAN YTHDF2 IN COMPLEX WITH JRNL TITL 2 AN M(6)A MONONUCLEOTIDE REVEALS AN AROMATIC CAGE FOR M(6)A JRNL TITL 3 RECOGNITION. JRNL REF CELL RES. V. 24 1490 2014 JRNL REFN ISSN 1001-0602 JRNL PMID 25412658 JRNL DOI 10.1038/CR.2014.153 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23209 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1247 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1704 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2416 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.218 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.198 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.553 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2553 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2353 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3455 ; 1.121 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5397 ; 0.725 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 299 ; 6.211 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;29.140 ;23.516 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 434 ;15.311 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;14.570 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2881 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 650 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1193 ; 1.184 ; 2.651 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1192 ; 1.181 ; 2.650 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1490 ; 2.030 ; 3.967 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4RDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087215. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 69.914 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.53500 REMARK 200 R SYM FOR SHELL (I) : 0.53500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM TARTRATE, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE, PH 5.6, 2M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.65333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.82667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.74000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.91333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 94.56667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 386 REMARK 465 GLY A 387 REMARK 465 SER A 388 REMARK 465 SER A 389 REMARK 465 TYR A 390 REMARK 465 HIS A 391 REMARK 465 HIS A 392 REMARK 465 HIS A 393 REMARK 465 HIS A 394 REMARK 465 HIS A 395 REMARK 465 HIS A 396 REMARK 465 SER A 397 REMARK 465 SER A 398 REMARK 465 GLY A 399 REMARK 465 HIS A 549 REMARK 465 THR A 550 REMARK 465 THR A 551 REMARK 465 SER A 552 REMARK 465 MET B 386 REMARK 465 GLY B 387 REMARK 465 SER B 388 REMARK 465 SER B 389 REMARK 465 TYR B 390 REMARK 465 HIS B 391 REMARK 465 HIS B 392 REMARK 465 HIS B 393 REMARK 465 HIS B 394 REMARK 465 HIS B 395 REMARK 465 HIS B 396 REMARK 465 SER B 397 REMARK 465 SER B 398 REMARK 465 GLY B 399 REMARK 465 GLU B 400 REMARK 465 HIS B 549 REMARK 465 THR B 550 REMARK 465 THR B 551 REMARK 465 SER B 552 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 A 408 CG CD CE NZ REMARK 470 LYS A 548 CG CD CE NZ REMARK 470 LYS B 408 CG CD CE NZ REMARK 470 TYR B 418 OH REMARK 470 LYS B 548 CG CD CE NZ 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 HIS A 406 -11.62 75.57 REMARK 500 SER A 434 -167.74 -109.67 REMARK 500 ASP A 489 46.18 -95.30 REMARK 500 SER B 434 -167.65 -109.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6MD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6MD B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RDO RELATED DB: PDB DBREF 4RDN A 408 552 UNP Q9Y5A9 YTHD2_HUMAN 408 552 DBREF 4RDN B 408 552 UNP Q9Y5A9 YTHD2_HUMAN 408 552 SEQADV 4RDN MET A 386 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLY A 387 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER A 388 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER A 389 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN TYR A 390 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 391 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 392 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 393 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 394 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 395 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 396 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER A 397 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER A 398 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLY A 399 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLU A 400 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN ASN A 401 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN LEU A 402 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN TYR A 403 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN PHE A 404 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLN A 405 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS A 406 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN MET A 407 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN MET B 386 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLY B 387 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER B 388 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER B 389 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN TYR B 390 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 391 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 392 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 393 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 394 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 395 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 396 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER B 397 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN SER B 398 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLY B 399 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLU B 400 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN ASN B 401 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN LEU B 402 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN TYR B 403 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN PHE B 404 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN GLN B 405 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN HIS B 406 UNP Q9Y5A9 EXPRESSION TAG SEQADV 4RDN MET B 407 UNP Q9Y5A9 EXPRESSION TAG SEQRES 1 A 167 MET GLY SER SER TYR HIS HIS HIS HIS HIS HIS SER SER SEQRES 2 A 167 GLY GLU ASN LEU TYR PHE GLN HIS MET LYS HIS GLY ARG SEQRES 3 A 167 VAL PHE ILE ILE LYS SER TYR SER GLU ASP ASP ILE HIS SEQRES 4 A 167 ARG SER ILE LYS TYR ASN ILE TRP CYS SER THR GLU HIS SEQRES 5 A 167 GLY ASN LYS ARG LEU ASP ALA ALA TYR ARG SER MET ASN SEQRES 6 A 167 GLY LYS GLY PRO VAL TYR LEU LEU PHE SER VAL ASN GLY SEQRES 7 A 167 SER GLY HIS PHE CYS GLY VAL ALA GLU MET LYS SER ALA SEQRES 8 A 167 VAL ASP TYR ASN THR CYS ALA GLY VAL TRP SER GLN ASP SEQRES 9 A 167 LYS TRP LYS GLY ARG PHE ASP VAL ARG TRP ILE PHE VAL SEQRES 10 A 167 LYS ASP VAL PRO ASN SER GLN LEU ARG HIS ILE ARG LEU SEQRES 11 A 167 GLU ASN ASN GLU ASN LYS PRO VAL THR ASN SER ARG ASP SEQRES 12 A 167 THR GLN GLU VAL PRO LEU GLU LYS ALA LYS GLN VAL LEU SEQRES 13 A 167 LYS ILE ILE ALA SER TYR LYS HIS THR THR SER SEQRES 1 B 167 MET GLY SER SER TYR HIS HIS HIS HIS HIS HIS SER SER SEQRES 2 B 167 GLY GLU ASN LEU TYR PHE GLN HIS MET LYS HIS GLY ARG SEQRES 3 B 167 VAL PHE ILE ILE LYS SER TYR SER GLU ASP ASP ILE HIS SEQRES 4 B 167 ARG SER ILE LYS TYR ASN ILE TRP CYS SER THR GLU HIS SEQRES 5 B 167 GLY ASN LYS ARG LEU ASP ALA ALA TYR ARG SER MET ASN SEQRES 6 B 167 GLY LYS GLY PRO VAL TYR LEU LEU PHE SER VAL ASN GLY SEQRES 7 B 167 SER GLY HIS PHE CYS GLY VAL ALA GLU MET LYS SER ALA SEQRES 8 B 167 VAL ASP TYR ASN THR CYS ALA GLY VAL TRP SER GLN ASP SEQRES 9 B 167 LYS TRP LYS GLY ARG PHE ASP VAL ARG TRP ILE PHE VAL SEQRES 10 B 167 LYS ASP VAL PRO ASN SER GLN LEU ARG HIS ILE ARG LEU SEQRES 11 B 167 GLU ASN ASN GLU ASN LYS PRO VAL THR ASN SER ARG ASP SEQRES 12 B 167 THR GLN GLU VAL PRO LEU GLU LYS ALA LYS GLN VAL LEU SEQRES 13 B 167 LYS ILE ILE ALA SER TYR LYS HIS THR THR SER HET 6MD A 601 20 HET SO4 A 602 5 HET SO4 A 603 5 HET 6MD B 601 20 HET SO4 B 602 5 HET SO4 B 603 5 HETNAM 6MD N-METHYLADENOSINE HETNAM SO4 SULFATE ION FORMUL 3 6MD 2(C11 H15 N5 O4) FORMUL 4 SO4 4(O4 S 2-) FORMUL 9 HOH *233(H2 O) HELIX 1 1 SER A 419 ASN A 430 1 12 HELIX 2 2 THR A 435 ASN A 450 1 16 HELIX 3 3 SER A 508 LEU A 510 5 3 HELIX 4 4 PRO A 522 SER A 526 5 5 HELIX 5 5 PRO A 533 TYR A 547 1 15 HELIX 6 6 SER B 419 ASN B 430 1 12 HELIX 7 7 THR B 435 ASN B 450 1 16 HELIX 8 8 SER B 508 LEU B 510 5 3 HELIX 9 9 PRO B 522 SER B 526 5 5 HELIX 10 10 PRO B 533 TYR B 547 1 15 SHEET 1 A 6 ILE A 431 TRP A 432 0 SHEET 2 A 6 PHE A 495 PRO A 506 -1 O PHE A 495 N TRP A 432 SHEET 3 A 6 HIS A 466 MET A 473 -1 N VAL A 470 O ILE A 500 SHEET 4 A 6 VAL A 455 VAL A 461 -1 N LEU A 457 O ALA A 471 SHEET 5 A 6 ARG A 411 SER A 417 1 N PHE A 413 O LEU A 458 SHEET 6 A 6 GLU A 531 VAL A 532 -1 O VAL A 532 N VAL A 412 SHEET 1 B 6 ILE B 431 TRP B 432 0 SHEET 2 B 6 PHE B 495 PRO B 506 -1 O PHE B 495 N TRP B 432 SHEET 3 B 6 HIS B 466 MET B 473 -1 N VAL B 470 O ILE B 500 SHEET 4 B 6 VAL B 455 VAL B 461 -1 N LEU B 457 O ALA B 471 SHEET 5 B 6 ARG B 411 SER B 417 1 N PHE B 413 O LEU B 458 SHEET 6 B 6 GLU B 531 VAL B 532 -1 O VAL B 532 N VAL B 412 SITE 1 AC1 16 LYS A 416 SER A 417 TYR A 418 ASP A 422 SITE 2 AC1 16 TRP A 432 CYS A 433 THR A 435 ASN A 462 SITE 3 AC1 16 TRP A 486 LYS A 490 TRP A 491 ASP A 528 SITE 4 AC1 16 HOH A 706 HOH A 715 HOH A 788 HOH A 810 SITE 1 AC2 2 GLU A 436 HIS A 437 SITE 1 AC3 8 LYS A 416 VAL A 461 GLY A 463 SER A 464 SITE 2 AC3 8 GLY A 465 ASN A 507 HOH A 785 HOH A 803 SITE 1 AC4 14 LYS B 416 SER B 417 TYR B 418 ASP B 422 SITE 2 AC4 14 TRP B 432 CYS B 433 ASN B 462 TRP B 486 SITE 3 AC4 14 TRP B 491 ASP B 528 HOH B 705 HOH B 707 SITE 4 AC4 14 HOH B 771 HOH B 796 SITE 1 AC5 3 THR B 435 GLU B 436 HIS B 437 SITE 1 AC6 8 HOH A 792 LYS B 416 VAL B 461 GLY B 463 SITE 2 AC6 8 SER B 464 GLY B 465 ASN B 507 THR B 524 CRYST1 80.730 80.730 113.480 90.00 90.00 120.00 P 65 12 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 0.012387 0.007152 0.000000 0.00000 SCALE2 0.000000 0.014303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008812 0.00000