PDB Short entry for 4RCJ HEADER RNA BINDING PROTEIN/RNA 16-SEP-14 4RCJ TITLE CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN IN COMPLEX WITH 5MER M6A RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING FAMILY PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 365-554; COMPND 5 SYNONYM: DERMATOMYOSITIS ASSOCIATED WITH CANCER PUTATIVE AUTOANTIGEN COMPND 6 1, DACA-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3'); COMPND 10 CHAIN: B; COMPND 11 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: YTHDF1, C20ORF21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, RNA BINDING KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.TEMPEL,C.XU,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 4 20-SEP-23 4RCJ 1 SEQADV SEQRES LINK REVDAT 3 21-OCT-15 4RCJ 1 JRNL REVDAT 2 09-SEP-15 4RCJ 1 JRNL REVDAT 1 12-NOV-14 4RCJ 0 JRNL AUTH C.XU,K.LIU,H.AHMED,P.LOPPNAU,M.SCHAPIRA,J.MIN JRNL TITL STRUCTURAL BASIS FOR THE DISCRIMINATIVE RECOGNITION OF JRNL TITL 2 N6-METHYLADENOSINE RNA BY THE HUMAN YT521-B HOMOLOGY DOMAIN JRNL TITL 3 FAMILY OF PROTEINS. JRNL REF J.BIOL.CHEM. V. 290 24902 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26318451 JRNL DOI 10.1074/JBC.M115.680389 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 23124 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1164 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1519 REMARK 3 NUCLEIC ACID ATOMS : 91 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : 0.38000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.042 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARP/WARP WAS USED IN DENSITY REMARK 3 IMPROVEMENT MODE AFTER MOLECULAR REPLACEMENT. JLIGAND WAS USED REMARK 3 FOR PREPARATION OF NUCLEOTIDE LINK RESTRAINT TARGETS. COOT WAS REMARK 3 USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS REMARK 3 EVALUATED WITH MOLPROBITY. WEAK ELECTRON DENSITY NEAR THE 3'-END REMARK 3 OF THE MODELED OLIGONUCLEOTIDE SUGGESTS THE PRESENCE OF AN REMARK 3 ADDITIONAL NUCLEOTIDE. REMARK 4 REMARK 4 4RCJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791829 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.6 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: PDB ENTRY 4RCI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-3350, 0.2 M SODIUM CHLORIDE, REMARK 280 0.1 M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 20.01450 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 364 REMARK 465 ARG A 553 REMARK 465 GLN A 554 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 GLU A 381 CG CD OE1 OE2 REMARK 470 LYS A 387 CD CE NZ REMARK 470 SER A 430 OG REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 LYS A 527 CD CE NZ REMARK 470 GLU A 547 CD OE1 OE2 REMARK 470 LYS A 551 CD CE NZ REMARK 470 GLU A 552 CG CD OE1 OE2 REMARK 470 U B 5 C4' O4' C3' O3' C2' O2' C1' REMARK 470 U B 5 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U B 5 C6 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 G B 1 C5' - C4' - O4' ANGL. DEV. = 6.8 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 SER A 376 69.77 -109.16 REMARK 500 SER A 413 -163.17 -112.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RCI RELATED DB: PDB REMARK 900 RELATED ID: 4RCM RELATED DB: PDB DBREF 4RCJ A 365 554 UNP Q9BYJ9 YTHD1_HUMAN 365 554 DBREF 4RCJ B 1 5 PDB 4RCJ 4RCJ 1 5 SEQADV 4RCJ GLY A 364 UNP Q9BYJ9 EXPRESSION TAG SEQRES 1 A 191 GLY HIS PRO VAL LEU GLU LYS LEU LYS ALA ALA HIS SER SEQRES 2 A 191 TYR ASN PRO LYS GLU PHE GLU TRP ASN LEU LYS SER GLY SEQRES 3 A 191 ARG VAL PHE ILE ILE LYS SER TYR SER GLU ASP ASP ILE SEQRES 4 A 191 HIS ARG SER ILE LYS TYR SER ILE TRP CYS SER THR GLU SEQRES 5 A 191 HIS GLY ASN LYS ARG LEU ASP SER ALA PHE ARG CYS MET SEQRES 6 A 191 SER SER LYS GLY PRO VAL TYR LEU LEU PHE SER VAL ASN SEQRES 7 A 191 GLY SER GLY HIS PHE CYS GLY VAL ALA GLU MET LYS SER SEQRES 8 A 191 PRO VAL ASP TYR GLY THR SER ALA GLY VAL TRP SER GLN SEQRES 9 A 191 ASP LYS TRP LYS GLY LYS PHE ASP VAL GLN TRP ILE PHE SEQRES 10 A 191 VAL LYS ASP VAL PRO ASN ASN GLN LEU ARG HIS ILE ARG SEQRES 11 A 191 LEU GLU ASN ASN ASP ASN LYS PRO VAL THR ASN SER ARG SEQRES 12 A 191 ASP THR GLN GLU VAL PRO LEU GLU LYS ALA LYS GLN VAL SEQRES 13 A 191 LEU LYS ILE ILE SER SER TYR LYS HIS THR THR SER ILE SEQRES 14 A 191 PHE ASP ASP PHE ALA HIS TYR GLU LYS ARG GLN GLU GLU SEQRES 15 A 191 GLU GLU VAL VAL ARG LYS GLU ARG GLN SEQRES 1 B 5 G G 6MZ C U MODRES 4RCJ 6MZ B 3 A N6-METHYLADENOSINE-5'-MONOPHOSPHATE HET 6MZ B 3 23 HET UNX A 601 1 HET UNX A 602 1 HET UNX A 603 1 HET UNX A 604 1 HET UNX A 605 1 HET UNX A 606 1 HET UNX A 607 1 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 6MZ C11 H16 N5 O7 P FORMUL 3 UNX 7(X) FORMUL 10 HOH *177(H2 O) HELIX 1 1 HIS A 365 HIS A 375 1 11 HELIX 2 2 SER A 398 SER A 409 1 12 HELIX 3 3 THR A 414 SER A 429 1 16 HELIX 4 4 ASN A 487 LEU A 489 5 3 HELIX 5 5 LEU A 494 ASP A 498 5 5 HELIX 6 6 PRO A 501 SER A 505 5 5 HELIX 7 7 PRO A 512 TYR A 526 1 15 HELIX 8 8 SER A 531 ASP A 534 5 4 HELIX 9 9 ASP A 535 LYS A 551 1 17 SHEET 1 A 6 ILE A 410 TRP A 411 0 SHEET 2 A 6 PHE A 474 PRO A 485 -1 O PHE A 474 N TRP A 411 SHEET 3 A 6 HIS A 445 MET A 452 -1 N VAL A 449 O ILE A 479 SHEET 4 A 6 VAL A 434 VAL A 440 -1 N LEU A 436 O ALA A 450 SHEET 5 A 6 ARG A 390 SER A 396 1 N ILE A 394 O LEU A 437 SHEET 6 A 6 GLU A 510 VAL A 511 -1 O VAL A 511 N VAL A 391 LINK O3' G B 2 P 6MZ B 3 1555 1555 1.57 LINK O3' 6MZ B 3 P C B 4 1555 1555 1.66 CRYST1 37.648 40.029 59.308 90.00 93.41 90.00 P 1 21 1 2 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 0.026562 0.000000 0.001583 0.00000 SCALE2 0.000000 0.024982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016891 0.00000