HEADER RNA BINDING PROTEIN/RNA 09-NOV-15 5EN1 TITLE CRYSTAL STRUCTURE OF HNRNPA2B1 IN COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 12-195; COMPND 5 SYNONYM: HNRNP A2/B1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*GP*GP*AP*CP*UP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 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: HNRNPA2B1, HNRPA2B1; 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_TAXID: 9606 KEYWDS HNRNP, RRM, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.X.WU,S.C.SU,J.B.MA REVDAT 3 08-NOV-23 5EN1 1 REMARK REVDAT 2 07-FEB-18 5EN1 1 JRNL REMARK REVDAT 1 09-NOV-16 5EN1 0 JRNL AUTH B.X.WU,S.C.SU,D.P.PATIL,H.H.LIU,J.H.GAN,S.R.JAFFREY,J.B.MA JRNL TITL MOLECULAR BASIS FOR THE SPECIFIC AND MULTIVARIANT JRNL TITL 2 RECOGNITIONS OF RNA SUBSTRATES BY HUMAN HNRNP A2/B1 JRNL REF NAT COMMUN 2018 JRNL REFN ESSN 2041-1723 JRNL DOI 10.1038/S41467-017-02770-Z REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 5889 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 299 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) : 2.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 300 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1491 REMARK 3 NUCLEIC ACID ATOMS : 150 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.60000 REMARK 3 B22 (A**2) : 1.28000 REMARK 3 B33 (A**2) : -2.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.338 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.298 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.648 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1688 ; 0.011 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 1522 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2295 ; 1.615 ; 1.864 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3512 ; 1.417 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 183 ; 7.489 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;34.183 ;23.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 286 ;16.347 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.227 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 238 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1799 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 406 ; 0.002 ; 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): 735 ; 2.771 ; 4.157 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 734 ; 2.754 ; 4.154 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 917 ; 4.475 ; 6.219 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 918 ; 4.476 ; 6.225 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 953 ; 3.202 ; 4.835 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 952 ; 3.185 ; 4.826 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1379 ; 5.368 ; 7.130 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1838 ; 7.099 ;35.244 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1839 ; 7.100 ;35.293 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 REMARK 4 REMARK 4 5EN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6187 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 28.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: 1U1Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1M TRIS PH8.5, PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 61.31150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.31150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.19000 REMARK 290 SMTRY3 4 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: 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 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 LYS A 59 16.01 58.29 REMARK 500 LYS A 120 -126.18 60.10 REMARK 500 GLN A 148 -5.69 84.24 REMARK 500 ARG A 190 36.11 -81.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 5EN1 A 12 195 UNP P22626 ROA2_HUMAN 12 195 DBREF 5EN1 B 1 7 PDB 5EN1 5EN1 1 7 SEQRES 1 A 184 ARG LYS LYS ARG GLU LYS GLU GLN PHE ARG LYS LEU PHE SEQRES 2 A 184 ILE GLY GLY LEU SER PHE GLU THR THR GLU GLU SER LEU SEQRES 3 A 184 ARG ASN TYR TYR GLU GLN TRP GLY LYS LEU THR ASP CYS SEQRES 4 A 184 VAL VAL MET ARG ASP PRO ALA SER LYS ARG SER ARG GLY SEQRES 5 A 184 PHE GLY PHE VAL THR PHE SER SER MET ALA GLU VAL ASP SEQRES 6 A 184 ALA ALA MET ALA ALA ARG PRO HIS SER ILE ASP GLY ARG SEQRES 7 A 184 VAL VAL GLU PRO LYS ARG ALA VAL ALA ARG GLU GLU SER SEQRES 8 A 184 GLY LYS PRO GLY ALA HIS VAL THR VAL LYS LYS LEU PHE SEQRES 9 A 184 VAL GLY GLY ILE LYS GLU ASP THR GLU GLU HIS HIS LEU SEQRES 10 A 184 ARG ASP TYR PHE GLU GLU TYR GLY LYS ILE ASP THR ILE SEQRES 11 A 184 GLU ILE ILE THR ASP ARG GLN SER GLY LYS LYS ARG GLY SEQRES 12 A 184 PHE GLY PHE VAL THR PHE ASP ASP HIS ASP PRO VAL ASP SEQRES 13 A 184 LYS ILE VAL LEU GLN LYS TYR HIS THR ILE ASN GLY HIS SEQRES 14 A 184 ASN ALA GLU VAL ARG LYS ALA LEU SER ARG GLN GLU MET SEQRES 15 A 184 GLN GLU SEQRES 1 B 7 A G G A C U G FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 LYS A 17 PHE A 20 5 4 HELIX 2 AA2 THR A 33 GLU A 42 1 10 HELIX 3 AA3 SER A 71 ALA A 81 1 11 HELIX 4 AA4 ALA A 98 SER A 102 5 5 HELIX 5 AA5 GLU A 124 GLU A 133 1 10 HELIX 6 AA6 GLU A 134 GLY A 136 5 3 HELIX 7 AA7 ASP A 162 GLN A 172 1 11 HELIX 8 AA8 SER A 189 MET A 193 5 5 SHEET 1 AA1 5 LEU A 47 ARG A 54 0 SHEET 2 AA1 5 SER A 61 PHE A 69 -1 O ARG A 62 N MET A 53 SHEET 3 AA1 5 LYS A 22 GLY A 26 -1 N LEU A 23 O VAL A 67 SHEET 4 AA1 5 VAL A 90 ARG A 95 -1 O LYS A 94 N PHE A 24 SHEET 5 AA1 5 HIS A 84 SER A 85 -1 N HIS A 84 O VAL A 91 SHEET 1 AA2 5 ILE A 138 THR A 145 0 SHEET 2 AA2 5 LYS A 152 PHE A 160 -1 O THR A 159 N ASP A 139 SHEET 3 AA2 5 LYS A 113 GLY A 117 -1 N LEU A 114 O VAL A 158 SHEET 4 AA2 5 HIS A 180 LYS A 186 -1 O ARG A 185 N PHE A 115 SHEET 5 AA2 5 HIS A 175 ILE A 177 -1 N ILE A 177 O HIS A 180 CISPEP 1 ARG A 82 PRO A 83 0 5.88 CRYST1 122.623 46.380 37.516 90.00 96.02 90.00 C 1 2 1 4 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 0.008155 0.000000 0.000859 0.00000 SCALE2 0.000000 0.021561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026803 0.00000