HEADER RNA BINDING PROTEIN/RNA 16-JUN-21 7F3K TITLE CRYSTAL STRUCTURE OF HUMAN YBX2 CSD IN COMPLEX WITH M5C RNA IN SPACE TITLE 2 GROUP P21212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: Y-BOX-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CONTRIN,DNA-BINDING PROTEIN C,DBPC,GERM CELL-SPECIFIC Y-BOX- COMPND 5 BINDING PROTEIN,MSY2 HOMOLOG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*UP*CP*AP*UP*(5MC)P*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: YBX2, CSDA3, MSY2; 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 COMPLEX, PROTEIN-RNA, YBX, COLD-SHOCK DOMAIN, RNA BINDING PROTEIN, KEYWDS 2 RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,Y.HUANG REVDAT 2 29-NOV-23 7F3K 1 REMARK REVDAT 1 22-JUN-22 7F3K 0 JRNL AUTH Y.ZHANG,Y.HUANG JRNL TITL CRYSTAL STRUCTURE OF HUMAN YBX2 CSD IN COMPLEX WITH M5C RNA JRNL TITL 2 IN SPACE GROUP P21212 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.76 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1591 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 33.6900 - 3.9200 1.00 1318 152 0.1434 0.1749 REMARK 3 2 3.9100 - 3.1100 1.00 1345 141 0.1360 0.1437 REMARK 3 3 3.1100 - 2.7200 1.00 1338 145 0.1527 0.1972 REMARK 3 4 2.7100 - 2.4700 1.00 1333 139 0.1693 0.1780 REMARK 3 5 2.4700 - 2.2900 1.00 1332 147 0.1485 0.1973 REMARK 3 6 2.2900 - 2.1600 1.00 1321 149 0.1472 0.1568 REMARK 3 7 2.1600 - 2.0500 1.00 1338 146 0.1342 0.1794 REMARK 3 8 2.0500 - 1.9600 1.00 1313 133 0.1419 0.1813 REMARK 3 9 1.9600 - 1.8800 1.00 1330 155 0.1390 0.1877 REMARK 3 10 1.8800 - 1.8200 1.00 1336 133 0.1439 0.1947 REMARK 3 11 1.8200 - 1.7600 0.99 1301 151 0.1528 0.2044 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) : 0.148 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.812 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.32 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 : 0.007 853 REMARK 3 ANGLE : 1.105 1179 REMARK 3 CHIRALITY : 0.051 132 REMARK 3 PLANARITY : 0.006 135 REMARK 3 DIHEDRAL : 26.936 161 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 7F3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022772. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8891 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10400 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: PHENIX REMARK 200 STARTING MODEL: 6A6J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 3.2 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -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 37.87450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.56750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.87450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.56750 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 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 ALA A 85 REMARK 465 ASP A 86 REMARK 465 LYS A 87 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 ND2 ASN A 159 O HOH A 301 2.09 REMARK 500 NE ARG A 132 O HOH A 302 2.14 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 A 367 O HOH A 367 2545 1.81 REMARK 500 O HOH A 396 O HOH B 127 1565 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6A6J RELATED DB: PDB REMARK 900 ZEBRAFISH YBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 6A6L RELATED DB: PDB REMARK 900 YBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTX RELATED DB: PDB REMARK 900 YBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTS RELATED DB: PDB REMARK 900 YBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTT RELATED DB: PDB REMARK 900 YBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTV RELATED DB: PDB REMARK 900 YBX1 COMPLEXED WITH RNA DBREF 7F3K A 85 177 UNP Q9Y2T7 YBOX2_HUMAN 85 177 DBREF 7F3K B 1 6 PDB 7F3K 7F3K 1 6 SEQADV 7F3K THR A 92 UNP Q9Y2T7 ILE 92 ENGINEERED MUTATION SEQADV 7F3K LYS A 93 UNP Q9Y2T7 GLN 93 ENGINEERED MUTATION SEQRES 1 A 93 ALA ASP LYS PRO VAL LEU ALA THR LYS VAL LEU GLY THR SEQRES 2 A 93 VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE SEQRES 3 A 93 ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN SEQRES 4 A 93 THR ALA ILE LYS ARG ASN ASN PRO ARG LYS PHE LEU ARG SEQRES 5 A 93 SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL SEQRES 6 A 93 GLU GLY GLU LYS GLY ALA GLU ALA THR ASN VAL THR GLY SEQRES 7 A 93 PRO GLY GLY VAL PRO VAL LYS GLY SER ARG TYR ALA PRO SEQRES 8 A 93 ASN ARG SEQRES 1 B 6 U C A U 5MC U HET 5MC B 5 21 HET SO4 A 201 5 HET SO4 A 202 5 HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 5MC C10 H16 N3 O8 P FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *125(H2 O) HELIX 1 AA1 THR A 124 ILE A 126 5 3 HELIX 2 AA2 GLY A 162 VAL A 166 5 5 SHEET 1 AA1 6 ALA A 91 ASN A 102 0 SHEET 2 AA1 6 TYR A 107 ARG A 112 -1 O TYR A 107 N ASN A 102 SHEET 3 AA1 6 ASP A 118 HIS A 122 -1 O VAL A 119 N ILE A 110 SHEET 4 AA1 6 ALA A 155 THR A 161 1 O ALA A 157 N PHE A 120 SHEET 5 AA1 6 THR A 143 GLU A 150 -1 N VAL A 149 O GLU A 156 SHEET 6 AA1 6 ALA A 91 ASN A 102 -1 N ALA A 91 O VAL A 148 LINK O3' U B 4 P 5MC B 5 1555 1555 1.60 LINK O3' 5MC B 5 P U B 6 1555 1555 1.60 CRYST1 75.749 33.135 33.693 90.00 90.00 90.00 P 21 21 2 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 0.013201 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029680 0.00000