HEADER RNA BINDING PROTEIN/RNA 06-JUL-22 7YEX TITLE STRUCTURE OF MMIGF2BP3 IN COMPLEX WITH 8-MER RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR 2 MRNA-BINDING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGF2 MRNA-BINDING PROTEIN 3,IMP-3,MIMP-3,IGF-II MRNA-BINDING COMPND 5 PROTEIN 3,VICKZ FAMILY MEMBER 3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(P*CP*AP*CP*AP*CP*AP*CP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: IGF2BP3, VICKZ3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS IGF2BP3, IGF2BP, IMP3, RNA BINDING, M6A MODIFICATION, RNA BINDING KEYWDS 2 PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.J.LI,B.X.WU REVDAT 2 29-NOV-23 7YEX 1 REMARK REVDAT 1 12-JUL-23 7YEX 0 JRNL AUTH X.J.LI,B.X.WU JRNL TITL STRUCTURE OF MMIGF2BP3 IN COMPLEX WITH 8-MER RNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX-1.19.2-4158 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 13113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 668 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 2.1519 - 1.9977 0.87 0 0 0.2563 0.3020 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.43 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 1395 REMARK 3 ANGLE : 0.918 1913 REMARK 3 CHIRALITY : 0.057 219 REMARK 3 PLANARITY : 0.006 236 REMARK 3 DIHEDRAL : 15.647 841 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 7YEX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030774. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-21 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 : 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 : 13473 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.94300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.833 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: 7YEW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 20%W/V POLYETHYLENE REMARK 280 GLYCOL 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.09700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.72300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.09700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.72300 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 160 REMARK 465 ALA A 161 REMARK 465 C B 4 REMARK 465 A B 5 REMARK 465 C B 6 REMARK 465 A B 7 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 OE1 GLU A 69 O HOH A 201 2.19 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 MET A 1 53.50 -105.32 REMARK 500 LYS A 36 -148.65 -105.45 REMARK 500 ILE A 80 -94.69 -133.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YEX A 1 160 UNP Q9CPN8 IF2B3_MOUSE 1 160 DBREF 7YEX B 0 7 PDB 7YEX 7YEX 0 7 SEQADV 7YEX SER A 0 UNP Q9CPN8 EXPRESSION TAG SEQADV 7YEX ALA A 161 UNP Q9CPN8 EXPRESSION TAG SEQRES 1 A 162 SER MET ASN LYS LEU TYR ILE GLY ASN LEU SER ASP HIS SEQRES 2 A 162 ALA GLY PRO ALA ASP LEU GLU SER VAL PHE LYS ASP ALA SEQRES 3 A 162 LYS ILE PRO VAL ALA GLY PRO PHE LEU VAL LYS THR GLY SEQRES 4 A 162 TYR ALA PHE VAL ASP CYS PRO ASP GLU GLY TRP ALA LEU SEQRES 5 A 162 LYS ALA ILE GLU ALA LEU SER GLY LYS MET GLU LEU HIS SEQRES 6 A 162 GLY LYS PRO MET GLU VAL GLU HIS SER VAL PRO LYS ARG SEQRES 7 A 162 GLN ARG ILE ARG LYS LEU GLN ILE ARG ASN ILE PRO PRO SEQRES 8 A 162 HIS LEU GLN TRP GLU VAL LEU ASP SER LEU LEU VAL GLN SEQRES 9 A 162 TYR GLY VAL VAL GLU SER CYS GLU GLN VAL ASN THR ASP SEQRES 10 A 162 SER GLU THR ALA VAL VAL ASN VAL THR TYR SER SER LYS SEQRES 11 A 162 ASP GLN ALA ARG GLN ALA LEU ASP LYS LEU ASN GLY PHE SEQRES 12 A 162 GLN LEU GLU ASN PHE THR LEU LYS VAL ALA TYR ILE PRO SEQRES 13 A 162 ASP GLU THR ALA ALA ALA SEQRES 1 B 8 C A C A C A C A FORMUL 3 HOH *73(H2 O) HELIX 1 AA1 GLY A 14 ALA A 25 1 12 HELIX 2 AA2 ASP A 46 SER A 58 1 13 HELIX 3 AA3 PRO A 75 ARG A 79 5 5 HELIX 4 AA4 GLN A 93 VAL A 102 1 10 HELIX 5 AA5 SER A 128 ASN A 140 1 13 SHEET 1 AA1 4 LEU A 34 VAL A 35 0 SHEET 2 AA1 4 ALA A 40 ASP A 43 -1 O PHE A 41 N LEU A 34 SHEET 3 AA1 4 LYS A 3 GLY A 7 -1 N LEU A 4 O VAL A 42 SHEET 4 AA1 4 GLU A 69 HIS A 72 -1 O GLU A 71 N TYR A 5 SHEET 1 AA2 2 GLU A 62 LEU A 63 0 SHEET 2 AA2 2 LYS A 66 PRO A 67 -1 O LYS A 66 N LEU A 63 SHEET 1 AA3 4 VAL A 107 GLN A 112 0 SHEET 2 AA3 4 ALA A 120 TYR A 126 -1 O THR A 125 N GLU A 108 SHEET 3 AA3 4 LYS A 82 ILE A 88 -1 N ILE A 85 O VAL A 122 SHEET 4 AA3 4 LYS A 150 TYR A 153 -1 O LYS A 150 N ARG A 86 SHEET 1 AA4 2 GLN A 143 LEU A 144 0 SHEET 2 AA4 2 PHE A 147 THR A 148 -1 O PHE A 147 N LEU A 144 CRYST1 40.439 64.194 73.446 90.00 90.00 90.00 P 2 21 21 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 0.024729 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015578 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013615 0.00000