PDB Short entry for 1WKW HEADER TRANSLATION/PROTEIN BINDING 10-JUN-04 1WKW TITLE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF EIF4E-M7GPPPA-4EBP1 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 27-217; COMPND 5 SYNONYM: EIF4E, EIF-4E, MRNA CAP-BINDING PROTEIN, EIF-4F 25 KDA COMPND 6 SUBUNIT; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E BINDING PROTEIN COMPND 10 1; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 47-66; COMPND 13 SYNONYM: 4E BINDING PROTEIN 1, 4E-BP1, EIF4E-BINDING PROTEIN 1, PHAS- COMPND 14 I; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSLATION, INITIATION FACTOR, CAP-BINDING PROTEIN, MRNA-CAP, KEYWDS 2 TRANSLATION-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.TOMOO,Y.MATSUSHITA,H.FUJISAKI,X.SHEN,H.MIYAGAWA,K.KITAMURA,K.MIURA, AUTHOR 2 T.ISHIDA REVDAT 5 13-MAR-24 1WKW 1 REMARK REVDAT 4 11-OCT-17 1WKW 1 REMARK REVDAT 3 24-FEB-09 1WKW 1 VERSN REVDAT 2 24-JAN-06 1WKW 1 JRNL REVDAT 1 10-JUN-05 1WKW 0 JRNL AUTH K.TOMOO,Y.MATSUSHITA,H.FUJISAKI,F.ABIKO,X.SHEN,T.TANIGUCHI, JRNL AUTH 2 H.MIYAGAWA,K.KITAMURA,K.MIURA,T.ISHIDA JRNL TITL STRUCTURAL BASIS FOR MRNA CAP-BINDING REGULATION OF JRNL TITL 2 EUKARYOTIC INITIATION FACTOR 4E BY 4E-BINDING PROTEIN, JRNL TITL 3 STUDIED BY SPECTROSCOPIC, X-RAY CRYSTAL STRUCTURAL, AND JRNL TITL 4 MOLECULAR DYNAMICS SIMULATION METHODS JRNL REF BIOCHIM.BIOPHYS.ACTA V.1753 191 2005 JRNL REFN ISSN 0006-3002 JRNL PMID 16271312 JRNL DOI 10.1016/J.BBAPAP.2005.07.023 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10130 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1163 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1735 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023688. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL24XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.836 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ISOPROPANOL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 19.18000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.77000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.59000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 VAL A 217 O 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 ASP A 51 -13.36 -156.43 REMARK 500 LYS A 52 38.41 34.25 REMARK 500 SER A 53 29.38 -161.17 REMARK 500 ILE A 63 -67.75 -102.42 REMARK 500 PHE A 66 149.79 -175.82 REMARK 500 ASP A 143 -152.51 54.48 REMARK 500 LYS A 206 -85.21 -78.60 REMARK 500 SER A 207 96.66 -165.36 REMARK 500 SER A 209 5.29 51.60 REMARK 500 THR A 210 113.98 60.76 REMARK 500 THR B 50 -78.41 -58.73 REMARK 500 ARG B 51 164.06 62.37 REMARK 500 ARG B 56 -72.25 -44.11 REMARK 500 CYS B 62 18.25 -63.64 REMARK 500 ARG B 63 -168.19 59.07 REMARK 500 ASN B 64 145.97 84.83 REMARK 500 SER B 65 93.53 19.08 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 GTA A 1000 DBREF 1WKW A 27 217 UNP P06730 IF4E_HUMAN 27 217 DBREF 1WKW B 47 66 UNP Q13541 4EBP1_HUMAN 47 66 SEQRES 1 A 191 GLU VAL ALA ASN PRO GLU HIS TYR ILE LYS HIS PRO LEU SEQRES 2 A 191 GLN ASN ARG TRP ALA LEU TRP PHE PHE LYS ASN ASP LYS SEQRES 3 A 191 SER LYS THR TRP GLN ALA ASN LEU ARG LEU ILE SER LYS SEQRES 4 A 191 PHE ASP THR VAL GLU ASP PHE TRP ALA LEU TYR ASN HIS SEQRES 5 A 191 ILE GLN LEU SER SER ASN LEU MET PRO GLY CYS ASP TYR SEQRES 6 A 191 SER LEU PHE LYS ASP GLY ILE GLU PRO MET TRP GLU ASP SEQRES 7 A 191 GLU LYS ASN LYS ARG GLY GLY ARG TRP LEU ILE THR LEU SEQRES 8 A 191 ASN LYS GLN GLN ARG ARG SER ASP LEU ASP ARG PHE TRP SEQRES 9 A 191 LEU GLU THR LEU LEU CYS LEU ILE GLY GLU SER PHE ASP SEQRES 10 A 191 ASP TYR SER ASP ASP VAL CYS GLY ALA VAL VAL ASN VAL SEQRES 11 A 191 ARG ALA LYS GLY ASP LYS ILE ALA ILE TRP THR THR GLU SEQRES 12 A 191 CYS GLU ASN ARG GLU ALA VAL THR HIS ILE GLY ARG VAL SEQRES 13 A 191 TYR LYS GLU ARG LEU GLY LEU PRO PRO LYS ILE VAL ILE SEQRES 14 A 191 GLY TYR GLN SER HIS ALA ASP THR ALA THR LYS SER GLY SEQRES 15 A 191 SER THR THR LYS ASN ARG PHE VAL VAL SEQRES 1 B 20 PRO GLY GLY THR ARG ILE ILE TYR ASP ARG LYS PHE LEU SEQRES 2 B 20 MET GLU CYS ARG ASN SER PRO HET GTA A1000 51 HETNAM GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE HETSYN GTA 7-METHYL-GPPPA FORMUL 3 GTA C21 H30 N10 O17 P3 1+ FORMUL 4 HOH *89(H2 O) HELIX 1 1 ASN A 30 ILE A 35 1 6 HELIX 2 2 THR A 55 ALA A 58 5 4 HELIX 3 3 VAL A 69 HIS A 78 1 10 HELIX 4 4 LEU A 81 LEU A 85 5 5 HELIX 5 5 GLN A 120 ASP A 125 1 6 HELIX 6 6 ASP A 125 GLY A 139 1 15 HELIX 7 7 PHE A 142 ASP A 147 5 6 HELIX 8 8 ASN A 172 GLY A 188 1 17 HELIX 9 9 ALA A 201 THR A 203 5 3 HELIX 10 10 ASP B 55 CYS B 62 1 8 SHEET 1 A 8 LEU A 60 THR A 68 0 SHEET 2 A 8 PRO A 38 PHE A 48 -1 N PHE A 47 O ARG A 61 SHEET 3 A 8 ASP A 90 LYS A 95 -1 O SER A 92 N TRP A 46 SHEET 4 A 8 VAL A 149 ASN A 155 -1 O ALA A 152 N LEU A 93 SHEET 5 A 8 LYS A 162 THR A 167 -1 O TRP A 166 N GLY A 151 SHEET 6 A 8 GLY A 111 THR A 116 -1 N ILE A 115 O ILE A 163 SHEET 7 A 8 GLY A 196 SER A 199 -1 O GLN A 198 N ARG A 112 SHEET 8 A 8 PHE A 215 VAL A 216 -1 O PHE A 215 N TYR A 197 SITE 1 AC1 19 TRP A 56 MET A 101 TRP A 102 GLU A 103 SITE 2 AC1 19 ARG A 157 LYS A 162 PRO A 191 LYS A 192 SITE 3 AC1 19 ILE A 193 VAL A 194 ALA A 204 THR A 205 SITE 4 AC1 19 LYS A 206 SER A 207 GLY A 208 THR A 211 SITE 5 AC1 19 VAL A 217 HOH A1010 HOH A1066 CRYST1 87.770 87.770 38.360 90.00 90.00 90.00 P 43 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 0.011393 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026069 0.00000