PDB Short entry for 3AM7 HEADER TRANSLATION/PROTEIN BINDING 17-AUG-10 3AM7 TITLE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF EIF4E-M7GTP-4EBP2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-217; COMPND 5 SYNONYM: EIF-4E, EIF4E, 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 2; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 47-65; COMPND 13 SYNONYM: EIF4E-BINDING PROTEIN 2, 4E-BP2; COMPND 14 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: EIF4E, EIF4EL1, EIF4F; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: EIF4EBP2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAP, TRANSLATION, PROTEIN-PROTEIN COMPLEX, TRANSLATION-PROTEIN KEYWDS 2 BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.TOMOO,A.FUKUYO,Y.IN,T.ISHIDA REVDAT 2 12-APR-23 3AM7 1 JRNL REMARK REVDAT 1 17-AUG-11 3AM7 0 JRNL AUTH A.FUKUYO,Y.IN,T.ISHIDA,K.TOMOO JRNL TITL STRUCTURAL SCAFFOLD FOR EIF4E BINDING SELECTIVITY OF 4E-BP JRNL TITL 2 ISOFORMS: CRYSTAL STRUCTURE OF EIF4E BINDING REGION OF JRNL TITL 3 4E-BP2 AND ITS COMPARISON WITH THAT OF 4E-BP1. JRNL REF J.PEPT.SCI. V. 17 650 2011 JRNL REFN ISSN 1075-2617 JRNL PMID 21661078 JRNL DOI 10.1002/PSC.1384 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 14502 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) : 0.230 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 734 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 : 1725 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 93 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 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) : 0.685 REMARK 3 BOND ANGLES (DEGREES) : 2.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.310 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 3AM7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000029422. 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 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16434 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 43.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.810 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 43.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.81 REMARK 200 R MERGE FOR SHELL (I) : 0.10100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 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 (%): 58.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-MME 2000, 0.1M MES, 0.2M REMARK 280 AMMONIUM SULFATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.0K 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 18.87500 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 28.31250 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 9.43750 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: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 LEU A 60 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 TYR A 34 -0.72 -140.27 REMARK 500 LYS A 52 -37.97 63.45 REMARK 500 LYS A 54 161.99 -49.98 REMARK 500 ILE A 63 -68.08 -94.28 REMARK 500 ASP A 67 27.68 -146.92 REMARK 500 ASP A 143 -138.00 54.99 REMARK 500 LYS A 206 -57.03 -168.56 REMARK 500 SER A 207 10.58 172.39 REMARK 500 SER A 209 49.37 17.83 REMARK 500 THR A 210 93.34 37.14 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 MGP A 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WKW RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH 4EBP SUBTYPE DBREF 3AM7 A 27 217 UNP P06730 IF4E_HUMAN 27 217 DBREF 3AM7 B 47 65 UNP Q13542 4EBP2_HUMAN 47 65 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 19 PRO GLY GLY THR ARG ILE ILE TYR ASP ARG LYS PHE LEU SEQRES 2 B 19 LEU ASP ARG ARG ASN SER HET MGP A1000 33 HETNAM MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE FORMUL 3 MGP C11 H19 N5 O14 P3 1+ FORMUL 4 HOH *93(H2 O) HELIX 1 1 ASN A 30 TYR A 34 5 5 HELIX 2 2 VAL A 69 ILE A 79 1 11 HELIX 3 3 LEU A 81 LEU A 85 5 5 HELIX 4 4 GLN A 120 ASP A 125 1 6 HELIX 5 5 ASP A 125 GLY A 139 1 15 HELIX 6 6 PHE A 142 ASP A 147 5 6 HELIX 7 7 ASN A 172 GLY A 188 1 17 HELIX 8 8 ALA A 201 THR A 203 5 3 HELIX 9 9 ASP B 55 ASP B 61 1 7 SHEET 1 A 8 LEU A 62 THR A 68 0 SHEET 2 A 8 PRO A 38 LYS A 49 -1 N LEU A 45 O ILE A 63 SHEET 3 A 8 CYS A 89 LYS A 95 -1 O SER A 92 N TRP A 46 SHEET 4 A 8 VAL A 149 ASN A 155 -1 O VAL A 154 N TYR A 91 SHEET 5 A 8 LYS A 162 THR A 167 -1 O LYS A 162 N ASN A 155 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 16 HOH A 18 HOH A 21 TRP A 56 MET A 101 SITE 2 AC1 16 TRP A 102 GLU A 103 ARG A 157 LYS A 159 SITE 3 AC1 16 LYS A 162 PRO A 191 LYS A 192 VAL A 194 SITE 4 AC1 16 VAL A 217 HOH A 234 HOH A 241 HOH A 271 CRYST1 87.840 87.840 37.750 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 0.011384 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026490 0.00000