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 3 29-MAY-24 3AM7 1 REMARK
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
(ATOM LINES ARE NOT SHOWN.)
END
