PDB Short entry for 2GPQ HEADER TRANSLATION 18-APR-06 2GPQ TITLE CAP-FREE STRUCTURE OF EIF4E SUGGESTS BASIS FOR ITS ALLOSTERIC TITLE 2 REGULATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EIF4E, EIF-4E, MRNA CAP-BINDING PROTEIN, EIF-4F 25 KDA COMPND 5 SUBUNIT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS TRANSLATION REGULATION, EIF4E, APO FORM, TRANSLATION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR L.VOLPON,M.J.OSBORNE,K.L.B.BORDEN REVDAT 3 09-MAR-22 2GPQ 1 REMARK REVDAT 2 24-FEB-09 2GPQ 1 VERSN REVDAT 1 14-NOV-06 2GPQ 0 JRNL AUTH L.VOLPON,M.J.OSBORNE,I.TOPISIROVIC,N.SIDDIQUI,K.L.BORDEN JRNL TITL CAP-FREE STRUCTURE OF EIF4E SUGGESTS A BASIS FOR JRNL TITL 2 CONFORMATIONAL REGULATION BY ITS LIGANDS. JRNL REF EMBO J. V. 25 5138 2006 JRNL REFN ISSN 0261-4189 JRNL PMID 17036047 JRNL DOI 10.1038/SJ.EMBOJ.7601380 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CNS 1.1 REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1973 RESTRAINTS, 1697 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 276 DIHEDRAL ANGLE RESTRAINTS, 160 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS REMARK 4 REMARK 4 2GPQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037403. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3MM EIF4E U-98% 15N, U-13C; REMARK 210 50MM PHOSPHATE BUFFER; 100MM REMARK 210 NACL; 1MM DTT; 0.02% NAN3; 90% REMARK 210 H2O, 10% D2O; 0.3MM EIF4E U-98% REMARK 210 15N, U-95% D; 50MM PHOSPHATE REMARK 210 BUFFER; 100MM NACL; 1MM DTT; REMARK 210 0.02% NAN3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA; HNCO; HCCH-TOCSY; 3D 15N REMARK 210 -EDITED NOESY; 3D-13C-EDITED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, SPARKY 3.112 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 O THR A 177 H ARG A 181 1.60 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 1 ALA A 2 131.32 -175.11 REMARK 500 1 GLU A 7 129.80 -175.28 REMARK 500 1 THR A 16 -43.21 -164.14 REMARK 500 1 GLU A 20 79.80 61.91 REMARK 500 1 GLU A 23 161.11 60.62 REMARK 500 1 SER A 24 -74.37 -153.60 REMARK 500 1 ASN A 25 109.15 -176.75 REMARK 500 1 GLN A 26 30.92 -149.88 REMARK 500 1 TYR A 34 64.43 172.58 REMARK 500 1 LYS A 52 67.39 -67.03 REMARK 500 1 SER A 53 -35.26 172.94 REMARK 500 1 SER A 64 171.37 179.49 REMARK 500 1 LEU A 81 37.62 163.96 REMARK 500 1 ASN A 84 33.10 -145.24 REMARK 500 1 LEU A 85 39.60 -97.77 REMARK 500 1 PRO A 100 65.54 -67.82 REMARK 500 1 TRP A 102 -68.05 -127.35 REMARK 500 1 GLU A 140 141.00 169.33 REMARK 500 1 SER A 141 -65.07 65.56 REMARK 500 1 ASP A 143 -162.24 49.35 REMARK 500 1 ALA A 158 -85.34 58.24 REMARK 500 1 LYS A 192 -68.03 -178.39 REMARK 500 1 ALA A 204 30.02 -97.95 REMARK 500 1 THR A 205 -68.91 -162.32 REMARK 500 1 LYS A 206 -169.20 45.84 REMARK 500 1 SER A 207 105.92 60.28 REMARK 500 1 THR A 210 -74.54 -121.18 REMARK 500 1 THR A 211 -168.47 -111.48 REMARK 500 1 LYS A 212 77.59 -66.26 REMARK 500 1 ASN A 213 89.59 -177.32 REMARK 500 1 ARG A 214 50.65 127.79 REMARK 500 2 GLU A 20 88.46 -69.49 REMARK 500 2 THR A 22 168.14 57.30 REMARK 500 2 ASN A 25 81.16 -177.31 REMARK 500 2 VAL A 28 144.28 -179.81 REMARK 500 2 ALA A 29 -90.27 -85.90 REMARK 500 2 ASN A 30 -57.96 163.83 REMARK 500 2 GLU A 32 115.71 -167.84 REMARK 500 2 HIS A 33 -46.93 -178.59 REMARK 500 2 TYR A 34 134.60 -180.00 REMARK 500 2 SER A 53 -33.24 179.37 REMARK 500 2 SER A 64 166.71 179.62 REMARK 500 2 ILE A 79 82.12 -157.73 REMARK 500 2 LEU A 81 -165.35 44.88 REMARK 500 2 SER A 82 -65.40 70.37 REMARK 500 2 GLU A 140 37.02 -177.09 REMARK 500 2 SER A 141 -58.53 -178.12 REMARK 500 2 ASP A 143 -163.34 68.08 REMARK 500 2 TYR A 145 46.64 -87.39 REMARK 500 2 ALA A 158 -87.14 55.64 REMARK 500 REMARK 500 THIS ENTRY HAS 316 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2GPQ A 1 217 UNP P06730 IF4E_HUMAN 1 217 SEQRES 1 A 217 MET ALA THR VAL GLU PRO GLU THR THR PRO THR PRO ASN SEQRES 2 A 217 PRO PRO THR THR GLU GLU GLU LYS THR GLU SER ASN GLN SEQRES 3 A 217 GLU VAL ALA ASN PRO GLU HIS TYR ILE LYS HIS PRO LEU SEQRES 4 A 217 GLN ASN ARG TRP ALA LEU TRP PHE PHE LYS ASN ASP LYS SEQRES 5 A 217 SER LYS THR TRP GLN ALA ASN LEU ARG LEU ILE SER LYS SEQRES 6 A 217 PHE ASP THR VAL GLU ASP PHE TRP ALA LEU TYR ASN HIS SEQRES 7 A 217 ILE GLN LEU SER SER ASN LEU MET PRO GLY CYS ASP TYR SEQRES 8 A 217 SER LEU PHE LYS ASP GLY ILE GLU PRO MET TRP GLU ASP SEQRES 9 A 217 GLU LYS ASN LYS ARG GLY GLY ARG TRP LEU ILE THR LEU SEQRES 10 A 217 ASN LYS GLN GLN ARG ARG SER ASP LEU ASP ARG PHE TRP SEQRES 11 A 217 LEU GLU THR LEU LEU CYS LEU ILE GLY GLU SER PHE ASP SEQRES 12 A 217 ASP TYR SER ASP ASP VAL CYS GLY ALA VAL VAL ASN VAL SEQRES 13 A 217 ARG ALA LYS GLY ASP LYS ILE ALA ILE TRP THR THR GLU SEQRES 14 A 217 CYS GLU ASN ARG GLU ALA VAL THR HIS ILE GLY ARG VAL SEQRES 15 A 217 TYR LYS GLU ARG LEU GLY LEU PRO PRO LYS ILE VAL ILE SEQRES 16 A 217 GLY TYR GLN SER HIS ALA ASP THR ALA THR LYS SER GLY SEQRES 17 A 217 SER THR THR LYS ASN ARG PHE VAL VAL HELIX 1 1 VAL A 69 GLN A 80 1 12 HELIX 2 2 GLU A 105 GLY A 110 1 6 HELIX 3 3 GLN A 120 ARG A 122 5 3 HELIX 4 4 SER A 124 GLU A 140 1 17 HELIX 5 5 PHE A 142 ASP A 147 5 6 HELIX 6 6 ASN A 172 GLY A 188 1 17 HELIX 7 7 ALA A 201 THR A 205 5 5 SHEET 1 A 7 LEU A 60 THR A 68 0 SHEET 2 A 7 PRO A 38 LYS A 49 -1 N LEU A 45 O SER A 64 SHEET 3 A 7 CYS A 89 LYS A 95 -1 O SER A 92 N TRP A 46 SHEET 4 A 7 VAL A 149 ARG A 157 -1 O VAL A 154 N TYR A 91 SHEET 5 A 7 GLY A 160 THR A 167 -1 O TRP A 166 N GLY A 151 SHEET 6 A 7 GLY A 111 ASN A 118 -1 N ILE A 115 O ILE A 163 SHEET 7 A 7 GLY A 196 SER A 199 -1 O GLY A 196 N LEU A 114 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000