PDB Short entry for 1IPB HEADER RNA BINDING PROTEIN 08-MAY-01 1IPB TITLE CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7- TITLE 2 METHYL GPPPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E; COMPND 3 CHAIN: A; COMPND 4 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEMEX KEYWDS INITIATION FACTOR, PROTEIN BIOSYNTHESIS, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.TOMOO,X.SHEN,K.OKABE,Y.NOZOE,S.FUKUHARA,S.MORINO,T.ISHIDA, AUTHOR 2 T.TANIGUCHI,H.HASEGAWA,A.TERASHIMA,M.SASAKI,Y.KATSUYA,K.KITAMURA, AUTHOR 3 H.MIYOSHI,M.ISHIKAWA,K.MIURA REVDAT 5 27-DEC-23 1IPB 1 REMARK REVDAT 4 04-OCT-17 1IPB 1 REMARK REVDAT 3 24-FEB-09 1IPB 1 VERSN REVDAT 2 13-JAN-04 1IPB 1 JRNL REVDAT 1 08-MAY-02 1IPB 0 JRNL AUTH K.TOMOO,X.SHEN,K.OKABE,Y.NOZOE,S.FUKUHARA,S.MORINO,T.ISHIDA, JRNL AUTH 2 T.TANIGUCHI,H.HASEGAWA,A.TERASHIMA,M.SASAKI,Y.KATSUYA, JRNL AUTH 3 K.KITAMURA,H.MIYOSHI,M.ISHIKAWA,K.MIURA JRNL TITL CRYSTAL STRUCTURES OF 7-METHYLGUANOSINE 5'-TRIPHOSPHATE JRNL TITL 2 (M(7)GTP)- AND JRNL TITL 3 P(1)-7-METHYLGUANOSINE-P(3)-ADENOSINE-5',5'-TRIPHOSPHATE JRNL TITL 4 (M(7)GPPPA)-BOUND HUMAN FULL-LENGTH EUKARYOTIC INITIATION JRNL TITL 5 FACTOR 4E: BIOLOGICAL IMPORTANCE OF THE C-TERMINAL FLEXIBLE JRNL TITL 6 REGION JRNL REF BIOCHEM.J. V. 362 539 2002 JRNL REFN ISSN 0264-6021 JRNL PMID 11879179 JRNL DOI 10.1042/0264-6021:3620539 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17165 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) : 0.196 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1657 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 : 1572 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 138 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) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.24 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.685 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 1IPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000005145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL 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) : NULL 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: NULL 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 (%): 59.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 19.25500 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 28.88250 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 9.62750 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: 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 VAL A 4 REMARK 465 GLU A 5 REMARK 465 PRO A 6 REMARK 465 GLU A 7 REMARK 465 THR A 8 REMARK 465 THR A 9 REMARK 465 PRO A 10 REMARK 465 THR A 11 REMARK 465 PRO A 12 REMARK 465 ASN A 13 REMARK 465 PRO A 14 REMARK 465 PRO A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 GLU A 19 REMARK 465 GLU A 20 REMARK 465 LYS A 21 REMARK 465 THR A 22 REMARK 465 GLU A 23 REMARK 465 SER A 24 REMARK 465 ASN A 25 REMARK 465 GLN A 26 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 -15.13 -142.08 REMARK 500 ILE A 63 -72.57 -97.81 REMARK 500 ASP A 67 23.34 -142.30 REMARK 500 ASP A 143 -115.12 44.54 REMARK 500 SER A 207 94.01 -50.20 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IPC RELATED DB: PDB REMARK 900 1IPC CONTAINS THE SAME PROTEIN COMPLEXED WITH 7-METHYL GTP DBREF 1IPB 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 HET GTA A1000 51 HETNAM GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE HETSYN GTA 7-METHYL-GPPPA FORMUL 2 GTA C21 H30 N10 O17 P3 1+ FORMUL 3 HOH *138(H2 O) HELIX 1 1 ASN A 30 TYR A 34 5 5 HELIX 2 2 TRP A 56 ALA A 58 5 3 HELIX 3 3 VAL A 69 ILE A 79 1 11 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 SHEET 1 A 8 LEU A 60 THR A 68 0 SHEET 2 A 8 PRO A 38 PHE A 48 -1 N LEU A 39 O ASP A 67 SHEET 3 A 8 ASP A 90 LYS A 95 -1 O ASP A 90 N PHE A 48 SHEET 4 A 8 VAL A 149 ASN A 155 -1 O CYS A 150 N LYS A 95 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 O GLY A 111 N THR A 167 SHEET 7 A 8 GLY A 196 SER A 199 -1 O GLY A 196 N LEU A 114 SHEET 8 A 8 PHE A 215 VAL A 216 -1 O PHE A 215 N TYR A 197 SITE 1 AC1 23 TRP A 56 GLN A 57 MET A 101 TRP A 102 SITE 2 AC1 23 GLU A 103 ARG A 157 LYS A 162 PRO A 191 SITE 3 AC1 23 LYS A 192 ILE A 193 VAL A 194 ALA A 204 SITE 4 AC1 23 THR A 205 LYS A 206 SER A 207 VAL A 217 SITE 5 AC1 23 HOH A1013 HOH A1034 HOH A1045 HOH A1074 SITE 6 AC1 23 HOH A1089 HOH A1097 HOH A1113 CRYST1 89.260 89.260 38.510 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 0.011203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025967 0.00000