PDB Short entry for 1D7Q HEADER GENE REGULATION 19-OCT-99 1D7Q TITLE HUMAN TRANSLATION INITIATION FACTOR EIF1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (N-TERMINAL HISTIDINE TAG); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRANSLATION INITIATION FACTOR 1A; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: HISTIDINE TAG IS ENGINEERED INTO THE VECTOR THAT IS SOURCE 4 EXPRESSED WITH THE PROTEIN; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PQE31 KEYWDS OB-FOLD, BETA-BARREL, RNA-BINDING PROTEIN, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.L.BATTISTE,T.V.PESTOVA,C.U.T.HELLEN,G.WAGNER REVDAT 5 16-FEB-22 1D7Q 1 REMARK REVDAT 4 24-FEB-09 1D7Q 1 VERSN REVDAT 3 01-APR-03 1D7Q 1 JRNL REVDAT 2 05-MAY-00 1D7Q 1 REMARK ATOM REVDAT 1 17-MAR-00 1D7Q 0 JRNL AUTH J.L.BATTISTE,T.V.PESTOVA,C.U.HELLEN,G.WAGNER JRNL TITL THE EIF1A SOLUTION STRUCTURE REVEALS A LARGE RNA-BINDING JRNL TITL 2 SURFACE IMPORTANT FOR SCANNING FUNCTION. JRNL REF MOL.CELL V. 5 109 2000 JRNL REFN ISSN 1097-2765 JRNL PMID 10678173 JRNL DOI 10.1016/S1097-2765(00)80407-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.V.PESTOVA,S.I.BORUKHOV,C.U.T.HELLEN REMARK 1 TITL EUKARYOTIC RIBOSOMES REQUIRE INITIATION FACTORS 1 AND 1A TO REMARK 1 TITL 2 LOCATE INITIATION CODONS REMARK 1 REF NATURE V. 394 854 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/29703 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, X-PLOR 3.851 REMARK 3 AUTHORS : VARIAN (VNMR), A.T. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 CALCULATIONS WERE RESTRAINED WITH THE FOLLOWING NMR DATA. NOE REMARK 3 DISTANCE REMARK 3 RESTRAINTS INTRA-RESIDUE 607 INTER-RESIDUE SEQUENTIAL (IJ=1) 266 REMARK 3 INTER-RESIDUE REMARK 3 MEDIUM (IJ <= 4) 105 INTER-RESIDUE LONG (IJ > 4) 342 HYDROGENS REMARK 3 BONDS: PROTEIN REMARK 3 BACKBONE 40 DIHEDRAL ANGLES: PHI 65 PSI 65 NO NOE VIOLATIONS >0.3 REMARK 3 A IN FINAL REMARK 3 STRUCTURES. RMS DEVIATIONS OF THE ENSEMBLE SUPERPOSITION TO THE REMARK 3 AVERAGE REMARK 3 STRUCTURE ARE: BACKBONE 39-131 0.57 A SECONDARY STRUCTURE 0.23 A REMARK 3 HEAVY ATOMS REMARK 3 39-131 1.17 A SECONDARY STRUCTURE 0.72 A BOND LENGTHS 0.0016 A REMARK 3 BOND ANGLES REMARK 3 0.345 DEGREE IMPROPER ANGLES 0.259 DEGREE. NOTE THAT RESIDUES 1-38 REMARK 3 AND 132-143 HAD NO LONG REMARK 3 RANGE NOES AND ARE DISORDERED IN THE CALCULATED STRUCTURES. REMARK 4 REMARK 4 1D7Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009868. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 7.5; 7.5; 7.5; 7.5 REMARK 210 IONIC STRENGTH : 500MM; 500MM; 500MM; 500MM REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8MM U-13C,15N EIF1A, 10MM REMARK 210 PHOSPHATE BUFFER, PH 7.5, 500MM REMARK 210 NACL, 1MM DTT, 0.1MM EDTA; 0.5MM REMARK 210 U-15N EIF1A, 10MM PHOSPHATE REMARK 210 BUFFER, PH 7.5, 500MM NACL, 1MM REMARK 210 DTT, 0.1MM EDTA; 1.2MM EIF1A, REMARK 210 10MM PHOSPHATE BUFFER, PH 7.5, REMARK 210 500MM NACL, 1MM DTT, 0.1MM EDTA; REMARK 210 0.4MM 15N-LYSINE EIF1A, 10MM REMARK 210 PHOSPHATE BUFFER, PH 7.5, 500MM REMARK 210 NACL, 1MM DTT, 0.1MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, XEASY 1.2, X-PLOR REMARK 210 3.851, TALOS 1.0 REMARK 210 METHOD USED : STRUCTURES WERE CALCULATED USING REMARK 210 SIMULATED ANNEALING/MOLECULAR REMARK 210 DYNAMICS FROM AN EXTENDED REMARK 210 CONFORMATION WITH RANDOM PHI/PSI REMARK 210 ANGLES. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 REMARK 210 REMARK 210 REMARK: REMARK 210 THE PROTEIN WAS ASSIGNED FROM THE TRIPLE RESONANCE EXPERIMENTS REMARK 210 HNCA, HN(CO)CA, REMARK 210 HNCO, HN(CA)CO, CBCA(CO)NH, HBHA(CBCACO)NH, H(CCCO)NH, (H)C(CCO)NH, REMARK 210 AND HCCH- REMARK 210 TOCSY. VAL AND LEU METHYL GROUPS WERE STEREOSPECIFICALLY ASSIGNED REMARK 210 FROM REMARK 210 ANALYSIS OF MULTIPLET COUPLINGS IN AN HSQC OF 10% 13C-LABELED REMARK 210 PROTEIN. REMARK 210 BACKBONE DIHEDRAL ANGLES WERE ESTIMATED USING THE PROGRAM TALOS REMARK 210 AND BACKBONE REMARK 210 HETERONUCLEAR CHEMICAL SHIFTS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 C MET B 14 N PRO A 15 1.35 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 SER B 4 -75.34 -170.15 REMARK 500 1 HIS B 5 78.01 -166.03 REMARK 500 1 HIS B 6 -70.74 68.29 REMARK 500 1 HIS B 7 109.18 -163.67 REMARK 500 1 HIS B 10 85.00 59.28 REMARK 500 1 ASN A 17 93.83 60.22 REMARK 500 1 LYS A 20 -67.08 -152.12 REMARK 500 1 LYS A 23 36.12 -159.57 REMARK 500 1 ARG A 25 -65.58 69.41 REMARK 500 1 ARG A 26 128.56 64.27 REMARK 500 1 ASN A 32 97.26 61.63 REMARK 500 1 SER A 34 32.63 -159.36 REMARK 500 1 LYS A 36 132.17 -177.57 REMARK 500 1 GLU A 38 87.02 -158.76 REMARK 500 1 LEU A 55 -155.83 -103.79 REMARK 500 1 ASN A 57 -43.81 -159.76 REMARK 500 1 SER A 87 68.62 -151.08 REMARK 500 1 ARG A 95 -8.08 82.03 REMARK 500 1 ASP A 99 -175.61 82.99 REMARK 500 1 ASN A 100 -60.93 69.62 REMARK 500 1 GLU A 130 145.24 63.13 REMARK 500 1 THR A 131 -46.71 -148.80 REMARK 500 1 ASP A 132 145.52 63.13 REMARK 500 1 THR A 133 76.81 -67.76 REMARK 500 1 PHE A 134 118.99 61.91 REMARK 500 1 PRO A 136 174.67 -51.11 REMARK 500 1 ASP A 138 -83.19 61.52 REMARK 500 1 ASP A 139 71.25 47.30 REMARK 500 1 GLU A 141 140.30 63.58 REMARK 500 1 PHE A 144 -80.53 62.73 REMARK 500 1 ILE A 147 82.94 65.35 REMARK 500 1 ASP A 149 -69.06 68.50 REMARK 500 1 ASP A 151 -67.09 68.41 REMARK 500 1 GLU A 152 154.88 64.79 REMARK 500 1 ASP A 153 -65.74 69.48 REMARK 500 2 HIS B 8 -36.75 -177.87 REMARK 500 2 HIS B 9 100.40 -47.90 REMARK 500 2 ASP B 12 75.64 67.99 REMARK 500 2 LYS A 16 102.00 61.69 REMARK 500 2 LYS A 20 53.66 -154.07 REMARK 500 2 ASN A 24 152.39 62.56 REMARK 500 2 ARG A 25 43.80 -95.55 REMARK 500 2 ARG A 27 -76.51 65.61 REMARK 500 2 LYS A 29 -51.19 -158.96 REMARK 500 2 ASN A 30 -67.22 68.91 REMARK 500 2 GLU A 31 128.48 64.37 REMARK 500 2 ASN A 32 123.80 62.37 REMARK 500 2 GLU A 33 59.60 -108.11 REMARK 500 2 SER A 34 29.34 -141.42 REMARK 500 2 GLU A 38 78.52 -118.91 REMARK 500 REMARK 500 THIS ENTRY HAS 532 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D7Q A 15 157 UNP P47813 IF1AX_HUMAN 1 143 DBREF 1D7Q B 1 14 PDB 1D7Q 1D7Q 1 14 SEQRES 1 B 14 MET ARG GLY SER HIS HIS HIS HIS HIS HIS THR ASP PRO SEQRES 2 B 14 MET SEQRES 1 A 143 PRO LYS ASN LYS GLY LYS GLY GLY LYS ASN ARG ARG ARG SEQRES 2 A 143 GLY LYS ASN GLU ASN GLU SER GLU LYS ARG GLU LEU VAL SEQRES 3 A 143 PHE LYS GLU ASP GLY GLN GLU TYR ALA GLN VAL ILE LYS SEQRES 4 A 143 MET LEU GLY ASN GLY ARG LEU GLU ALA MET CYS PHE ASP SEQRES 5 A 143 GLY VAL LYS ARG LEU CYS HIS ILE ARG GLY LYS LEU ARG SEQRES 6 A 143 LYS LYS VAL TRP ILE ASN THR SER ASP ILE ILE LEU VAL SEQRES 7 A 143 GLY LEU ARG ASP TYR GLN ASP ASN LYS ALA ASP VAL ILE SEQRES 8 A 143 LEU LYS TYR ASN ALA ASP GLU ALA ARG SER LEU LYS ALA SEQRES 9 A 143 TYR GLY GLU LEU PRO GLU HIS ALA LYS ILE ASN GLU THR SEQRES 10 A 143 ASP THR PHE GLY PRO GLY ASP ASP ASP GLU ILE GLN PHE SEQRES 11 A 143 ASP ASP ILE GLY ASP ASP ASP GLU ASP ILE ASP ASP ILE HELIX 1 1 GLY A 76 LYS A 81 5 6 HELIX 2 2 GLU A 112 GLY A 120 1 9 SHEET 1 A 5 VAL A 68 HIS A 73 0 SHEET 2 A 5 ARG A 59 CYS A 64 -1 N LEU A 60 O CYS A 72 SHEET 3 A 5 GLN A 46 MET A 54 -1 O GLN A 50 N MET A 63 SHEET 4 A 5 ILE A 89 GLY A 93 -1 O ILE A 90 N ALA A 49 SHEET 5 A 5 ASP A 103 TYR A 108 -1 O ASP A 103 N GLY A 93 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