PDB Short entry for 2NLW HEADER TRANSLATION 20-OCT-06 2NLW TITLE SOLUTION STRUCTURE OF THE RRM DOMAIN OF HUMAN EUKARYOTIC INITIATION TITLE 2 FACTOR 3B COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF; COMPND 5 SYNONYM: EIF-3 ETA, EIF3 P116, EIF3 P110, EIF3B, PRT1 HOMOLOG, HPRT1; COMPND 6 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: EIF3S9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TRANSLATION INITIATION, EUKARYOTIC INITIATION FACTOR 3 COMPLEX, RNA KEYWDS 2 RECOGNITION MOTIF, TRANSLATION EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR L.ELANTAK,A.G.TZAKOS,N.LOCKER,P.J.LUKAVSKY REVDAT 5 27-DEC-23 2NLW 1 REMARK REVDAT 4 16-MAR-22 2NLW 1 REMARK REVDAT 3 24-FEB-09 2NLW 1 VERSN REVDAT 2 08-JUL-08 2NLW 1 JRNL REVDAT 1 06-FEB-07 2NLW 0 JRNL AUTH L.ELANTAK,A.G.TZAKOS,N.LOCKER,P.J.LUKAVSKY JRNL TITL STRUCTURE OF EIF3B RNA RECOGNITION MOTIF AND ITS INTERACTION JRNL TITL 2 WITH EIF3J: STRUCTURAL INSIGHTS INTO THE RECRUITMENT OF JRNL TITL 3 EIF3B TO THE 40 S RIBOSOMAL SUBUNIT. JRNL REF J.BIOL.CHEM. V. 282 8165 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17190833 JRNL DOI 10.1074/JBC.M610860200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NLW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040022. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 300MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM EIF3B-RRM UNLABELED, 20MM REMARK 210 HEPES, 90% H2O, 10% D2O; 0.8MM REMARK 210 EIF3B-RRM U-15N, 20MM HEPES, 90% REMARK 210 H2O, 10% D2O; 0.8MM EIF3B-RRM U- REMARK 210 15N,13C, 20MM HEPES, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, SPARKY 3.98, CYANA REMARK 210 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 REFINEMENT BY RESTRAINED REMARK 210 MOLECULAR DYNAMICS IN A HYDRATED REMARK 210 ENVIRONMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 OD2 ASP A 21 HH11 ARG A 93 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 PRO A 71 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 2 PRO A 71 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 3 PRO A 71 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 4 PRO A 71 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 7 PRO A 71 C - N - CA ANGL. DEV. = 11.1 DEGREES REMARK 500 8 PRO A 71 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 9 PRO A 71 C - N - CA ANGL. DEV. = 11.4 DEGREES REMARK 500 10 PRO A 71 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 11 PRO A 71 C - N - CA ANGL. DEV. = 11.5 DEGREES REMARK 500 12 PRO A 71 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 13 PRO A 71 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 15 PRO A 71 C - N - CA ANGL. DEV. = 11.3 DEGREES 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 ASN A 22 89.18 41.50 REMARK 500 1 THR A 60 129.19 -34.66 REMARK 500 1 PRO A 71 6.90 -36.64 REMARK 500 1 ALA A 72 63.31 84.56 REMARK 500 1 LYS A 88 -91.47 45.41 REMARK 500 1 HIS A 90 99.61 -62.54 REMARK 500 1 LEU A 96 -166.56 -102.76 REMARK 500 2 ASN A 22 92.03 46.58 REMARK 500 2 GLN A 25 -165.82 -61.84 REMARK 500 2 PRO A 71 8.05 -37.66 REMARK 500 2 ALA A 72 67.42 87.47 REMARK 500 2 ASN A 80 -71.91 -62.23 REMARK 500 2 ALA A 81 124.13 -177.30 REMARK 500 2 LYS A 88 -81.79 -36.20 REMARK 500 2 THR A 98 28.19 -72.29 REMARK 500 2 PHE A 100 35.06 -92.35 REMARK 500 2 ASP A 101 62.12 -150.81 REMARK 500 3 ASN A 22 97.92 45.70 REMARK 500 3 GLU A 55 -176.78 -173.98 REMARK 500 3 THR A 60 92.26 -56.95 REMARK 500 3 PRO A 71 8.71 -37.48 REMARK 500 3 ALA A 72 62.21 84.84 REMARK 500 3 ASN A 80 -63.68 -92.86 REMARK 500 3 LYS A 88 -95.56 40.24 REMARK 500 4 VAL A 3 29.25 -63.91 REMARK 500 4 ASP A 6 28.62 -78.37 REMARK 500 4 ASN A 22 104.76 31.68 REMARK 500 4 LYS A 61 176.26 -59.49 REMARK 500 4 PRO A 71 9.27 -35.52 REMARK 500 4 ALA A 72 65.20 87.11 REMARK 500 4 ASN A 80 -77.31 -81.96 REMARK 500 4 LYS A 88 -103.54 38.23 REMARK 500 5 VAL A 3 12.25 -146.94 REMARK 500 5 ASN A 22 90.57 44.27 REMARK 500 5 GLU A 56 114.85 -162.20 REMARK 500 5 LYS A 61 167.92 179.87 REMARK 500 5 ALA A 72 7.78 25.31 REMARK 500 5 PHE A 100 66.52 -59.14 REMARK 500 6 VAL A 3 -33.54 67.23 REMARK 500 6 GLU A 10 20.12 -74.61 REMARK 500 6 ASN A 22 95.37 42.57 REMARK 500 6 ASP A 29 18.04 55.90 REMARK 500 6 THR A 49 -61.22 -126.38 REMARK 500 6 THR A 60 108.00 -28.79 REMARK 500 6 ALA A 72 4.47 25.07 REMARK 500 6 PHE A 97 58.45 -108.14 REMARK 500 6 THR A 98 78.80 -47.69 REMARK 500 6 ASP A 99 -45.70 -141.06 REMARK 500 6 ASP A 101 74.11 -105.47 REMARK 500 6 TYR A 103 -69.04 -140.41 REMARK 500 REMARK 500 THIS ENTRY HAS 129 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 71 ALA A 72 5 142.13 REMARK 500 PRO A 71 ALA A 72 6 144.98 REMARK 500 PRO A 71 ALA A 72 14 144.25 REMARK 500 PRO A 71 ALA A 72 16 148.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 15 ARG A 93 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2NLW A 1 105 UNP P55884 IF39_HUMAN 170 274 SEQRES 1 A 105 GLY ASP VAL LEU LYS ASP ARG PRO GLN GLU ALA ASP GLY SEQRES 2 A 105 ILE ASP SER VAL ILE VAL VAL ASP ASN VAL PRO GLN VAL SEQRES 3 A 105 GLY PRO ASP ARG LEU GLU LYS LEU LYS ASN VAL ILE HIS SEQRES 4 A 105 LYS ILE PHE SER LYS PHE GLY LYS ILE THR ASN ASP PHE SEQRES 5 A 105 TYR PRO GLU GLU ASP GLY LYS THR LYS GLY TYR ILE PHE SEQRES 6 A 105 LEU GLU TYR ALA SER PRO ALA HIS ALA VAL ASP ALA VAL SEQRES 7 A 105 LYS ASN ALA ASP GLY TYR LYS LEU ASP LYS GLN HIS THR SEQRES 8 A 105 PHE ARG VAL ASN LEU PHE THR ASP PHE ASP LYS TYR MET SEQRES 9 A 105 THR HELIX 1 1 GLU A 32 SER A 43 1 12 HELIX 2 2 LYS A 44 GLY A 46 5 3 HELIX 3 3 ALA A 72 ALA A 81 1 10 SHEET 1 A 5 ILE A 48 PHE A 52 0 SHEET 2 A 5 TYR A 63 TYR A 68 -1 O GLU A 67 N ASN A 50 SHEET 3 A 5 VAL A 17 ASP A 21 -1 N ILE A 18 O LEU A 66 SHEET 4 A 5 THR A 91 ASN A 95 -1 O ASN A 95 N VAL A 19 SHEET 5 A 5 TYR A 84 LYS A 85 -1 N TYR A 84 O PHE A 92 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