HEADER TRANSLATION 01-JUL-10 3NS5 TITLE CRYSTAL STRUCTURE OF THE RNA RECOGNITION MOTIF OF YEAST EIF3B RESIDUES TITLE 2 76-161 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 76-161; COMPND 5 SYNONYM: EIF3B, EUKARYOTIC TRANSLATION INITIATION FACTOR 3 90 KDA COMPND 6 SUBUNIT, EIF3 P90, TRANSLATION INITIATION FACTOR EIF3 P90 SUBUNIT, COMPND 7 CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: CDC63, PRT1, YOR361C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.KHOSHNEVIS,P.NEUMANN,R.FICNER REVDAT 4 06-SEP-23 3NS5 1 SEQADV REVDAT 3 25-APR-12 3NS5 1 JRNL VERSN REVDAT 2 23-FEB-11 3NS5 1 JRNL REVDAT 1 06-OCT-10 3NS5 0 JRNL AUTH S.KHOSHNEVIS,P.NEUMANN,R.FICNER JRNL TITL CRYSTAL STRUCTURE OF THE RNA RECOGNITION MOTIF OF YEAST JRNL TITL 2 TRANSLATION INITIATION FACTOR EIF3B REVEALS DIFFERENCES TO JRNL TITL 3 HUMAN EIF3B. JRNL REF PLOS ONE V. 5 12784 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20862284 JRNL DOI 10.1371/JOURNAL.PONE.0012784 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.1_357 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.600 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 5584 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 3.2728 - 2.5981 0.99 2574 138 0.2796 0.3635 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 11.14 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.620 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63010 REMARK 3 B22 (A**2) : 3.86990 REMARK 3 B33 (A**2) : -3.23980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.001 1420 REMARK 3 ANGLE : 0.480 1902 REMARK 3 CHIRALITY : 0.033 218 REMARK 3 PLANARITY : 0.002 232 REMARK 3 DIHEDRAL : 9.774 540 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 4.6678 2.3827 17.7549 REMARK 3 T TENSOR REMARK 3 T11: 0.0813 T22: 0.0720 REMARK 3 T33: 0.0456 T12: -0.0094 REMARK 3 T13: 0.0055 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 0.4050 L22: 1.0064 REMARK 3 L33: 0.3751 L12: -0.6505 REMARK 3 L13: 0.0088 L23: -0.0464 REMARK 3 S TENSOR REMARK 3 S11: -0.1612 S12: -0.0067 S13: -0.0359 REMARK 3 S21: 0.2052 S22: 0.1443 S23: 0.0308 REMARK 3 S31: 0.0427 S32: -0.0635 S33: 0.0910 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 0.8847 1.1908 -2.8641 REMARK 3 T TENSOR REMARK 3 T11: 0.0514 T22: 0.0072 REMARK 3 T33: 0.0808 T12: 0.0462 REMARK 3 T13: -0.0138 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 0.4965 L22: 0.4492 REMARK 3 L33: 0.2057 L12: -0.0954 REMARK 3 L13: -0.0013 L23: -0.1966 REMARK 3 S TENSOR REMARK 3 S11: -0.0909 S12: 0.0838 S13: -0.0207 REMARK 3 S21: -0.1474 S22: -0.0065 S23: -0.0411 REMARK 3 S31: 0.0329 S32: 0.0940 S33: -0.0470 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060212. 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5632 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.598 REMARK 200 RESOLUTION RANGE LOW (A) : 34.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : 0.32000 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3NS6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33% PEG4000 AND 0.1 M NA-CITRATE (PH REMARK 280 5.6) IN A SITTING DROP PLATE AT 20 DEGREES. 1UL OF PROTEIN AT REMARK 280 THE CONCENTRATION OF 17 MG/ML WAS MIXED WITH 1 UL OF RESERVOIR, REMARK 280 VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 15.14000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.14000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.07000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 71 REMARK 465 GLY B 71 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 77 CA REMARK 480 GLN B 77 CA 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 PRO A 85 128.66 -38.85 REMARK 500 ASP A 150 -156.17 -156.81 REMARK 500 SER B 133 -179.41 -173.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NS6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RNA RECOGNITION MOTIF OF YEAST EIF3B DBREF 3NS5 A 76 161 UNP P06103 EIF3B_YEAST 76 161 DBREF 3NS5 B 76 161 UNP P06103 EIF3B_YEAST 76 161 SEQADV 3NS5 GLY A 71 UNP P06103 EXPRESSION TAG SEQADV 3NS5 PRO A 72 UNP P06103 EXPRESSION TAG SEQADV 3NS5 LEU A 73 UNP P06103 EXPRESSION TAG SEQADV 3NS5 GLY A 74 UNP P06103 EXPRESSION TAG SEQADV 3NS5 SER A 75 UNP P06103 EXPRESSION TAG SEQADV 3NS5 GLY B 71 UNP P06103 EXPRESSION TAG SEQADV 3NS5 PRO B 72 UNP P06103 EXPRESSION TAG SEQADV 3NS5 LEU B 73 UNP P06103 EXPRESSION TAG SEQADV 3NS5 GLY B 74 UNP P06103 EXPRESSION TAG SEQADV 3NS5 SER B 75 UNP P06103 EXPRESSION TAG SEQRES 1 A 91 GLY PRO LEU GLY SER ASP GLN TYR ILE VAL VAL ASN GLY SEQRES 2 A 91 ALA PRO VAL ILE PRO SER ALA LYS VAL PRO VAL LEU LYS SEQRES 3 A 91 LYS ALA LEU THR SER LEU PHE SER LYS ALA GLY LYS VAL SEQRES 4 A 91 VAL ASN MET GLU PHE PRO ILE ASP GLU ALA THR GLY LYS SEQRES 5 A 91 THR LYS GLY PHE LEU PHE VAL GLU CYS GLY SER MET ASN SEQRES 6 A 91 ASP ALA LYS LYS ILE ILE LYS SER PHE HIS GLY LYS ARG SEQRES 7 A 91 LEU ASP LEU LYS HIS ARG LEU PHE LEU TYR THR MET LYS SEQRES 1 B 91 GLY PRO LEU GLY SER ASP GLN TYR ILE VAL VAL ASN GLY SEQRES 2 B 91 ALA PRO VAL ILE PRO SER ALA LYS VAL PRO VAL LEU LYS SEQRES 3 B 91 LYS ALA LEU THR SER LEU PHE SER LYS ALA GLY LYS VAL SEQRES 4 B 91 VAL ASN MET GLU PHE PRO ILE ASP GLU ALA THR GLY LYS SEQRES 5 B 91 THR LYS GLY PHE LEU PHE VAL GLU CYS GLY SER MET ASN SEQRES 6 B 91 ASP ALA LYS LYS ILE ILE LYS SER PHE HIS GLY LYS ARG SEQRES 7 B 91 LEU ASP LEU LYS HIS ARG LEU PHE LEU TYR THR MET LYS FORMUL 3 HOH *50(H2 O) HELIX 1 1 PRO A 88 ALA A 90 5 3 HELIX 2 2 LYS A 91 LYS A 105 1 15 HELIX 3 3 SER A 133 HIS A 145 1 13 HELIX 4 4 PRO B 88 ALA B 90 5 3 HELIX 5 5 LYS B 91 SER B 104 1 14 HELIX 6 6 SER B 133 HIS B 145 1 13 SHEET 1 A 4 ASN A 111 GLU A 113 0 SHEET 2 A 4 LEU A 127 GLU A 130 -1 O GLU A 130 N ASN A 111 SHEET 3 A 4 TYR A 78 ASN A 82 -1 N VAL A 81 O LEU A 127 SHEET 4 A 4 PHE A 156 THR A 159 -1 O TYR A 158 N VAL A 80 SHEET 1 B 2 ILE A 116 ASP A 117 0 SHEET 2 B 2 LYS A 122 THR A 123 -1 O LYS A 122 N ASP A 117 SHEET 1 C 4 VAL B 109 GLU B 113 0 SHEET 2 C 4 PHE B 126 CYS B 131 -1 O PHE B 128 N GLU B 113 SHEET 3 C 4 TYR B 78 ASN B 82 -1 N VAL B 81 O LEU B 127 SHEET 4 C 4 PHE B 156 THR B 159 -1 O TYR B 158 N VAL B 80 SHEET 1 D 2 ILE B 116 ASP B 117 0 SHEET 2 D 2 LYS B 122 THR B 123 -1 O LYS B 122 N ASP B 117 CRYST1 30.280 68.140 81.890 90.00 90.00 90.00 P 21 21 21 8 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 0.033025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012212 0.00000