HEADER RIBOSOME 20-JUL-13 4BYR OBSLTE 10-DEC-14 4BYR 4V8Y TITLE CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET TITLE 2 EUKARYOTIC TRANSLATION INITIATION COMPLEX SPLIT 4BYL 4BYN 4BYO 4BYP 4BYQ 4BYR 4BYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 5B; COMPND 3 CHAIN: P; COMPND 4 FRAGMENT: DOMAIN 1 AND 2, RESIDUES 401-739; COMPND 5 SYNONYM: EIF-5B, TRANSLATION INITIATION FACTOR IF-2, INITIATION COMPND 6 FACTOR EIF5B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS RIBOSOME, RIBOSOME INITIATION COMPLEX, SINGLE PARTICLE ANALYSIS EXPDTA ELECTRON MICROSCOPY AUTHOR I.S.FERNANDEZ,X.C.BAI,T.HUSSAIN,A.C.KELLEY,J.R.LORSCH,V.RAMAKRISHNAN, AUTHOR 2 S.H.W.SCHERES REVDAT 3 10-DEC-14 4BYR 1 OBSLTE REVDAT 2 27-NOV-13 4BYR 1 JRNL REVDAT 1 20-NOV-13 4BYR 0 JRNL AUTH I.S.FERNANDEZ,X.C.BAI,T.HUSSAIN,A.C.KELLEY,J.R.LORSCH, JRNL AUTH 2 V.RAMAKRISHNAN,S.H.SCHERES JRNL TITL MOLECULAR ARCHITECTURE OF A EUKARYOTIC TRANSLATIONAL JRNL TITL 2 INITIATION COMPLEX. JRNL REF SCIENCE V. 342 40585 2013 JRNL REFN ISSN 0036-8075 JRNL PMID 24200810 JRNL DOI 10.1126/SCIENCE.1240585 REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND3, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : MDFF REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 1.77 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.3 REMARK 3 NUMBER OF PARTICLES : 40729 REMARK 3 CTF CORRECTION METHOD : EACH PARTICLE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: CROSS- REMARK 3 -CORRELATION BETWEEN CRYO-EM MAP AND CRYSTAL STRUCTURE REMARK 3 REMARK 3 OTHER DETAILS: USE A NEWLY DEVELOPED STATISTICAL MOVIE REMARK 3 PROCESSING APPROACH TO COMPENSATE FOR BEAM-INDUCED REMARK 3 MOVEMENT. REMARK 3 SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2421. REMARK 3 (DEPOSITION ID: 11807). REMARK 4 REMARK 4 4BYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 THIS ENTRY WITH OTHER SPLIT ENTRIES HAVE BEEN CONSOLIDATED INTO A REMARK 5 COMBINED FILE FOR COMPLETE REPRESENTATION. NO COORDINATES HAVE BEEN REMARK 5 CHANGED. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-SEP-13. REMARK 100 THE PDBE ID CODE IS EBI-57752. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : MIXED SYMMETRY REMARK 245 NAME OF SAMPLE : 80S-EIF5B-MET-ITRNAMET REMARK 245 EUKARYOTIC TRANSLATION REMARK 245 INITIATION COMPLEX WITH REMARK 245 TRNA IN THE PE-SITE AND REMARK 245 ONLY DENSITY FOR THE G REMARK 245 DOMAIN AND DOMAIN II REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.3 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- REMARK 245 CRYOGEN- ETHANE, HUMIDITY- REMARK 245 100, TEMPERATURE- 90, REMARK 245 INSTRUMENT- FEI VITROBOT REMARK 245 MARK II, METHOD- BLOT 2.5 REMARK 245 SECONDS BEFORE PLUNGING, REMARK 245 SAMPLE BUFFER : 3MM HEPES-KOH, 6.6 MM REMARK 245 TRIS-ACETATE PH 7.2, REMARK 245 3 MM NH4CL, 6.6 MM NH4- REMARK 245 ACETATE, 48 MM K-ACETATE, REMARK 245 4 MM MG-ACETATE, 2. REMARK 245 4 MM DTT REMARK 245 PH : 7.2 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 15-JAN-13 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1012 REMARK 245 TEMPERATURE (KELVIN) : 85 REMARK 245 MICROSCOPE MODEL : OTHER REMARK 245 DETECTOR TYPE : FEI FALCON ( REMARK 245 BACKTHINNED) REMARK 245 MINIMUM DEFOCUS (NM) : 1900 REMARK 245 MAXIMUM DEFOCUS (NM) : 3900 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 16 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 REMARK 245 CALIBRATED MAGNIFICATION : 79096 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: P 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 THR P 16 PB GCP P 1340 2.13 REMARK 500 C THR P 16 C3B GCP P 1340 1.68 REMARK 500 O THR P 16 PB GCP P 1340 1.69 REMARK 500 O THR P 16 O1B GCP P 1340 1.60 REMARK 500 O THR P 16 C3B GCP P 1340 1.73 REMARK 500 CG2 THR P 16 C5' GCP P 1340 1.68 REMARK 500 HB THR P 16 O3A GCP P 1340 1.54 REMARK 500 HG23 THR P 16 O5' GCP P 1340 1.26 REMARK 500 HG23 THR P 16 C5' GCP P 1340 0.76 REMARK 500 N GLY P 17 PG GCP P 1340 2.05 REMARK 500 N GLY P 17 O1G GCP P 1340 2.10 REMARK 500 N GLY P 17 C3B GCP P 1340 1.57 REMARK 500 CA GLY P 17 PG GCP P 1340 0.90 REMARK 500 CA GLY P 17 O1G GCP P 1340 0.92 REMARK 500 CA GLY P 17 O3G GCP P 1340 2.17 REMARK 500 CA GLY P 17 C3B GCP P 1340 1.64 REMARK 500 C GLY P 17 PG GCP P 1340 1.38 REMARK 500 C GLY P 17 O1G GCP P 1340 2.00 REMARK 500 C GLY P 17 O3G GCP P 1340 1.16 REMARK 500 C GLY P 17 C3B GCP P 1340 1.58 REMARK 500 O GLY P 17 PG GCP P 1340 1.98 REMARK 500 O GLY P 17 O3G GCP P 1340 0.74 REMARK 500 HA2 GLY P 17 PG GCP P 1340 0.73 REMARK 500 HA2 GLY P 17 O1G GCP P 1340 1.47 REMARK 500 HA2 GLY P 17 O2G GCP P 1340 1.22 REMARK 500 HA3 GLY P 17 O1G GCP P 1340 0.41 REMARK 500 N LYS P 18 PB GCP P 1340 2.03 REMARK 500 N LYS P 18 O3G GCP P 1340 2.11 REMARK 500 N LYS P 18 C3B GCP P 1340 1.44 REMARK 500 N LYS P 18 O2B GCP P 1340 1.98 REMARK 500 CA LYS P 18 O2B GCP P 1340 1.38 REMARK 500 C LYS P 18 PB GCP P 1340 1.83 REMARK 500 C LYS P 18 O3A GCP P 1340 1.75 REMARK 500 C LYS P 18 O2B GCP P 1340 1.23 REMARK 500 C LYS P 18 PA GCP P 1340 1.87 REMARK 500 C LYS P 18 O2A GCP P 1340 2.07 REMARK 500 O LYS P 18 PB GCP P 1340 2.09 REMARK 500 O LYS P 18 O3A GCP P 1340 1.10 REMARK 500 O LYS P 18 PA GCP P 1340 0.82 REMARK 500 O LYS P 18 O2A GCP P 1340 1.86 REMARK 500 O LYS P 18 O1A GCP P 1340 1.44 REMARK 500 H LYS P 18 C3B GCP P 1340 1.38 REMARK 500 HA LYS P 18 O2B GCP P 1340 1.34 REMARK 500 N THR P 19 O2B GCP P 1340 1.56 REMARK 500 N THR P 19 O2A GCP P 1340 2.15 REMARK 500 CA THR P 19 O2A GCP P 1340 2.07 REMARK 500 C THR P 19 O2A GCP P 1340 1.84 REMARK 500 N LYS P 20 O2A GCP P 1340 2.15 REMARK 500 CG LYS P 20 C2' GCP P 1340 1.80 REMARK 500 CG LYS P 20 N9 GCP P 1340 2.07 REMARK 500 REMARK 500 THIS ENTRY HAS 100 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU P 63 N GLU P 63 CA 1.381 REMARK 500 TRP P 210 CD2 TRP P 210 CE2 0.396 REMARK 500 TRP P 210 CD2 TRP P 210 CE3 0.521 REMARK 500 TRP P 210 CE2 TRP P 210 CZ2 0.543 REMARK 500 TRP P 210 CE3 TRP P 210 CZ3 0.448 REMARK 500 TRP P 210 CZ2 TRP P 210 CH2 0.454 REMARK 500 TRP P 210 CZ3 TRP P 210 CH2 0.386 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 THR P 16 N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 LYS P 18 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 GLU P 63 CB - CA - C ANGL. DEV. = -22.4 DEGREES REMARK 500 GLU P 63 N - CA - C ANGL. DEV. = 19.5 DEGREES REMARK 500 GLU P 63 N - CA - CB ANGL. DEV. = 19.5 DEGREES REMARK 500 GLU P 63 C - N - CA ANGL. DEV. = 21.2 DEGREES REMARK 500 SER P 82 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 PHE P 83 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR P 136 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP P 210 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 TRP P 210 CG - CD1 - NE1 ANGL. DEV. = 7.3 DEGREES REMARK 500 TRP P 210 NE1 - CE2 - CZ2 ANGL. DEV. = 6.9 DEGREES REMARK 500 GLY P 244 N - CA - C ANGL. DEV. = 16.8 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 HSO P 13 162.56 86.38 REMARK 500 THR P 16 77.97 -176.26 REMARK 500 GLN P 31 72.13 -111.61 REMARK 500 GLN P 41 -145.61 -74.05 REMARK 500 PRO P 48 152.29 -44.98 REMARK 500 THR P 56 140.14 166.02 REMARK 500 ALA P 60 -32.71 157.26 REMARK 500 GLU P 61 -4.48 -169.15 REMARK 500 THR P 66 10.33 -160.29 REMARK 500 LEU P 73 55.60 90.27 REMARK 500 THR P 77 -32.47 -149.49 REMARK 500 SER P 82 -122.40 28.58 REMARK 500 PHE P 83 70.69 94.50 REMARK 500 SER P 88 -103.23 67.59 REMARK 500 CYS P 94 -175.25 47.38 REMARK 500 ASN P 95 -151.84 53.95 REMARK 500 HSO P 105 -34.40 -140.39 REMARK 500 GLN P 109 -79.47 -57.80 REMARK 500 LYS P 131 142.81 70.71 REMARK 500 ILE P 132 22.59 -148.17 REMARK 500 ARG P 134 46.71 -96.19 REMARK 500 TYR P 136 137.25 -31.65 REMARK 500 ASP P 137 -14.07 66.66 REMARK 500 TRP P 138 166.23 -42.02 REMARK 500 SER P 154 172.95 -52.88 REMARK 500 ASN P 185 132.53 -33.93 REMARK 500 ASN P 187 132.80 46.06 REMARK 500 LYS P 190 -60.55 -93.35 REMARK 500 GLU P 203 103.67 -161.77 REMARK 500 SER P 221 -85.11 -147.91 REMARK 500 MET P 267 -10.05 -162.19 REMARK 500 THR P 280 134.88 99.49 REMARK 500 PRO P 281 -150.21 -83.03 REMARK 500 PRO P 283 -137.65 -72.61 REMARK 500 ARG P 285 118.11 79.70 REMARK 500 GLU P 286 98.57 177.81 REMARK 500 ARG P 288 7.51 -159.45 REMARK 500 LYS P 290 -178.03 51.18 REMARK 500 SER P 291 158.92 -48.63 REMARK 500 GLU P 313 -96.44 -131.97 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 PHE P 47 PRO P 48 147.71 REMARK 500 LEU P 227 SER P 228 -121.27 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 ARG P 4 0.08 SIDE CHAIN REMARK 500 TYR P 62 0.16 SIDE CHAIN REMARK 500 TYR P 165 0.07 SIDE CHAIN REMARK 500 TRP P 210 0.13 SIDE CHAIN REMARK 500 ARG P 219 0.08 SIDE CHAIN REMARK 500 ARG P 320 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP P 2 -10.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 TYR P 62 24.5 L L OUTSIDE RANGE REMARK 500 GLU P 63 18.5 L L OUTSIDE RANGE REMARK 500 CYS P 94 24.4 L L OUTSIDE RANGE REMARK 500 ASP P 137 24.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GCP P1340 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-2421 RELATED DB: EMDB REMARK 900 MOLECULAR ARCHITECTURE OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYL RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYN RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYO RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYP RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYQ RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYS RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYT RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYU RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYV RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYW RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYX RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX DBREF 4BYR P 1 339 UNP P39730 IF2P_YEAST 401 739 SEQRES 1 P 339 LYS ASP LEU ARG SER PRO ILE CYS CYS ILE LEU GLY HSO SEQRES 2 P 339 VAL ASP THR GLY LYS THR LYS LEU LEU ASP LYS ILE ARG SEQRES 3 P 339 GLN THR ASN VAL GLN GLY GLY GLU ALA GLY GLY ILE THR SEQRES 4 P 339 GLN GLN ILE GLY ALA THR TYR PHE PRO ILE ASP ALA ILE SEQRES 5 P 339 LYS ALA LYS THR LYS VAL MET ALA GLU TYR GLU LYS GLN SEQRES 6 P 339 THR PHE ASP VAL PRO GLY LEU LEU VAL ILE ASP THR PRO SEQRES 7 P 339 GLY HSO GLU SER PHE SER ASN LEU ARG SER ARG GLY SER SEQRES 8 P 339 SER LEU CYS ASN ILE ALA ILE LEU VAL ILE ASP ILE MET SEQRES 9 P 339 HSO GLY LEU GLU GLN GLN THR ILE GLU SER ILE LYS LEU SEQRES 10 P 339 LEU ARG ASP ARG LYS ALA PRO PHE VAL VAL ALA LEU ASN SEQRES 11 P 339 LYS ILE ASP ARG LEU TYR ASP TRP LYS ALA ILE PRO ASN SEQRES 12 P 339 ASN SER PHE ARG ASP SER PHE ALA LYS GLN SER ARG ALA SEQRES 13 P 339 VAL GLN GLU GLU PHE GLN SER ARG TYR SER LYS ILE GLN SEQRES 14 P 339 LEU GLU LEU ALA GLU GLN GLY LEU ASN SER GLU LEU TYR SEQRES 15 P 339 PHE GLN ASN LYS ASN MET SER LYS TYR VAL SER ILE VAL SEQRES 16 P 339 PRO THR SER ALA VAL THR GLY GLU GLY VAL PRO ASP LEU SEQRES 17 P 339 LEU TRP LEU LEU LEU GLU LEU THR GLN LYS ARG MET SER SEQRES 18 P 339 LYS GLN LEU MET TYR LEU SER HSO VAL GLU ALA THR ILE SEQRES 19 P 339 LEU GLU VAL LYS VAL VAL GLU GLY PHE GLY THR THR ILE SEQRES 20 P 339 ASP VAL ILE LEU SER ASN GLY TYR LEU ARG GLU GLY ASP SEQRES 21 P 339 ARG ILE VAL LEU CYS GLY MET ASN GLY PRO ILE VAL THR SEQRES 22 P 339 ASN ILE ARG ALA LEU LEU THR PRO GLN PRO LEU ARG GLU SEQRES 23 P 339 LEU ARG LEU LYS SER GLU TYR VAL HSO HSO LYS GLU VAL SEQRES 24 P 339 LYS ALA ALA LEU GLY VAL LYS ILE ALA ALA ASN ASP LEU SEQRES 25 P 339 GLU LYS ALA VAL SER GLY SER ARG LEU LEU VAL VAL GLY SEQRES 26 P 339 PRO GLU ASP ASP GLU ASP GLU LEU MET ASP ASP VAL MET SEQRES 27 P 339 ASP MODRES 4BYR HSO P 13 HIS HISTIDINOL MODRES 4BYR HSO P 80 HIS HISTIDINOL MODRES 4BYR HSO P 105 HIS HISTIDINOL MODRES 4BYR HSO P 229 HIS HISTIDINOL MODRES 4BYR HSO P 295 HIS HISTIDINOL MODRES 4BYR HSO P 296 HIS HISTIDINOL HET HSO P 13 17 HET HSO P 80 17 HET HSO P 105 17 HET HSO P 229 17 HET HSO P 295 17 HET HSO P 296 17 HET GCP P1340 32 HETNAM HSO HISTIDINOL HETNAM GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER FORMUL 2 HSO 6(C6 H10 N3 O 1+) FORMUL 3 GCP C11 H18 N5 O13 P3 HELIX 1 1 LYS P 20 GLN P 31 1 12 HELIX 2 2 PRO P 48 LYS P 55 1 8 HELIX 3 3 GLN P 110 LYS P 122 1 13 HELIX 4 4 SER P 145 GLN P 153 1 9 HELIX 5 5 SER P 154 LEU P 177 1 24 HELIX 6 6 GLY P 204 MET P 220 1 17 HELIX 7 7 SER P 221 LEU P 224 5 4 HELIX 8 8 GLY P 325 ASP P 339 1 15 SHEET 1 PA 7 ALA P 44 TYR P 46 0 SHEET 2 PA 7 LEU P 73 ASP P 76 -1 O VAL P 74 N THR P 45 SHEET 3 PA 7 CYS P 8 LEU P 11 1 O CYS P 8 N ILE P 75 SHEET 4 PA 7 ILE P 96 LEU P 99 1 O ILE P 96 N CYS P 9 SHEET 5 PA 7 VAL P 126 LEU P 129 1 O VAL P 126 N LEU P 99 SHEET 6 PA 7 VAL P 192 PRO P 196 1 O SER P 193 N VAL P 127 SHEET 7 PA 7 SER P 179 LEU P 181 1 O GLU P 180 N ILE P 194 SHEET 1 PB 7 GLU P 231 VAL P 239 0 SHEET 2 PB 7 THR P 245 ASN P 253 -1 O THR P 246 N LYS P 238 SHEET 3 PB 7 LEU P 303 ALA P 309 -1 O LEU P 303 N LEU P 251 SHEET 4 PB 7 PRO P 270 LEU P 279 -1 N ARG P 276 O ALA P 308 SHEET 5 PB 7 ARG P 261 CYS P 265 -1 O ILE P 262 N THR P 273 SHEET 6 PB 7 ARG P 320 VAL P 323 -1 O LEU P 322 N VAL P 263 SHEET 7 PB 7 GLU P 231 VAL P 239 -1 O ALA P 232 N LEU P 321 SHEET 1 PC 2 TYR P 255 ARG P 257 0 SHEET 2 PC 2 GLU P 298 LYS P 300 -1 O VAL P 299 N LEU P 256 LINK C GLY P 12 N HSO P 13 1555 1555 1.36 LINK C HSO P 13 N VAL P 14 1555 1555 1.34 LINK C GLY P 79 N HSO P 80 1555 1555 1.33 LINK C HSO P 80 N GLU P 81 1555 1555 1.35 LINK C MET P 104 N HSO P 105 1555 1555 1.35 LINK C HSO P 105 N GLY P 106 1555 1555 1.34 LINK C SER P 228 N HSO P 229 1555 1555 1.34 LINK C HSO P 229 N VAL P 230 1555 1555 1.35 LINK C VAL P 294 N HSO P 295 1555 1555 1.34 LINK C HSO P 295 N HSO P 296 1555 1555 1.35 LINK C HSO P 296 N LYS P 297 1555 1555 1.35 CISPEP 1 LEU P 72 LEU P 73 0 -8.87 CISPEP 2 HSO P 80 GLU P 81 0 3.96 CISPEP 3 GLU P 81 SER P 82 0 1.09 CISPEP 4 PHE P 83 SER P 84 0 1.36 CISPEP 5 LEU P 93 CYS P 94 0 -1.39 CISPEP 6 THR P 280 PRO P 281 0 7.07 SITE 1 AC1 12 THR P 16 GLY P 17 LYS P 18 THR P 19 SITE 2 AC1 12 LYS P 20 ASP P 23 PRO P 78 GLY P 79 SITE 3 AC1 12 LYS P 131 SER P 198 ALA P 199 VAL P 200 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