PDB Short entry for 2VRH HEADER RIBOSOME 07-APR-08 2VRH TITLE STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING TITLE 2 RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIGGER FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: BASED ON PDB 1W26_A. RESIDUES 22-62 WERE REPLACED WITH COMPND 6 THE CORRESPONDING RESIDUES OF PDB 1OMS_B; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 50S RIBOSOMAL PROTEIN L23; COMPND 9 CHAIN: B; COMPND 10 OTHER_DETAILS: BASED ON PDB 2AW4_T; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 50S RIBOSOMAL PROTEIN L24; COMPND 13 CHAIN: C; COMPND 14 FRAGMENT: RESIDUES 2-104; COMPND 15 OTHER_DETAILS: BASED ON PDB 2AW4_U; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: 50S RIBOSOMAL PROTEIN L29; COMPND 18 CHAIN: D; COMPND 19 OTHER_DETAILS: BASED ON PDB 2AW4_X SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 OTHER_DETAILS: BASED ON PDB 1W26_A; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 OTHER_DETAILS: BASED ON PDB 2AW4_T; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 562; SOURCE 14 OTHER_DETAILS: BASED ON PDB 2AW4_U; SOURCE 15 MOL_ID: 4; SOURCE 16 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 17 ORGANISM_TAXID: 562; SOURCE 18 OTHER_DETAILS: BASED ON PDB 2AW4_X KEYWDS RIBOSOME, TRIGGER FACTOR, RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN, CO- KEYWDS 2 TRANSLATIONAL PROTEIN FOLDING, ROTAMASE, CHAPERONE, ISOMERASE, CELL KEYWDS 3 CYCLE, RNA-BINDING, RRNA-BINDING, CELL DIVISION, RIBOSOME-NASCENT KEYWDS 4 CHAIN COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, B, C, D AUTHOR F.MERZ,D.BOEHRINGER,C.SCHAFFITZEL,S.PREISSLER,A.HOFFMANN,T.MAIER, AUTHOR 2 A.RUTKOWSKA,J.LOZZA,N.BAN,B.BUKAU,E.DEUERLING REVDAT 5 23-AUG-17 2VRH 1 REMARK REVDAT 4 07-AUG-13 2VRH 1 REMARK CRYST1 SCALE1 SCALE2 REVDAT 4 2 1 SCALE3 REVDAT 3 14-DEC-11 2VRH 1 REMARK VERSN REVDAT 2 24-FEB-09 2VRH 1 VERSN REVDAT 1 17-JUN-08 2VRH 0 JRNL AUTH F.MERZ,D.BOEHRINGER,C.SCHAFFITZEL,S.PREISSLER,A.HOFFMANN, JRNL AUTH 2 T.MAIER,A.RUTKOWSKA,J.LOZZA,N.BAN,B.BUKAU,E.DEUERLING JRNL TITL MOLECULAR MECHANISM AND STRUCTURE OF TRIGGER FACTOR BOUND TO JRNL TITL 2 THE TRANSLATING RIBOSOME. JRNL REF EMBO J. V. 27 1622 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18497744 JRNL DOI 10.1038/EMBOJ.2008.89 REMARK 2 REMARK 2 RESOLUTION. 19.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : MOLREP, IMAGIC, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2AW4 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--RIGID BODY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 4.233 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 19.00 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: FITTING OF CRYSTAL STRUCTURES INTO MAP EMD-1499 REMARK 4 REMARK 4 2VRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290035874. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : STRUCTURE OF THE E. COLI REMARK 245 TRIGGER FACTOR BOUND TO A REMARK 245 TRANSLATING RIBOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 50 MM HEPES-KOH PH 7.5, 100 MM REMARK 245 KCL, 25 MM MGCL2, 0.5 MG/ML REMARK 245 CHLORAMPHENICOL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 88.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI 20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : NULL REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 50000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ALA A 432 REMARK 465 GLU B 100 REMARK 465 LYS C 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P9Y RELATED DB: PDB REMARK 900 RIBOSOME BINDING OF E. COLI TRIGGER FACTOR MUTANT F44L. REMARK 900 RELATED ID: 2J28 RELATED DB: PDB REMARK 900 MODEL OF E. COLI SRP BOUND TO 70S RNCS REMARK 900 RELATED ID: 2VHM RELATED DB: PDB REMARK 900 STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME REMARK 900 RELATED ID: 2WWQ RELATED DB: PDB REMARK 900 E.COLI 70S RIBOSOME STALLED DURING TRANSLATION OF TNAC LEADER REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1P86 RELATED DB: PDB REMARK 900 REAL SPACE REFINED COORDINATES OF THE 50S SUBUNIT FITTEDINTO THE REMARK 900 LOW RESOLUTION CRYO-EM MAP OF THE INITIATION-LIKESTATE OF E. COLI REMARK 900 70S RIBOSOME REMARK 900 RELATED ID: 2AW4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROMESCHERICHIA COLI AT REMARK 900 3.5 A RESOLUTION. THIS FILE CONTAINSTHE 50S SUBUNIT OF ONE 70S REMARK 900 RIBOSOME. THE ENTIRE CRYSTALSTRUCTURE CONTAINS TWO 70S RIBOSOMES REMARK 900 AND IS DESCRIBED INREMARK 400. REMARK 900 RELATED ID: 1W26 RELATED DB: PDB REMARK 900 TRIGGER FACTOR IN COMPLEX WITH THE RIBOSOME FORMS A MOLECULAR REMARK 900 CRADLE FOR NASCENT PROTEINS REMARK 900 RELATED ID: 1W2B RELATED DB: PDB REMARK 900 TRIGGER FACTOR RIBOSOME BINDING DOMAIN IN COMPLEX WITH 50S REMARK 900 RELATED ID: 1P85 RELATED DB: PDB REMARK 900 REAL SPACE REFINED COORDINATES OF THE 50S SUBUNIT FITTEDINTO THE REMARK 900 LOW RESOLUTION CRYO-EM MAP OF THE EF -G.GTP STATEOF E. COLI 70S REMARK 900 RIBOSOME REMARK 900 RELATED ID: 2VHN RELATED DB: PDB REMARK 900 STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME REMARK 900 RELATED ID: 1OMS RELATED DB: PDB REMARK 900 STRUCTURE DETERMINATION BY MAD: E.COLI TRIGGER FACTORBINDING AT THE REMARK 900 RIBOSOMAL EXIT TUNNEL. REMARK 900 RELATED ID: 2AWB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROMESCHERICHIA COLI AT REMARK 900 3.5 A RESOLUTION. THIS FILE CONTAINSTHE 50S SUBUNIT OF THE SECOND REMARK 900 70S RIBOSOME. THE ENTIRECRYSTAL STRUCTURE CONTAINS TWO 70S REMARK 900 RIBOSOMES AND ISDESCRIBED IN REMARK 400. REMARK 900 RELATED ID: 1L1P RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PPIASE DOMAIN FROM E. COLITRIGGER FACTOR REMARK 900 RELATED ID: EMD-1499 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING REMARK 900 RIBOSOME DBREF 2VRH A 1 432 UNP P0A850 TIG_ECOLI 1 432 DBREF 2VRH B 1 100 UNP Q0TCE3 RL23_ECOL5 1 100 DBREF 2VRH C 1 103 UNP P60624 RL24_ECOLI 2 104 DBREF 2VRH D 1 63 UNP P0A7M6 RL29_ECOLI 1 63 SEQRES 1 A 432 MSE GLN VAL SER VAL GLU THR THR GLN GLY LEU GLY ARG SEQRES 2 A 432 ARG VAL THR ILE THR ILE ALA ALA ASP SER ILE GLU THR SEQRES 3 A 432 ALA VAL LYS SER GLU LEU VAL ASN VAL ALA LYS LYS VAL SEQRES 4 A 432 ARG ILE ASP GLY PHE ARG LYS GLY LYS VAL PRO MSE ASN SEQRES 5 A 432 ILE VAL ALA GLN ARG TYR GLY ALA SER VAL ARG GLN ASP SEQRES 6 A 432 VAL LEU GLY ASP LEU MSE SER ARG ASN PHE ILE ASP ALA SEQRES 7 A 432 ILE ILE LYS GLU LYS ILE ASN PRO ALA GLY ALA PRO THR SEQRES 8 A 432 TYR VAL PRO GLY GLU TYR LYS LEU GLY GLU ASP PHE THR SEQRES 9 A 432 TYR SER VAL GLU PHE GLU VAL TYR PRO GLU VAL GLU LEU SEQRES 10 A 432 GLN GLY LEU GLU ALA ILE GLU VAL GLU LYS PRO ILE VAL SEQRES 11 A 432 GLU VAL THR ASP ALA ASP VAL ASP GLY MSE LEU ASP THR SEQRES 12 A 432 LEU ARG LYS GLN GLN ALA THR TRP LYS GLU LYS ASP GLY SEQRES 13 A 432 ALA VAL GLU ALA GLU ASP ARG VAL THR ILE ASP PHE THR SEQRES 14 A 432 GLY SER VAL ASP GLY GLU GLU PHE GLU GLY GLY LYS ALA SEQRES 15 A 432 SER ASP PHE VAL LEU ALA MSE GLY GLN GLY ARG MSE ILE SEQRES 16 A 432 PRO GLY PHE GLU ASP GLY ILE LYS GLY HIS LYS ALA GLY SEQRES 17 A 432 GLU GLU PHE THR ILE ASP VAL THR PHE PRO GLU GLU TYR SEQRES 18 A 432 HIS ALA GLU ASN LEU LYS GLY LYS ALA ALA LYS PHE ALA SEQRES 19 A 432 ILE ASN LEU LYS LYS VAL GLU GLU ARG GLU LEU PRO GLU SEQRES 20 A 432 LEU THR ALA GLU PHE ILE LYS ARG PHE GLY VAL GLU ASP SEQRES 21 A 432 GLY SER VAL GLU GLY LEU ARG ALA GLU VAL ARG LYS ASN SEQRES 22 A 432 MSE GLU ARG GLU LEU LYS SER ALA ILE ARG ASN ARG VAL SEQRES 23 A 432 LYS SER GLN ALA ILE GLU GLY LEU VAL LYS ALA ASN ASP SEQRES 24 A 432 ILE ASP VAL PRO ALA ALA LEU ILE ASP SER GLU ILE ASP SEQRES 25 A 432 VAL LEU ARG ARG GLN ALA ALA GLN ARG PHE GLY GLY ASN SEQRES 26 A 432 GLU LYS GLN ALA LEU GLU LEU PRO ARG GLU LEU PHE GLU SEQRES 27 A 432 GLU GLN ALA LYS ARG ARG VAL VAL VAL GLY LEU LEU LEU SEQRES 28 A 432 GLY GLU VAL ILE ARG THR ASN GLU LEU LYS ALA ASP GLU SEQRES 29 A 432 GLU ARG VAL LYS GLY LEU ILE GLU GLU MSE ALA SER ALA SEQRES 30 A 432 TYR GLU ASP PRO LYS GLU VAL ILE GLU PHE TYR SER LYS SEQRES 31 A 432 ASN LYS GLU LEU MSE ASP ASN MSE ARG ASN VAL ALA LEU SEQRES 32 A 432 GLU GLU GLN ALA VAL GLU ALA VAL LEU ALA LYS ALA LYS SEQRES 33 A 432 VAL THR GLU LYS GLU THR THR PHE ASN GLU LEU MSE ASN SEQRES 34 A 432 GLN GLN ALA SEQRES 1 B 100 MET ILE ARG GLU GLU ARG LEU LEU LYS VAL LEU ARG ALA SEQRES 2 B 100 PRO HIS VAL SER GLU LYS ALA SER THR ALA MET GLU LYS SEQRES 3 B 100 SER ASN THR ILE VAL LEU LYS VAL ALA LYS ASP ALA THR SEQRES 4 B 100 LYS ALA GLU ILE LYS ALA ALA VAL GLN LYS LEU PHE GLU SEQRES 5 B 100 VAL GLU VAL GLU VAL VAL ASN THR LEU VAL VAL LYS GLY SEQRES 6 B 100 LYS VAL LYS ARG HIS GLY GLN ARG ILE GLY ARG ARG SER SEQRES 7 B 100 ASP TRP LYS LYS ALA TYR VAL THR LEU LYS GLU GLY GLN SEQRES 8 B 100 ASN LEU ASP PHE VAL GLY GLY ALA GLU SEQRES 1 C 103 ALA ALA LYS ILE ARG ARG ASP ASP GLU VAL ILE VAL LEU SEQRES 2 C 103 THR GLY LYS ASP LYS GLY LYS ARG GLY LYS VAL LYS ASN SEQRES 3 C 103 VAL LEU SER SER GLY LYS VAL ILE VAL GLU GLY ILE ASN SEQRES 4 C 103 LEU VAL LYS LYS HIS GLN LYS PRO VAL PRO ALA LEU ASN SEQRES 5 C 103 GLN PRO GLY GLY ILE VAL GLU LYS GLU ALA ALA ILE GLN SEQRES 6 C 103 VAL SER ASN VAL ALA ILE PHE ASN ALA ALA THR GLY LYS SEQRES 7 C 103 ALA ASP ARG VAL GLY PHE ARG PHE GLU ASP GLY LYS LYS SEQRES 8 C 103 VAL ARG PHE PHE LYS SER ASN SER GLU THR ILE LYS SEQRES 1 D 63 MET LYS ALA LYS GLU LEU ARG GLU LYS SER VAL GLU GLU SEQRES 2 D 63 LEU ASN THR GLU LEU LEU ASN LEU LEU ARG GLU GLN PHE SEQRES 3 D 63 ASN LEU ARG MET GLN ALA ALA SER GLY GLN LEU GLN GLN SEQRES 4 D 63 SER HIS LEU LEU LYS GLN VAL ARG ARG ASP VAL ALA ARG SEQRES 5 D 63 VAL LYS THR LEU LEU ASN GLU LYS ALA GLY ALA MODRES 2VRH MSE A 1 MET SELENOMETHIONINE MODRES 2VRH MSE A 51 MET SELENOMETHIONINE MODRES 2VRH MSE A 71 MET SELENOMETHIONINE MODRES 2VRH MSE A 140 MET SELENOMETHIONINE MODRES 2VRH MSE A 189 MET SELENOMETHIONINE MODRES 2VRH MSE A 194 MET SELENOMETHIONINE MODRES 2VRH MSE A 274 MET SELENOMETHIONINE MODRES 2VRH MSE A 374 MET SELENOMETHIONINE MODRES 2VRH MSE A 395 MET SELENOMETHIONINE MODRES 2VRH MSE A 398 MET SELENOMETHIONINE MODRES 2VRH MSE A 428 MET SELENOMETHIONINE HET MSE A 1 1 HET MSE A 51 1 HET MSE A 71 1 HET MSE A 140 1 HET MSE A 189 1 HET MSE A 194 1 HET MSE A 274 1 HET MSE A 374 1 HET MSE A 395 1 HET MSE A 398 1 HET MSE A 428 1 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 11(C5 H11 N O2 SE) 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 HETATM 1 CA MSE A 1 537.518 425.216 415.313 1.00117.02 C