HEADER RIBOSOME 07-JAN-19 6J45 TITLE CRYSTAL STRUCTURE OF E. COLI PEPTIDE DEFORMYLASE ENZYME AND CHAPERONE TITLE 2 TRIGGER FACTOR FITTED INTO THE CRYO-EM DENSITY MAP OF THE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: P; COMPND 4 SYNONYM: PDF,POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRIGGER FACTOR; COMPND 9 CHAIN: Q; COMPND 10 SYNONYM: TF,PPIASE; COMPND 11 EC: 5.2.1.8; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI H591; SOURCE 3 ORGANISM_TAXID: 656408; SOURCE 4 GENE: DEF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI H591; SOURCE 9 ORGANISM_TAXID: 656408; SOURCE 10 GENE: TIG; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E. COLI 70S RIBOSOME, PROTEIN BIOGENESIS, CHAPERONE, PEPTIDE KEYWDS 2 DEFORMYLASE, TRIGGER FACTOR, POLYPEPTIDE EXIT TUNNEL, PPIASE, KEYWDS 3 RIBOSOME EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN P, Q AUTHOR J.SENGUPTA,S.BHAKTA,S.AKBAR REVDAT 2 27-MAR-24 6J45 1 REMARK REVDAT 1 17-APR-19 6J45 0 JRNL AUTH S.BHAKTA,S.AKBAR,J.SENGUPTA JRNL TITL CRYO-EM STRUCTURES REVEAL RELOCALIZATION OF METAP IN THE JRNL TITL 2 PRESENCE OF OTHER PROTEIN BIOGENESIS FACTORS AT THE JRNL TITL 3 RIBOSOMAL TUNNEL EXIT. JRNL REF J. MOL. BIOL. V. 431 1426 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 30753870 JRNL DOI 10.1016/J.JMB.2019.02.002 REMARK 2 REMARK 2 RESOLUTION. 12.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1BS7 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 : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.20 REMARK 3 NUMBER OF PARTICLES : 20900 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6J45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010429. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : E. COLI 70S RIBOSOME IN COMPLEX REMARK 245 WITH ENZYME PEPTIDE DEFORMYLASE REMARK 245 AND CHAPERONE TRIGGER FACTOR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : THE COMPLEX WAS PREPARED BY REMARK 245 INCUBATING E. COLI 70S RIBOSOME WITH PEPTIDE DEFORMYLASE, REMARK 245 METHIONINE AMINOPEPTIDASE AND TRIGGER FACTOR IN THAT SEQUENCE. REMARK 245 HOWEVER, CRYO EM RECONSTRUCTION OF THE COMPLEX SHOWED NO DENSITY REMARK 245 CORRESPONDING TO METHIONINE AMINOPEPTIDASE NEAR THE RIBOSOMAL REMARK 245 TUNNEL EXIT. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI POLARA 300 REMARK 245 DETECTOR TYPE : FEI EAGLE (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL 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 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: P, Q 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 MET P 0 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-9750 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF E. COLI 70S RIBOSOME IN COMPLEX WITH PEPTIDE REMARK 900 DEFORMYLASE ENZYME REMARK 900 RELATED ID: EMD-9752 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF E. COLI 70S RIBOSOME IN COMPLEX WITH REMARK 900 METHIONINE AMINOPEPTIDASE ENZYME REMARK 900 RELATED ID: EMD-9753 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF PEPTIDE DEFORMYLASE AND METHIONINE REMARK 900 AMINOPEPTIDASE BOUND TO THE E. COLI 70S RIBOSOME REMARK 900 RELATED ID: EMD-9759 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF METHIONINE AMINOPEPTIDASE ENZYME AND REMARK 900 CHAPERONE TRIGGER FACTOR BOUND TO THE E. COLI 70S RIBOSOME REMARK 900 RELATED ID: EMD-9778 RELATED DB: EMDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI PEPTIDE DEFORMYLASE ENZYME AND REMARK 900 CHAPERONE TRIGGER FACTOR FITTED INTO THE CRYO-EM DENSITY MAP OF THE REMARK 900 COMPLEX DBREF 6J45 P 0 168 UNP F4VJS7 F4VJS7_ECOLX 1 169 DBREF 6J45 Q 1 432 UNP F4VAM2 F4VAM2_ECOLX 1 432 SEQRES 1 P 169 MET SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG SEQRES 2 P 169 LEU ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA SEQRES 3 P 169 GLU ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET SEQRES 4 P 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 P 169 ASP ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU SEQRES 6 P 169 ASN ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU SEQRES 7 P 169 LEU GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 P 169 LEU SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA SEQRES 9 P 169 GLU LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 P 169 PRO PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 P 169 ILE GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE SEQRES 12 P 169 MET ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG SEQRES 13 P 169 GLN LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SEQRES 1 Q 432 MET GLN VAL SER VAL GLU THR THR GLN GLY LEU GLY ARG SEQRES 2 Q 432 ARG VAL THR ILE THR ILE ALA ALA ASP SER ILE GLU THR SEQRES 3 Q 432 ALA VAL LYS SER GLU LEU VAL ASN VAL ALA LYS LYS VAL SEQRES 4 Q 432 ARG ILE ASP GLY PHE ARG LYS GLY LYS VAL PRO MET ASN SEQRES 5 Q 432 ILE VAL ALA GLN ARG TYR GLY ALA SER VAL ARG GLN ASP SEQRES 6 Q 432 VAL LEU GLY ASP LEU MET SER ARG ASN PHE ILE ASP ALA SEQRES 7 Q 432 ILE ILE LYS GLU LYS ILE ASN PRO ALA GLY ALA PRO THR SEQRES 8 Q 432 TYR VAL PRO GLY GLU TYR LYS LEU GLY GLU ASP PHE THR SEQRES 9 Q 432 TYR SER VAL GLU PHE GLU VAL TYR PRO GLU VAL GLU LEU SEQRES 10 Q 432 GLN GLY LEU GLU ALA ILE GLU VAL GLU LYS PRO ILE VAL SEQRES 11 Q 432 GLU VAL THR ASP ALA ASP VAL ASP GLY MET LEU ASP THR SEQRES 12 Q 432 LEU ARG LYS GLN GLN ALA THR TRP LYS GLU LYS ASP GLY SEQRES 13 Q 432 ALA VAL GLU ALA GLU ASP ARG VAL THR ILE ASP PHE THR SEQRES 14 Q 432 GLY SER VAL ASP GLY GLU GLU PHE GLU GLY GLY LYS ALA SEQRES 15 Q 432 SER ASP PHE VAL LEU ALA MET GLY GLN GLY ARG MET ILE SEQRES 16 Q 432 PRO GLY PHE GLU ASP GLY ILE LYS GLY HIS LYS ALA GLY SEQRES 17 Q 432 GLU GLU PHE THR ILE ASP VAL THR PHE PRO GLU GLU TYR SEQRES 18 Q 432 HIS ALA GLU ASN LEU LYS GLY LYS ALA ALA LYS PHE ALA SEQRES 19 Q 432 ILE ASN LEU LYS LYS VAL GLU GLU ARG GLU LEU PRO GLU SEQRES 20 Q 432 LEU THR ALA GLU PHE ILE LYS ARG PHE GLY VAL GLU ASP SEQRES 21 Q 432 GLY SER VAL GLU GLY LEU ARG ALA GLU VAL ARG LYS ASN SEQRES 22 Q 432 MET GLU ARG GLU LEU LYS SER ALA ILE ARG ASN ARG VAL SEQRES 23 Q 432 LYS SER GLN ALA ILE GLU GLY LEU VAL LYS ALA ASN ASP SEQRES 24 Q 432 ILE ASP VAL PRO ALA ALA LEU ILE ASP SER GLU ILE ASP SEQRES 25 Q 432 VAL LEU ARG ARG GLN ALA ALA GLN ARG PHE GLY GLY ASN SEQRES 26 Q 432 GLU LYS GLN ALA LEU GLU LEU PRO ARG GLU LEU PHE GLU SEQRES 27 Q 432 GLU GLN ALA LYS ARG ARG VAL VAL VAL GLY LEU LEU LEU SEQRES 28 Q 432 GLY GLU VAL ILE ARG THR ASN GLU LEU LYS ALA ASP GLU SEQRES 29 Q 432 GLU ARG VAL LYS GLY LEU ILE GLU GLU MET ALA SER ALA SEQRES 30 Q 432 TYR GLU ASP PRO LYS GLU VAL ILE GLU PHE TYR SER LYS SEQRES 31 Q 432 ASN LYS GLU LEU MET ASP ASN MET ARG ASN VAL ALA LEU SEQRES 32 Q 432 GLU GLU GLN ALA VAL GLU ALA VAL LEU ALA LYS ALA LYS SEQRES 33 Q 432 VAL THR GLU LYS GLU THR THR PHE ASN GLU LEU MET ASN SEQRES 34 Q 432 GLN GLN ALA 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