HEADER PROTEIN TRANSPORT 03-AUG-05 2AKH TITLE NORMAL MODE-BASED FLEXIBLE FITTED COORDINATES OF A NON-TRANSLOCATING TITLE 2 SECYEG PROTEIN-CONDUCTING CHANNEL INTO THE CRYO-EM MAP OF A SECYEG- TITLE 3 NASCENT CHAIN-70S RIBOSOME COMPLEX FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-EXPORT MEMBRANE PROTEIN SECG; COMPND 3 CHAIN: X, A; COMPND 4 SYNONYM: PREPROTEIN TRANSLOCASE BAND 1 SUBUNIT, P12; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PREPROTEIN TRANSLOCASE SECY SUBUNIT; COMPND 8 CHAIN: Y, B; COMPND 9 FRAGMENT: PLUG TMH 2A DELETED; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: PREPROTEIN TRANSLOCASE SECE SUBUNIT; COMPND 14 CHAIN: Z, C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: SECG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 GENE: SECY, PRLA; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 15 ORGANISM_TAXID: 562; SOURCE 16 GENE: SECE, PRLG; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TRANSPORT, TRANSLOCATION, TRANSMEMBRANE, TRANSPORT EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN X, Y, Z, A, B, C AUTHOR K.M.MITRA,C.SCHAFFITZEL,T.SHAIKH,F.TAMA,S.JENNI,C.L.BROOKS III,N.BAN, AUTHOR 2 J.FRANK REVDAT 4 14-FEB-24 2AKH 1 REMARK REVDAT 3 18-JUL-18 2AKH 1 REMARK REVDAT 2 24-FEB-09 2AKH 1 VERSN REVDAT 1 15-NOV-05 2AKH 0 JRNL AUTH K.MITRA,C.SCHAFFITZEL,T.SHAIKH,F.TAMA,S.JENNI,C.L.BROOKS, JRNL AUTH 2 N.BAN,J.FRANK JRNL TITL STRUCTURE OF THE E. COLI PROTEIN-CONDUCTING CHANNEL BOUND TO JRNL TITL 2 A TRANSLATING RIBOSOME. JRNL REF NATURE V. 438 318 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 16292303 JRNL DOI 10.1038/NATURE04133 REMARK 2 REMARK 2 RESOLUTION. 14.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RSR2000, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT, R-FACTOR REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--NORMAL MODE-BASED FLEXIBLE FITTING REMARK 3 REFINEMENT PROTOCOL--NORMAL MODE-BASED FLEXIBLE FITTING, REAL REMARK 3 SPACE REFINEMENT 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) : 14.90 REMARK 3 NUMBER OF PARTICLES : 53325 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THE RESOLUTION IS BASED ON FSC AT 0.5 CUT-OFF REMARK 4 REMARK 4 2AKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034000. 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 : PROTEIN-CONDUCTING CHANNEL; REMARK 245 PROTEIN TRANSLOCASE ACTIVITY; REMARK 245 PROTEIN TRANSLOCASE ACTIVITY; REMARK 245 PROTEIN TRANSLOCASE ACTIVITY 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 : NULL REMARK 245 SAMPLE DETAILS : DIMER OF SECYEG HETEROTRIMER; REMARK 245 DIMER OF SECYEG HETEROTRIMER; DIMER OF SECYEG HETEROTRIMER REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 09-MAR-04 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4300.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.26 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1100.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 39000 REMARK 245 CALIBRATED MAGNIFICATION : 39000 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y, Z, A, B, C 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1143 RELATED DB: EMDB REMARK 900 CRYO-EM MAP OF THE E. COLI PROTEIN-CONDUCTING CHANNEL BOUND TO A REMARK 900 TRANSLATING RIBOSOME REMARK 900 RELATED ID: 2AKI RELATED DB: PDB REMARK 900 NORMAL MODE-BASED FLEXIBLE FITTED COORDINATES OF A TRANSLOCATING REMARK 900 SECYEG PROTEIN-CONDUCTING CHANNEL INTO THE CRYO-EM MAP OF A SECYEG- REMARK 900 NASCENT CHAIN-70S RIBOSOME COMPLEX FROM E. COLI DBREF 2AKH X 1 77 UNP P33582 SECG_ECOLI 1 77 DBREF 2AKH A 1 77 UNP P33582 SECG_ECOLI 1 77 DBREF 2AKH Y 1 39 UNP P03844 SECY_ECOLI 1 39 DBREF 2AKH Y 76 436 UNP P03844 SECY_ECOLI 76 436 DBREF 2AKH B 1 400 UNP P03844 SECY_ECOLI 1 436 DBREF 2AKH B 76 436 UNP P03844 SECY_ECOLI 76 436 DBREF 2AKH Z 17 127 UNP P16920 SECE_ECOLI 17 127 DBREF 2AKH C 17 127 UNP P16920 SECE_ECOLI 17 127 SEQRES 1 X 77 MET TYR GLU ALA LEU LEU VAL VAL PHE LEU ILE VAL ALA SEQRES 2 X 77 ILE GLY LEU VAL GLY LEU ILE MET LEU GLN GLN GLY LYS SEQRES 3 X 77 GLY ALA ASP MET GLY ALA SER PHE GLY ALA GLY ALA SER SEQRES 4 X 77 ALA THR LEU PHE GLY SER SER GLY SER GLY ASN PHE MET SEQRES 5 X 77 THR ARG MET THR ALA LEU LEU ALA THR LEU PHE PHE ILE SEQRES 6 X 77 ILE SER LEU VAL LEU GLY ASN ILE ASN SER ASN LYS SEQRES 1 Y 400 MET ALA LYS GLN PRO GLY LEU ASP PHE GLN SER ALA LYS SEQRES 2 Y 400 GLY GLY LEU GLY GLU LEU LYS ARG ARG LEU LEU PHE VAL SEQRES 3 Y 400 ILE GLY ALA LEU ILE VAL PHE ARG ILE GLY SER PHE ILE SEQRES 4 Y 400 SER ILE PHE ALA LEU GLY ILE MET PRO TYR ILE SER ALA SEQRES 5 Y 400 SER ILE ILE ILE GLN LEU LEU THR VAL VAL HIS PRO THR SEQRES 6 Y 400 LEU ALA GLU ILE LYS LYS GLU GLY GLU SER GLY ARG ARG SEQRES 7 Y 400 LYS ILE SER GLN TYR THR ARG TYR GLY THR LEU VAL LEU SEQRES 8 Y 400 ALA ILE PHE GLN SER ILE GLY ILE ALA THR GLY LEU PRO SEQRES 9 Y 400 ASN MET PRO GLY MET GLN GLY LEU VAL ILE ASN PRO GLY SEQRES 10 Y 400 PHE ALA PHE TYR PHE THR ALA VAL VAL SER LEU VAL THR SEQRES 11 Y 400 GLY THR MET PHE LEU MET TRP LEU GLY GLU GLN ILE THR SEQRES 12 Y 400 GLU ARG GLY ILE GLY ASN GLY ILE SER ILE ILE ILE PHE SEQRES 13 Y 400 ALA GLY ILE VAL ALA GLY LEU PRO PRO ALA ILE ALA HIS SEQRES 14 Y 400 THR ILE GLU GLN ALA ARG GLN GLY ASP LEU HIS PHE LEU SEQRES 15 Y 400 VAL LEU LEU LEU VAL ALA VAL LEU VAL PHE ALA VAL THR SEQRES 16 Y 400 PHE PHE VAL VAL PHE VAL GLU ARG GLY GLN ARG ARG ILE SEQRES 17 Y 400 VAL VAL ASN TYR ALA LYS ARG GLN GLN GLY ARG ARG VAL SEQRES 18 Y 400 TYR ALA ALA GLN SER THR HIS LEU PRO LEU LYS VAL ASN SEQRES 19 Y 400 MET ALA GLY VAL ILE PRO ALA ILE PHE ALA SER SER ILE SEQRES 20 Y 400 ILE LEU PHE PRO ALA THR ILE ALA SER TRP PHE GLY GLY SEQRES 21 Y 400 GLY THR GLY TRP ASN TRP LEU THR THR ILE SER LEU TYR SEQRES 22 Y 400 LEU GLN PRO GLY GLN PRO LEU TYR VAL LEU LEU TYR ALA SEQRES 23 Y 400 SER ALA ILE ILE PHE PHE CYS PHE PHE TYR THR ALA LEU SEQRES 24 Y 400 VAL PHE ASN PRO ARG GLU THR ALA ASP ASN LEU LYS LYS SEQRES 25 Y 400 SER GLY ALA PHE VAL PRO GLY ILE ARG PRO GLY GLU GLN SEQRES 26 Y 400 THR ALA LYS TYR ILE ASP LYS VAL MET THR ARG LEU THR SEQRES 27 Y 400 LEU VAL GLY ALA LEU TYR ILE THR PHE ILE CYS LEU ILE SEQRES 28 Y 400 PRO GLU PHE MET ARG ASP ALA MET LYS VAL PRO PHE TYR SEQRES 29 Y 400 PHE GLY GLY THR SER LEU LEU ILE VAL VAL VAL VAL ILE SEQRES 30 Y 400 MET ASP PHE MET ALA GLN VAL GLN THR LEU MET MET SER SEQRES 31 Y 400 SER GLN TYR GLU SER ALA LEU LYS LYS ALA SEQRES 1 Z 111 MET LYS TRP VAL VAL VAL VAL ALA LEU LEU LEU VAL ALA SEQRES 2 Z 111 ILE VAL GLY ASN TYR LEU TYR ARG ASP ILE MET LEU PRO SEQRES 3 Z 111 LEU ARG ALA LEU ALA VAL VAL ILE LEU ILE ALA ALA ALA SEQRES 4 Z 111 GLY GLY VAL ALA LEU LEU THR THR LYS GLY LYS ALA THR SEQRES 5 Z 111 VAL ALA PHE ALA ARG GLU ALA ARG THR GLU VAL ARG LYS SEQRES 6 Z 111 VAL ILE TRP PRO THR ARG GLN GLU THR LEU HIS THR THR SEQRES 7 Z 111 LEU ILE VAL ALA ALA VAL THR ALA VAL MET SER LEU ILE SEQRES 8 Z 111 LEU TRP GLY LEU ASP GLY ILE LEU VAL ARG LEU VAL SER SEQRES 9 Z 111 PHE ILE THR GLY LEU ARG PHE SEQRES 1 A 77 MET TYR GLU ALA LEU LEU VAL VAL PHE LEU ILE VAL ALA SEQRES 2 A 77 ILE GLY LEU VAL GLY LEU ILE MET LEU GLN GLN GLY LYS SEQRES 3 A 77 GLY ALA ASP MET GLY ALA SER PHE GLY ALA GLY ALA SER SEQRES 4 A 77 ALA THR LEU PHE GLY SER SER GLY SER GLY ASN PHE MET SEQRES 5 A 77 THR ARG MET THR ALA LEU LEU ALA THR LEU PHE PHE ILE SEQRES 6 A 77 ILE SER LEU VAL LEU GLY ASN ILE ASN SER ASN LYS SEQRES 1 B 400 MET ALA LYS GLN PRO GLY LEU ASP PHE GLN SER ALA LYS SEQRES 2 B 400 GLY GLY LEU GLY GLU LEU LYS ARG ARG LEU LEU PHE VAL SEQRES 3 B 400 ILE GLY ALA LEU ILE VAL PHE ARG ILE GLY SER PHE ILE SEQRES 4 B 400 SER ILE PHE ALA LEU GLY ILE MET PRO TYR ILE SER ALA SEQRES 5 B 400 SER ILE ILE ILE GLN LEU LEU THR VAL VAL HIS PRO THR SEQRES 6 B 400 LEU ALA GLU ILE LYS LYS GLU GLY GLU SER GLY ARG ARG SEQRES 7 B 400 LYS ILE SER GLN TYR THR ARG TYR GLY THR LEU VAL LEU SEQRES 8 B 400 ALA ILE PHE GLN SER ILE GLY ILE ALA THR GLY LEU PRO SEQRES 9 B 400 ASN MET PRO GLY MET GLN GLY LEU VAL ILE ASN PRO GLY SEQRES 10 B 400 PHE ALA PHE TYR PHE THR ALA VAL VAL SER LEU VAL THR SEQRES 11 B 400 GLY THR MET PHE LEU MET TRP LEU GLY GLU GLN ILE THR SEQRES 12 B 400 GLU ARG GLY ILE GLY ASN GLY ILE SER ILE ILE ILE PHE SEQRES 13 B 400 ALA GLY ILE VAL ALA GLY LEU PRO PRO ALA ILE ALA HIS SEQRES 14 B 400 THR ILE GLU GLN ALA ARG GLN GLY ASP LEU HIS PHE LEU SEQRES 15 B 400 VAL LEU LEU LEU VAL ALA VAL LEU VAL PHE ALA VAL THR SEQRES 16 B 400 PHE PHE VAL VAL PHE VAL GLU ARG GLY GLN ARG ARG ILE SEQRES 17 B 400 VAL VAL ASN TYR ALA LYS ARG GLN GLN GLY ARG ARG VAL SEQRES 18 B 400 TYR ALA ALA GLN SER THR HIS LEU PRO LEU LYS VAL ASN SEQRES 19 B 400 MET ALA GLY VAL ILE PRO ALA ILE PHE ALA SER SER ILE SEQRES 20 B 400 ILE LEU PHE PRO ALA THR ILE ALA SER TRP PHE GLY GLY SEQRES 21 B 400 GLY THR GLY TRP ASN TRP LEU THR THR ILE SER LEU TYR SEQRES 22 B 400 LEU GLN PRO GLY GLN PRO LEU TYR VAL LEU LEU TYR ALA SEQRES 23 B 400 SER ALA ILE ILE PHE PHE CYS PHE PHE TYR THR ALA LEU SEQRES 24 B 400 VAL PHE ASN PRO ARG GLU THR ALA ASP ASN LEU LYS LYS SEQRES 25 B 400 SER GLY ALA PHE VAL PRO GLY ILE ARG PRO GLY GLU GLN SEQRES 26 B 400 THR ALA LYS TYR ILE ASP LYS VAL MET THR ARG LEU THR SEQRES 27 B 400 LEU VAL GLY ALA LEU TYR ILE THR PHE ILE CYS LEU ILE SEQRES 28 B 400 PRO GLU PHE MET ARG ASP ALA MET LYS VAL PRO PHE TYR SEQRES 29 B 400 PHE GLY GLY THR SER LEU LEU ILE VAL VAL VAL VAL ILE SEQRES 30 B 400 MET ASP PHE MET ALA GLN VAL GLN THR LEU MET MET SER SEQRES 31 B 400 SER GLN TYR GLU SER ALA LEU LYS LYS ALA SEQRES 1 C 111 MET LYS TRP VAL VAL VAL VAL ALA LEU LEU LEU VAL ALA SEQRES 2 C 111 ILE VAL GLY ASN TYR LEU TYR ARG ASP ILE MET LEU PRO SEQRES 3 C 111 LEU ARG ALA LEU ALA VAL VAL ILE LEU ILE ALA ALA ALA SEQRES 4 C 111 GLY GLY VAL ALA LEU LEU THR THR LYS GLY LYS ALA THR SEQRES 5 C 111 VAL ALA PHE ALA ARG GLU ALA ARG THR GLU VAL ARG LYS SEQRES 6 C 111 VAL ILE TRP PRO THR ARG GLN GLU THR LEU HIS THR THR SEQRES 7 C 111 LEU ILE VAL ALA ALA VAL THR ALA VAL MET SER LEU ILE SEQRES 8 C 111 LEU TRP GLY LEU ASP GLY ILE LEU VAL ARG LEU VAL SER SEQRES 9 C 111 PHE ILE THR GLY LEU ARG PHE 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