HEADER PROTEIN TRANSPORT 03-AUG-05 2AKI
TITLE NORMAL MODE-BASED FLEXIBLE FITTED COORDINATES OF A 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 OMITTED;
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.MITRA,C.SCHAFFITZEL,T.SHAIKH,F.TAMA,S.JENNI,C.L.BROOKS III,N.BAN,
AUTHOR 2 J.FRANK
REVDAT 4 14-FEB-24 2AKI 1 REMARK
REVDAT 3 18-JUL-18 2AKI 1 REMARK
REVDAT 2 24-FEB-09 2AKI 1 VERSN
REVDAT 1 15-NOV-05 2AKI 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 2AKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-05.
REMARK 100 THE DEPOSITION ID IS D_1000034001.
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: 2AKH RELATED DB: PDB
REMARK 900 NORMAL MODE-BASED FLEXIBLE FITTED COORDINATES OF A NON-
REMARK 900 TRANSLOCATING SECYEG PROTEIN-CONDUCTING CHANNEL INTO THE CRYO-EM
REMARK 900 MAP OF A SECYEG-NASCENT CHAIN-70S RIBOSOME COMPLEX FROM E. COLI
DBREF 2AKI X 1 77 UNP P33582 SECG_ECOLI 1 77
DBREF 2AKI A 1 77 UNP P33582 SECG_ECOLI 1 77
DBREF 2AKI Y 1 39 UNP P03844 SECY_ECOLI 1 39
DBREF 2AKI Y 76 436 UNP P03844 SECY_ECOLI 76 436
DBREF 2AKI B 1 400 UNP P03844 SECY_ECOLI 1 436
DBREF 2AKI B 76 436 UNP P03844 SECY_ECOLI 76 436
DBREF 2AKI Z 17 127 UNP P16920 SECE_ECOLI 17 127
DBREF 2AKI 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
(ATOM LINES ARE NOT SHOWN.)
END