HEADER LYASE/HYDROLASE 16-JUN-14 4UPF TITLE ASSEMBLY PRINCIPLES OF THE UNIQUE CAGE FORMED BY THE ATPASE RAVA TITLE 2 HEXAMER AND THE LYSINE DECARBOXYLASE LDCI DECAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE DECARBOXYLASE, INDUCIBLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LDC, INDUCIBLE LYSINE DECARBOXYLASE; COMPND 5 EC: 4.1.1.18; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ATPASE RAVA; COMPND 9 CHAIN: D; COMPND 10 FRAGMENT: LARA DOMAIN RESIDUES 329-440; COMPND 11 SYNONYM: REGULATORY ATPASE VARIANT A; COMPND 12 EC: 3.6.3.1; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655; SOURCE 3 ORGANISM_TAXID: 511145; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: CF1693 SOURCE 7; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655; SOURCE 11 ORGANISM_TAXID: 511145; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_VARIANT: GOLD PLYSS; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_VECTOR: P11 KEYWDS LYASE-HYDROLASE COMPLEX, LYSINE DECARBOXYLASE, AAA+ ATPASE, ACID KEYWDS 2 STRESS RESPONSE EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, D AUTHOR H.MALET,K.LIU,M.EL BAKKOURI,S.W.S.CHAN,G.EFFANTIN,M.BACIA,W.A.HOURY, AUTHOR 2 I.GUTSCHE REVDAT 4 08-MAY-24 4UPF 1 REMARK REVDAT 3 30-AUG-17 4UPF 1 REMARK REVDAT 2 10-SEP-14 4UPF 1 JRNL REVDAT 1 20-AUG-14 4UPF 0 JRNL AUTH H.MALET,K.LIU,M.EL BAKKOURI,S.W.S.CHAN,G.EFFANTIN,M.BACIA, JRNL AUTH 2 W.A.HOURY,I.GUTSCHE JRNL TITL ASSEMBLY PRINCIPLES OF A UNIQUE CAGE FORMED BY HEXAMERIC AND JRNL TITL 2 DECAMERIC E. COLI PROTEINS. JRNL REF ELIFE V. 3 03653 2014 JRNL REFN ESSN 2050-084X JRNL PMID 25097238 JRNL DOI 10.7554/ELIFE.03653 REMARK 2 REMARK 2 RESOLUTION. 7.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND, FLEX-EM, SITUS, EMAN, EMAN, REMARK 3 FPM, IMAGIC, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3N75 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--FLEXIBLE FOR 3N75, RIGID FOR 3NBX REMARK 3 REFINEMENT PROTOCOL--X-RAY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.464 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 7.500 REMARK 3 NUMBER OF PARTICLES : 23540 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: CROSS-COMMON LINE, PROJECTION MATCHING SUBMISSION REMARK 3 BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2681. (DEPOSITION ID: REMARK 3 12595). REMARK 4 REMARK 4 4UPF 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_1290060953. 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 : COMPLEX BETWEEN A DECAMER OF REMARK 245 INDUCIBLE LYSINE DECARBOXYLASE REMARK 245 LDCI AND TEN LARA DOMAINS OF REMARK 245 THE ATPASE RAVA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.60 REMARK 245 SAMPLE SUPPORT DETAILS : OTHER REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- CRYOGEN- REMARK 245 ETHANE, HUMIDITY- 100, REMARK 245 TEMPERATURE- 91, INSTRUMENT- REMARK 245 FEI VITROBOT MARK III, METHOD- REMARK 245 BLOT FOR 2 SECONDS BEFORE REMARK 245 PLUNGING REMARK 245 SAMPLE BUFFER : 50MM MES PH 6.5, 100MM NACL, REMARK 245 0.2MM PLP, 1MM DTT, 0.01% REMARK 245 GLUTARALDEHYDE REMARK 245 PH : 6.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 14-SEP-12 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 91.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : GATAN ULTRASCAN 4000 (4K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2700.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : -0.10 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 51660 REMARK 245 CALIBRATED MAGNIFICATION : 51660 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : AUTOMATIC DATA ACQUISITION REMARK 245 WITH FEI EPU SOFTWARE 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: A, 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 LYS A 367 REMARK 465 GLU A 712 REMARK 465 SER A 713 REMARK 465 LYS A 714 REMARK 465 LYS A 715 REMARK 465 GLY D 326 REMARK 465 HIS D 327 REMARK 465 MET D 328 REMARK 465 GLN D 329 REMARK 465 GLN D 330 REMARK 465 SER D 331 REMARK 465 ASP D 332 REMARK 465 LYS D 333 REMARK 465 THR D 334 REMARK 465 ALA D 335 REMARK 465 LEU D 336 REMARK 465 THR D 337 REMARK 465 VAL D 338 REMARK 465 ILE D 339 REMARK 465 ARG D 340 REMARK 465 LEU D 341 REMARK 465 GLY D 342 REMARK 465 GLY D 343 REMARK 465 ILE D 344 REMARK 465 PHE D 345 REMARK 465 SER D 346 REMARK 465 ARG D 347 REMARK 465 ARG D 348 REMARK 465 GLN D 349 REMARK 465 GLN D 350 REMARK 465 TYR D 351 REMARK 465 GLN D 352 REMARK 465 LEU D 353 REMARK 465 PRO D 354 REMARK 465 VAL D 355 REMARK 465 ASN D 356 REMARK 465 VAL D 357 REMARK 465 THR D 358 REMARK 465 ALA D 359 REMARK 465 SER D 360 REMARK 465 PRO D 435 REMARK 465 GLY D 436 REMARK 465 SER D 437 REMARK 465 SER D 438 REMARK 465 ALA D 439 REMARK 465 GLU D 440 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UPB RELATED DB: PDB REMARK 900 ELECTRON CRYO-MICROSCOPY OF THE COMPLEX FORMED BETWEEN THE REMARK 900 HEXAMERIC ATPASE RAVA AND THE DECAMERIC INDUCIBLE DECARBOXYLASE LDCI REMARK 900 RELATED ID: EMD-2681 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE LARA DOMAIN (FROM GLN329 TO GLU440) WAS PCR AMPLIFIED REMARK 999 FROM THE P11-RAVA PLASMID. THE PCR PRODUCT WAS DIGESTED REMARK 999 WITH NDEI AND BAMHI (NEB) AND LIGATED INTO AN EMPTY P11 REMARK 999 VECTOR TO PRODUCE P11-LARA. THE RESULTING CONSTRUCT HAS AN REMARK 999 N-TERMINAL HIS6-TAG FOLLOWED BY A TOBACCO ETCH VIRUS (TEV) REMARK 999 CUT SITE THAT LEAVES THE THREE RESIDUES GHM AT THE REMARK 999 TERMINUS OF THE CONSTRUCT AFTER TEV CLEAVAGE. DBREF 4UPF A 1 715 UNP P0A9H3 LDCI_ECOLI 1 715 DBREF 4UPF D 329 440 UNP P31473 RAVA_ECOLI 329 440 SEQADV 4UPF GLY D 326 UNP P31473 EXPRESSION TAG SEQADV 4UPF HIS D 327 UNP P31473 EXPRESSION TAG SEQADV 4UPF MET D 328 UNP P31473 EXPRESSION TAG SEQRES 1 A 715 MET ASN VAL ILE ALA ILE LEU ASN HIS MET GLY VAL TYR SEQRES 2 A 715 PHE LYS GLU GLU PRO ILE ARG GLU LEU HIS ARG ALA LEU SEQRES 3 A 715 GLU ARG LEU ASN PHE GLN ILE VAL TYR PRO ASN ASP ARG SEQRES 4 A 715 ASP ASP LEU LEU LYS LEU ILE GLU ASN ASN ALA ARG LEU SEQRES 5 A 715 CYS GLY VAL ILE PHE ASP TRP ASP LYS TYR ASN LEU GLU SEQRES 6 A 715 LEU CYS GLU GLU ILE SER LYS MET ASN GLU ASN LEU PRO SEQRES 7 A 715 LEU TYR ALA PHE ALA ASN THR TYR SER THR LEU ASP VAL SEQRES 8 A 715 SER LEU ASN ASP LEU ARG LEU GLN ILE SER PHE PHE GLU SEQRES 9 A 715 TYR ALA LEU GLY ALA ALA GLU ASP ILE ALA ASN LYS ILE SEQRES 10 A 715 LYS GLN THR THR ASP GLU TYR ILE ASN THR ILE LEU PRO SEQRES 11 A 715 PRO LEU THR LYS ALA LEU PHE LYS TYR VAL ARG GLU GLY SEQRES 12 A 715 LYS TYR THR PHE CYS THR PRO GLY HIS MET GLY GLY THR SEQRES 13 A 715 ALA PHE GLN LYS SER PRO VAL GLY SER LEU PHE TYR ASP SEQRES 14 A 715 PHE PHE GLY PRO ASN THR MET LYS SER ASP ILE SER ILE SEQRES 15 A 715 SER VAL SER GLU LEU GLY SER LEU LEU ASP HIS SER GLY SEQRES 16 A 715 PRO HIS LYS GLU ALA GLU GLN TYR ILE ALA ARG VAL PHE SEQRES 17 A 715 ASN ALA ASP ARG SER TYR MET VAL THR ASN GLY THR SER SEQRES 18 A 715 THR ALA ASN LYS ILE VAL GLY MET TYR SER ALA PRO ALA SEQRES 19 A 715 GLY SER THR ILE LEU ILE ASP ARG ASN CYS HIS LYS SER SEQRES 20 A 715 LEU THR HIS LEU MET MET MET SER ASP VAL THR PRO ILE SEQRES 21 A 715 TYR PHE ARG PRO THR ARG ASN ALA TYR GLY ILE LEU GLY SEQRES 22 A 715 GLY ILE PRO GLN SER GLU PHE GLN HIS ALA THR ILE ALA SEQRES 23 A 715 LYS ARG VAL LYS GLU THR PRO ASN ALA THR TRP PRO VAL SEQRES 24 A 715 HIS ALA VAL ILE THR ASN SER THR TYR ASP GLY LEU LEU SEQRES 25 A 715 TYR ASN THR ASP PHE ILE LYS LYS THR LEU ASP VAL LYS SEQRES 26 A 715 SER ILE HIS PHE ASP SER ALA TRP VAL PRO TYR THR ASN SEQRES 27 A 715 PHE SER PRO ILE TYR GLU GLY LYS CYS GLY MET SER GLY SEQRES 28 A 715 GLY ARG VAL GLU GLY LYS VAL ILE TYR GLU THR GLN SER SEQRES 29 A 715 THR HIS LYS LEU LEU ALA ALA PHE SER GLN ALA SER MET SEQRES 30 A 715 ILE HIS VAL LYS GLY ASP VAL ASN GLU GLU THR PHE ASN SEQRES 31 A 715 GLU ALA TYR MET MET HIS THR THR THR SER PRO HIS TYR SEQRES 32 A 715 GLY ILE VAL ALA SER THR GLU THR ALA ALA ALA MET MET SEQRES 33 A 715 LYS GLY ASN ALA GLY LYS ARG LEU ILE ASN GLY SER ILE SEQRES 34 A 715 GLU ARG ALA ILE LYS PHE ARG LYS GLU ILE LYS ARG LEU SEQRES 35 A 715 ARG THR GLU SER ASP GLY TRP PHE PHE ASP VAL TRP GLN SEQRES 36 A 715 PRO ASP HIS ILE ASP THR THR GLU CYS TRP PRO LEU ARG SEQRES 37 A 715 SER ASP SER THR TRP HIS GLY PHE LYS ASN ILE ASP ASN SEQRES 38 A 715 GLU HIS MET TYR LEU ASP PRO ILE LYS VAL THR LEU LEU SEQRES 39 A 715 THR PRO GLY MET GLU LYS ASP GLY THR MET SER ASP PHE SEQRES 40 A 715 GLY ILE PRO ALA SER ILE VAL ALA LYS TYR LEU ASP GLU SEQRES 41 A 715 HIS GLY ILE VAL VAL GLU LYS THR GLY PRO TYR ASN LEU SEQRES 42 A 715 LEU PHE LEU PHE SER ILE GLY ILE ASP LYS THR LYS ALA SEQRES 43 A 715 LEU SER LEU LEU ARG ALA LEU THR ASP PHE LYS ARG ALA SEQRES 44 A 715 PHE ASP LEU ASN LEU ARG VAL LYS ASN MET LEU PRO SER SEQRES 45 A 715 LEU TYR ARG GLU ASP PRO GLU PHE TYR GLU ASN MET ARG SEQRES 46 A 715 ILE GLN GLU LEU ALA GLN ASN ILE HIS LYS LEU ILE VAL SEQRES 47 A 715 HIS HIS ASN LEU PRO ASP LEU MET TYR ARG ALA PHE GLU SEQRES 48 A 715 VAL LEU PRO THR MET VAL MET THR PRO TYR ALA ALA PHE SEQRES 49 A 715 GLN LYS GLU LEU HIS GLY MET THR GLU GLU VAL TYR LEU SEQRES 50 A 715 ASP GLU MET VAL GLY ARG ILE ASN ALA ASN MET ILE LEU SEQRES 51 A 715 PRO TYR PRO PRO GLY VAL PRO LEU VAL MET PRO GLY GLU SEQRES 52 A 715 MET ILE THR GLU GLU SER ARG PRO VAL LEU GLU PHE LEU SEQRES 53 A 715 GLN MET LEU CYS GLU ILE GLY ALA HIS TYR PRO GLY PHE SEQRES 54 A 715 GLU THR ASP ILE HIS GLY ALA TYR ARG GLN ALA ASP GLY SEQRES 55 A 715 ARG TYR THR VAL LYS VAL LEU LYS GLU GLU SER LYS LYS SEQRES 1 D 115 GLY HIS MET GLN GLN SER ASP LYS THR ALA LEU THR VAL SEQRES 2 D 115 ILE ARG LEU GLY GLY ILE PHE SER ARG ARG GLN GLN TYR SEQRES 3 D 115 GLN LEU PRO VAL ASN VAL THR ALA SER THR LEU THR LEU SEQRES 4 D 115 LEU LEU GLN LYS PRO LEU LYS LEU HIS ASP MET GLU VAL SEQRES 5 D 115 VAL HIS ILE SER PHE GLU ARG SER ALA LEU GLU GLN TRP SEQRES 6 D 115 LEU SER LYS GLY GLY GLU ILE ARG GLY LYS LEU ASN GLY SEQRES 7 D 115 ILE GLY PHE ALA GLN LYS LEU ASN LEU GLU VAL ASP SER SEQRES 8 D 115 ALA GLN HIS LEU VAL VAL ARG ASP VAL SER LEU GLN GLY SEQRES 9 D 115 SER THR LEU ALA LEU PRO GLY SER SER ALA GLU 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