HEADER MEMBRANE PROTEIN 05-MAR-25 9NN6 TITLE E. COLI CIR IN COMPLEX WITH THE RBD OF MICROCIN V COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN I RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COLICIN-V; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: MICROCIN-V BACTERIOCIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CIRA, CIR, FEUA, B2155, JW2142; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ENTEROBACTERIACEAE; SOURCE 9 ORGANISM_TAXID: 543; SOURCE 10 GENE: CVAC; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TONB-DEPENDENT RECEPTOR, BETA BARREL, ANTIMICROBIAL PROTEIN, MCCV, KEYWDS 2 MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.A.MAURAKIS,I.BOTOS,S.K.BUCHANAN REVDAT 2 22-OCT-25 9NN6 1 JRNL REVDAT 1 24-SEP-25 9NN6 0 JRNL AUTH S.A.MAURAKIS,A.C.O'DONNELL,I.BOTOS,R.GHIRLANDO,B.W.DAVIES, JRNL AUTH 2 S.K.BUCHANAN JRNL TITL STRUCTURAL INSIGHTS INTO CIR-MEDIATED KILLING BY THE JRNL TITL 2 ANTIMICROBIAL PROTEIN MICROCIN V. JRNL REF COMMUN BIOL V. 8 1449 2025 JRNL REFN ESSN 2399-3642 JRNL PMID 41068465 JRNL DOI 10.1038/S42003-025-08846-7 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX 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 : 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 102419 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9NN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000293556. 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 CIR IN COMPLEX WITH THE REMARK 245 RBD OF MICROCIN V REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE +5 WAIT TIME 0 BLOT REMARK 245 TOTAL 1 BLOT TIME 5 SECONDS REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 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) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 5965.00 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: A, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 198 -61.06 -122.31 REMARK 500 ASP A 268 -174.82 57.95 REMARK 500 ASN A 329 57.43 39.85 REMARK 500 SER A 395 74.44 -160.40 REMARK 500 VAL A 494 -62.06 67.03 REMARK 500 GLN A 501 -2.03 70.48 REMARK 500 THR A 508 36.24 -97.90 REMARK 500 LYS A 544 118.49 -161.69 REMARK 500 ASN A 559 48.60 33.29 REMARK 500 THR A 572 116.29 -160.79 REMARK 500 SER A 588 148.22 -172.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49565 RELATED DB: EMDB REMARK 900 E. COLI CIR IN COMPLEX WITH THE RBD OF MICROCIN V DBREF 9NN6 A 32 663 UNP P17315 CIRA_ECOLI 32 663 DBREF 9NN6 B 57 88 UNP P22522 CEAV_ECOLX 72 103 SEQADV 9NN6 MET A 338 UNP P17315 TRP 338 ENGINEERED MUTATION SEQADV 9NN6 MET A 343 UNP P17315 LEU 343 ENGINEERED MUTATION SEQADV 9NN6 MET A 589 UNP P17315 PHE 589 ENGINEERED MUTATION SEQADV 9NN6 MET A 591 UNP P17315 VAL 591 ENGINEERED MUTATION SEQRES 1 A 632 THR MET VAL VAL THR ALA SER SER VAL GLU GLN ASN LEU SEQRES 2 A 632 LYS ASP ALA PRO ALA SER ILE SER VAL ILE THR GLN GLU SEQRES 3 A 632 ASP LEU GLN ARG LYS PRO VAL GLN ASN LEU LYS ASP VAL SEQRES 4 A 632 LEU LYS GLU VAL PRO GLY VAL GLN LEU THR ASN GLU GLY SEQRES 5 A 632 ASP ASN ARG LYS GLY VAL SER ILE ARG GLY LEU ASP SER SEQRES 6 A 632 SER TYR THR LEU ILE LEU VAL ASP GLY LYS ARG VAL ASN SEQRES 7 A 632 SER ARG ASN ALA VAL PHE ARG HIS ASN ASP PHE ASP LEU SEQRES 8 A 632 ASN TRP ILE PRO VAL ASP SER ILE GLU ARG ILE GLU VAL SEQRES 9 A 632 VAL ARG GLY PRO MET SER SER LEU TYR GLY SER ASP ALA SEQRES 10 A 632 LEU GLY GLY VAL VAL ASN ILE ILE THR LYS LYS ILE GLY SEQRES 11 A 632 GLN LYS TRP SER GLY THR VAL THR VAL ASP THR THR ILE SEQRES 12 A 632 GLN GLU HIS ARG ASP ARG GLY ASP THR TYR ASN GLY GLN SEQRES 13 A 632 PHE PHE THR SER GLY PRO LEU ILE ASP GLY VAL LEU GLY SEQRES 14 A 632 MET LYS ALA TYR GLY SER LEU ALA LYS ARG GLU LYS ASP SEQRES 15 A 632 ASP PRO GLN ASN SER THR THR THR ASP THR GLY GLU THR SEQRES 16 A 632 PRO ARG ILE GLU GLY PHE SER SER ARG ASP GLY ASN VAL SEQRES 17 A 632 GLU PHE ALA TRP THR PRO ASN GLN ASN HIS ASP PHE THR SEQRES 18 A 632 ALA GLY TYR GLY PHE ASP ARG GLN ASP ARG ASP SER ASP SEQRES 19 A 632 SER LEU ASP LYS ASN ARG LEU GLU ARG GLN ASN TYR SER SEQRES 20 A 632 VAL SER HIS ASN GLY ARG TRP ASP TYR GLY THR SER GLU SEQRES 21 A 632 LEU LYS TYR TYR GLY GLU LYS VAL GLU ASN LYS ASN PRO SEQRES 22 A 632 GLY ASN SER SER PRO ILE THR SER GLU SER ASN THR VAL SEQRES 23 A 632 ASP GLY LYS TYR THR LEU PRO LEU THR ALA ILE ASN GLN SEQRES 24 A 632 PHE LEU THR VAL GLY GLY GLU MET ARG HIS ASP LYS MET SEQRES 25 A 632 SER ASP ALA VAL ASN LEU THR GLY GLY THR SER SER LYS SEQRES 26 A 632 THR SER ALA SER GLN TYR ALA LEU PHE VAL GLU ASP GLU SEQRES 27 A 632 TRP ARG ILE PHE GLU PRO LEU ALA LEU THR THR GLY VAL SEQRES 28 A 632 ARG MET ASP ASP HIS GLU THR TYR GLY GLU HIS TRP SER SEQRES 29 A 632 PRO ARG ALA TYR LEU VAL TYR ASN ALA THR ASP THR VAL SEQRES 30 A 632 THR VAL LYS GLY GLY TRP ALA THR ALA PHE LYS ALA PRO SEQRES 31 A 632 SER LEU LEU GLN LEU SER PRO ASP TRP THR SER ASN SER SEQRES 32 A 632 CYS ARG GLY ALA CYS LYS ILE VAL GLY SER PRO ASP LEU SEQRES 33 A 632 LYS PRO GLU THR SER GLU SER TRP GLU LEU GLY LEU TYR SEQRES 34 A 632 TYR MET GLY GLU GLU GLY TRP LEU GLU GLY VAL GLU SER SEQRES 35 A 632 SER VAL THR VAL PHE ARG ASN ASP VAL LYS ASP ARG ILE SEQRES 36 A 632 SER ILE SER ARG THR SER ASP VAL ASN ALA ALA PRO GLY SEQRES 37 A 632 TYR GLN ASN PHE VAL GLY PHE GLU THR GLY ALA ASN GLY SEQRES 38 A 632 ARG ARG ILE PRO VAL PHE SER TYR TYR ASN VAL ASN LYS SEQRES 39 A 632 ALA ARG ILE GLN GLY VAL GLU THR GLU LEU LYS ILE PRO SEQRES 40 A 632 PHE ASN ASP GLU TRP LYS LEU SER ILE ASN TYR THR TYR SEQRES 41 A 632 ASN ASP GLY ARG ASP VAL SER ASN GLY GLU ASN LYS PRO SEQRES 42 A 632 LEU SER ASP LEU PRO PHE HIS THR ALA ASN GLY THR LEU SEQRES 43 A 632 ASP TRP LYS PRO LEU ALA LEU GLU ASP TRP SER MET TYR SEQRES 44 A 632 MET SER GLY HIS TYR THR GLY GLN LYS ARG ALA ASP SER SEQRES 45 A 632 ALA THR ALA LYS THR PRO GLY GLY TYR THR ILE TRP ASN SEQRES 46 A 632 THR GLY ALA ALA TRP GLN VAL THR LYS ASP VAL LYS LEU SEQRES 47 A 632 ARG ALA GLY VAL LEU ASN LEU GLY ASP LYS ASP LEU SER SEQRES 48 A 632 ARG ASP ASP TYR SER TYR ASN GLU ASP GLY ARG ARG TYR SEQRES 49 A 632 PHE MET ALA VAL ASP TYR ARG PHE SEQRES 1 B 32 LYS GLN LYS PRO GLU GLY ILE PRO SER GLU ALA TRP ASN SEQRES 2 B 32 TYR ALA ALA GLY ARG LEU CYS ASN TRP SER PRO ASN ASN SEQRES 3 B 32 LEU SER ASP VAL CYS LEU HELIX 1 AA1 THR A 55 LYS A 62 1 8 HELIX 2 AA2 ASN A 66 LYS A 72 1 7 HELIX 3 AA3 ASP A 95 SER A 97 5 3 HELIX 4 AA4 ASP A 119 ASN A 123 5 5 HELIX 5 AA5 PRO A 126 ASP A 128 5 3 HELIX 6 AA6 SER A 422 SER A 427 1 6 HELIX 7 AA7 ALA A 496 GLN A 501 5 6 HELIX 8 AA8 SER A 558 GLU A 561 5 4 HELIX 9 AA9 SER A 642 SER A 647 1 6 SHEET 1 AA1 2 VAL A 34 THR A 36 0 SHEET 2 AA1 2 GLU A 41 ASN A 43 -1 O GLN A 42 N VAL A 35 SHEET 1 AA2 5 SER A 50 ILE A 54 0 SHEET 2 AA2 5 ILE A 130 ARG A 137 -1 O VAL A 135 N SER A 52 SHEET 3 AA2 5 GLY A 151 THR A 157 -1 O VAL A 152 N VAL A 136 SHEET 4 AA2 5 THR A 99 VAL A 103 1 N LEU A 100 O VAL A 153 SHEET 5 AA2 5 LYS A 106 VAL A 108 -1 O VAL A 108 N ILE A 101 SHEET 1 AA3 2 VAL A 77 GLY A 83 0 SHEET 2 AA3 2 ARG A 86 ILE A 91 -1 O SER A 90 N GLN A 78 SHEET 1 AA424 LYS A 563 PRO A 564 0 SHEET 2 AA424 TRP A 543 ASP A 556 -1 N ASP A 556 O LYS A 563 SHEET 3 AA424 HIS A 571 TRP A 579 -1 O ASP A 578 N LYS A 544 SHEET 4 AA424 TRP A 587 THR A 596 -1 O MET A 591 N LEU A 577 SHEET 5 AA424 TYR A 612 TRP A 621 -1 O ASN A 616 N SER A 592 SHEET 6 AA424 VAL A 627 LEU A 634 -1 O ALA A 631 N ALA A 619 SHEET 7 AA424 ARG A 654 PHE A 663 -1 O ALA A 658 N ARG A 630 SHEET 8 AA424 SER A 165 GLN A 175 -1 N ILE A 174 O TYR A 655 SHEET 9 AA424 THR A 183 ILE A 195 -1 O GLN A 187 N THR A 169 SHEET 10 AA424 LEU A 199 ARG A 210 -1 O LYS A 209 N TYR A 184 SHEET 11 AA424 GLY A 231 TRP A 243 -1 O ALA A 242 N GLY A 200 SHEET 12 AA424 PHE A 251 SER A 264 -1 O ALA A 253 N PHE A 241 SHEET 13 AA424 ASP A 268 HIS A 281 -1 O ARG A 274 N ASP A 258 SHEET 14 AA424 THR A 289 ASN A 301 -1 O GLU A 300 N GLU A 273 SHEET 15 AA424 ILE A 310 LEU A 325 -1 O SER A 312 N VAL A 299 SHEET 16 AA424 GLN A 330 SER A 344 -1 O LEU A 332 N LEU A 323 SHEET 17 AA424 LYS A 356 TRP A 370 -1 O GLN A 361 N ARG A 339 SHEET 18 AA424 LEU A 376 HIS A 387 -1 O LEU A 378 N TRP A 370 SHEET 19 AA424 GLY A 391 TYR A 402 -1 O TYR A 399 N THR A 379 SHEET 20 AA424 THR A 409 LYS A 419 -1 O VAL A 410 N TYR A 402 SHEET 21 AA424 GLU A 450 MET A 462 -1 O GLY A 458 N LYS A 411 SHEET 22 AA424 GLU A 472 SER A 487 -1 O ASP A 481 N GLU A 453 SHEET 23 AA424 TYR A 521 ILE A 537 -1 O ILE A 528 N ASN A 480 SHEET 24 AA424 TRP A 543 ASP A 556 -1 O ILE A 547 N LEU A 535 SHEET 1 AA5 2 GLN A 216 ASN A 217 0 SHEET 2 AA5 2 GLU A 225 THR A 226 -1 O THR A 226 N GLN A 216 SHEET 1 AA6 4 THR A 431 SER A 434 0 SHEET 2 AA6 4 CYS A 439 VAL A 442 -1 O CYS A 439 N SER A 434 SHEET 3 AA6 4 ILE A 515 SER A 519 1 O PHE A 518 N LYS A 440 SHEET 4 AA6 4 PHE A 503 GLU A 507 -1 N VAL A 504 O VAL A 517 SHEET 1 AA7 2 TRP B 68 ASN B 69 0 SHEET 2 AA7 2 ARG B 74 LEU B 75 -1 O ARG B 74 N ASN B 69 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 TER 4975 PHE A 663 TER 5226 LEU B 88 MASTER 130 0 0 9 41 0 0 6 5224 2 0 52 END