HEADER TRANSPORT PROTEIN 05-SEP-24 9DIS TITLE CRYO-EM STRUCTURE OF THE HEME/HEMOGLOBIN TRANSPORTER CHUA, IN COMPLEX TITLE 2 WITH DE NOVO DESIGNED BINDER H3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHUA BINDER H3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: OUTER MEMBRANE HEME/HEMOGLOBIN RECEPTOR; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: C41 DE3; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI CFT073; SOURCE 9 ORGANISM_TAXID: 199310; SOURCE 10 GENE: CHUA, C4308; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: C41 DE3 KEYWDS TONB-DEPENDENT TRANSPORTER, CHUA, HEME, HEMOGLOBIN, OUTER-MEMBRANE, KEYWDS 2 DE NOVO DESIGNED PROTEIN, BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.FOX,H.VENUGOPAL,C.J.LUPTON,B.A.SPICER,R.GRINTER REVDAT 2 23-JUL-25 9DIS 1 JRNL REVDAT 1 21-MAY-25 9DIS 0 JRNL AUTH D.R.FOX,K.ASADOLLAHI,I.SAMUELS,B.A.SPICER,A.KROPP, JRNL AUTH 2 C.J.LUPTON,K.LIM,C.WANG,H.VENUGOPAL,M.DRAMICANIN,G.J.KNOTT, JRNL AUTH 3 R.GRINTER JRNL TITL INHIBITING HEME PIRACY BY PATHOGENIC ESCHERICHIA COLI USING JRNL TITL 2 DE NOVO-DESIGNED PROTEINS. JRNL REF NAT COMMUN V. 16 6066 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40634285 JRNL DOI 10.1038/S41467-025-60612-9 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 2.510 REMARK 3 NUMBER OF PARTICLES : 333575 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 9DIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288129. 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 : COMPLEX BETWEEN THE REMARK 245 HEME/HEMOGLOBIN TRANSPORTER REMARK 245 CHUA AND DE NOVO DESIGNED REMARK 245 BINDING PROTEIN G7 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : 4D-STEM REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 7000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LEU A 115 REMARK 465 GLU A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 THR B 9 REMARK 465 THR B 289 REMARK 465 GLY B 290 REMARK 465 SER B 291 REMARK 465 SER B 292 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP B 511 ND2 ASN B 528 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 47 -61.35 -95.91 REMARK 500 PRO B 27 45.33 -78.73 REMARK 500 ALA B 123 56.59 -97.81 REMARK 500 THR B 170 -167.99 -125.39 REMARK 500 ALA B 558 -137.30 53.92 REMARK 500 GLN B 600 -121.80 60.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-46917 RELATED DB: EMDB REMARK 900 THE CRYSTAL STRUCTURE ON THE HEME/HEMOGLOBIN TRANSPORTER CHUA, IN REMARK 900 COMPLEX WITH HEME DBREF 9DIS A 1 122 PDB 9DIS 9DIS 1 122 DBREF1 9DIS B 9 640 UNP A0A0H2VC22_ECOL6 DBREF2 9DIS B A0A0H2VC22 17 648 SEQRES 1 A 122 ALA LYS ALA GLU GLU ALA LYS ALA ARG ALA ALA ALA SER SEQRES 2 A 122 ARG GLU ALA ALA ILE ALA HIS VAL ARG GLU LEU LEU LYS SEQRES 3 A 122 GLU GLN SER ASP THR PRO GLU MET ALA GLU LEU LEU ARG SEQRES 4 A 122 LEU PHE GLU ALA ALA GLU ALA ALA ASP PRO LEU ALA ALA SEQRES 5 A 122 ALA ALA ILE ALA ALA SER TYR LEU ALA ILE GLN GLU TYR SEQRES 6 A 122 ALA THR ALA PRO PRO GLU THR ALA ALA THR PHE GLU LYS SEQRES 7 A 122 TYR ALA TYR ALA ALA ALA ALA GLU ALA GLU ALA SER PRO SEQRES 8 A 122 LEU PRO GLU ALA LYS ARG ALA ALA GLU LEU LEU ARG LYS SEQRES 9 A 122 LEU LEU ASP GLU ALA LYS ALA LYS ARG ALA LEU GLU HIS SEQRES 10 A 122 HIS HIS HIS HIS HIS SEQRES 1 B 632 THR GLU THR MET THR VAL THR ALA THR GLY ASN ALA ARG SEQRES 2 B 632 SER SER PHE GLU ALA PRO MET MET VAL SER VAL ILE ASP SEQRES 3 B 632 THR SER ALA PRO GLU ASN GLN THR ALA THR SER ALA THR SEQRES 4 B 632 ASP LEU LEU ARG HIS VAL PRO GLY ILE THR LEU ASP GLY SEQRES 5 B 632 THR GLY ARG THR ASN GLY GLN ASP VAL ASN MET ARG GLY SEQRES 6 B 632 TYR ASP HIS ARG GLY VAL LEU VAL LEU VAL ASP GLY VAL SEQRES 7 B 632 ARG GLN GLY THR ASP THR GLY HIS LEU ASN GLY THR PHE SEQRES 8 B 632 LEU ASP PRO ALA LEU ILE LYS ARG VAL GLU ILE VAL ARG SEQRES 9 B 632 GLY PRO SER ALA LEU LEU TYR GLY SER GLY ALA LEU GLY SEQRES 10 B 632 GLY VAL ILE SER TYR ASP THR VAL ASP ALA LYS ASP LEU SEQRES 11 B 632 LEU GLN GLU GLY GLN SER SER GLY PHE ARG VAL PHE GLY SEQRES 12 B 632 THR GLY GLY THR GLY ASP HIS SER LEU GLY LEU GLY ALA SEQRES 13 B 632 SER ALA PHE GLY ARG THR GLU ASN LEU ASP GLY ILE VAL SEQRES 14 B 632 ALA TRP SER SER ARG ASP ARG GLY ASP LEU ARG GLN SER SEQRES 15 B 632 ASN GLY GLU THR ALA PRO ASN ASP GLU SER ILE ASN ASN SEQRES 16 B 632 MET LEU ALA LYS GLY THR TRP GLN ILE ASP SER ALA GLN SEQRES 17 B 632 SER LEU SER GLY LEU VAL ARG TYR TYR ASN ASN ASP ALA SEQRES 18 B 632 ARG GLU PRO LYS ASN PRO GLN THR VAL GLU ALA SER ASP SEQRES 19 B 632 SER SER ASN PRO MET VAL ASP ARG SER THR ILE GLN ARG SEQRES 20 B 632 ASP ALA GLN LEU SER TYR LYS LEU ALA PRO GLN GLY ASN SEQRES 21 B 632 ASP TRP LEU ASN ALA ASP ALA LYS ILE TYR TRP SER GLU SEQRES 22 B 632 VAL ARG ILE ASN ALA GLN ASN THR GLY SER SER GLY GLU SEQRES 23 B 632 TYR ARG GLU GLN ILE THR LYS GLY ALA ARG LEU GLU ASN SEQRES 24 B 632 ARG SER THR LEU PHE ALA ASP SER PHE ALA SER HIS LEU SEQRES 25 B 632 LEU THR TYR GLY GLY GLU TYR TYR ARG GLN GLU GLN HIS SEQRES 26 B 632 PRO GLY GLY ALA THR THR GLY PHE PRO GLN ALA LYS ILE SEQRES 27 B 632 ASP PHE SER SER GLY TRP LEU GLN ASP GLU ILE THR LEU SEQRES 28 B 632 ARG ASP LEU PRO ILE THR LEU LEU GLY GLY THR ARG TYR SEQRES 29 B 632 ASP SER TYR ARG GLY SER SER ASP GLY TYR LYS ASP VAL SEQRES 30 B 632 ASP ALA ASP LYS TRP SER SER ARG ALA GLY MET THR ILE SEQRES 31 B 632 ASN PRO THR ASN TRP LEU MET LEU PHE GLY SER TYR ALA SEQRES 32 B 632 GLN ALA PHE ARG ALA PRO THR MET GLY GLU MET TYR ASN SEQRES 33 B 632 ASP SER LYS HIS PHE SER ILE GLY ARG PHE TYR THR ASN SEQRES 34 B 632 TYR TRP VAL PRO ASN PRO ASN LEU ARG PRO GLU THR ASN SEQRES 35 B 632 GLU THR GLN GLU TYR GLY PHE GLY LEU ARG PHE ASP ASP SEQRES 36 B 632 LEU MET LEU SER ASN ASP ALA LEU GLU PHE LYS ALA SER SEQRES 37 B 632 TYR PHE ASP THR LYS ALA LYS ASP TYR ILE SER THR THR SEQRES 38 B 632 VAL ASP PHE ALA ALA ALA THR THR MET SER TYR ASN VAL SEQRES 39 B 632 PRO ASN ALA LYS ILE TRP GLY TRP ASP VAL MET THR LYS SEQRES 40 B 632 TYR THR THR ASP LEU PHE SER LEU ASP VAL ALA TYR ASN SEQRES 41 B 632 ARG THR ARG GLY LYS ASP THR ASP THR GLY GLU TYR ILE SEQRES 42 B 632 SER SER ILE ASN PRO ASP THR VAL THR SER THR LEU ASN SEQRES 43 B 632 ILE PRO ILE ALA HIS SER GLY PHE SER VAL GLY TRP VAL SEQRES 44 B 632 GLY THR PHE ALA ASP ARG SER THR HIS ILE SER SER SER SEQRES 45 B 632 TYR SER LYS GLN PRO GLY TYR GLY VAL ASN ASP PHE TYR SEQRES 46 B 632 VAL SER TYR GLN GLY GLN GLN ALA LEU LYS GLY MET THR SEQRES 47 B 632 THR THR LEU VAL LEU GLY ASN ALA PHE ASP LYS GLU TYR SEQRES 48 B 632 TRP SER PRO GLN GLY ILE PRO GLN ASP GLY ARG ASN GLY SEQRES 49 B 632 LYS ILE PHE VAL SER TYR GLN TRP HELIX 1 AA1 ALA A 1 GLU A 27 1 27 HELIX 2 AA2 THR A 31 ASP A 48 1 18 HELIX 3 AA3 ASP A 48 THR A 67 1 20 HELIX 4 AA4 PRO A 69 SER A 90 1 22 HELIX 5 AA5 LEU A 92 ARG A 113 1 22 HELIX 6 AA6 ALA B 46 ARG B 51 5 6 HELIX 7 AA7 ASP B 101 ALA B 103 5 3 HELIX 8 AA8 SER B 115 GLY B 120 1 6 HELIX 9 AA9 ASP B 134 LEU B 139 1 6 HELIX 10 AB1 THR B 418 ASN B 424 1 7 HELIX 11 AB2 GLN B 599 LYS B 603 5 5 SHEET 1 AA1 2 MET B 12 THR B 13 0 SHEET 2 AA1 2 ARG B 21 SER B 22 -1 O ARG B 21 N THR B 13 SHEET 1 AA2 5 MET B 29 ASP B 34 0 SHEET 2 AA2 5 ILE B 105 ARG B 112 -1 O ILE B 110 N SER B 31 SHEET 3 AA2 5 GLY B 126 THR B 132 -1 O VAL B 127 N VAL B 111 SHEET 4 AA2 5 LEU B 80 VAL B 83 1 N LEU B 82 O TYR B 130 SHEET 5 AA2 5 VAL B 86 ARG B 87 -1 O VAL B 86 N VAL B 83 SHEET 1 AA3 2 ILE B 56 LEU B 58 0 SHEET 2 AA3 2 VAL B 69 MET B 71 -1 O ASN B 70 N THR B 57 SHEET 1 AA425 LYS B 427 ILE B 431 0 SHEET 2 AA425 TYR B 435 TRP B 439 -1 O ASN B 437 N PHE B 429 SHEET 3 AA425 THR B 496 THR B 517 1 O THR B 497 N TYR B 438 SHEET 4 AA425 SER B 522 LYS B 533 -1 O LYS B 533 N LYS B 506 SHEET 5 AA425 ASN B 545 PRO B 556 -1 O THR B 550 N ALA B 526 SHEET 6 AA425 PHE B 562 ALA B 571 -1 O PHE B 570 N VAL B 549 SHEET 7 AA425 TYR B 587 GLN B 597 -1 O VAL B 589 N THR B 569 SHEET 8 AA425 MET B 605 GLY B 612 -1 O LEU B 609 N VAL B 594 SHEET 9 AA425 ASN B 631 GLN B 639 -1 O LYS B 633 N VAL B 610 SHEET 10 AA425 SER B 145 GLY B 154 -1 N GLY B 151 O VAL B 636 SHEET 11 AA425 SER B 159 ARG B 169 -1 O PHE B 167 N GLY B 146 SHEET 12 AA425 LEU B 173 ARG B 184 -1 O GLY B 175 N GLY B 168 SHEET 13 AA425 ASP B 198 GLN B 211 -1 O ILE B 201 N ARG B 182 SHEET 14 AA425 GLN B 216 PRO B 232 -1 O LEU B 218 N TRP B 210 SHEET 15 AA425 MET B 247 LEU B 263 -1 O VAL B 248 N GLU B 231 SHEET 16 AA425 ASN B 272 GLN B 287 -1 O ALA B 273 N LEU B 263 SHEET 17 AA425 GLU B 294 LEU B 311 -1 O GLU B 306 N ASP B 274 SHEET 18 AA425 ALA B 317 GLY B 336 -1 O LEU B 321 N SER B 309 SHEET 19 AA425 ALA B 344 LEU B 359 -1 O PHE B 348 N TYR B 328 SHEET 20 AA425 ILE B 364 SER B 379 -1 O TYR B 372 N GLY B 351 SHEET 21 AA425 TYR B 382 ILE B 398 -1 O ALA B 387 N TYR B 375 SHEET 22 AA425 LEU B 404 ARG B 415 -1 O LEU B 406 N ILE B 398 SHEET 23 AA425 GLU B 448 ASP B 462 -1 O THR B 452 N ALA B 411 SHEET 24 AA425 ALA B 470 ASP B 491 -1 O LYS B 481 N GLU B 451 SHEET 25 AA425 THR B 496 THR B 517 -1 O VAL B 502 N TYR B 485 SHEET 1 AA5 2 LEU B 187 ARG B 188 0 SHEET 2 AA5 2 THR B 194 ALA B 195 -1 O ALA B 195 N LEU B 187 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 849 ALA A 114 TER 5723 TRP B 640 MASTER 156 0 0 11 36 0 0 6 5721 2 0 59 END