HEADER MEMBRANE PROTEIN 15-SEP-23 8QKK TITLE CRYO-EM STRUCTURE OF MMPL3 FROM MYCOBACTERIUM SMEGMATIS RECONSTITUTED TITLE 2 INTO PEPTIDISCS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TREHALOSE MONOMYCOLATE EXPORTER MMPL3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 GENE: MMPL3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C43; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: DELTA ACRB KEYWDS MYCOBACTERIUM, TREHALOSE MONOMYCOLATE, TMM, PEPTIDISC, MMPL3, KEYWDS 2 MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.COUSTON,Z.GUO,K.WANG,P.E.GOURDON,M.BLAISE REVDAT 2 13-DEC-23 8QKK 1 JRNL REVDAT 1 15-NOV-23 8QKK 0 JRNL AUTH J.COUSTON,Z.GUO,K.WANG,P.GOURDON,M.BLAISE JRNL TITL CRYO-EM STRUCTURE OF THE TREHALOSE MONOMYCOLATE TRANSPORTER, JRNL TITL 2 MMPL3, RECONSTITUTED INTO PEPTIDISCS. JRNL REF CURR RES STRUCT BIOL V. 6 00109 2023 JRNL REFN ESSN 2665-928X JRNL PMID 38034087 JRNL DOI 10.1016/J.CRSTBI.2023.100109 REMARK 2 REMARK 2 RESOLUTION. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, PHENIX, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7K7M REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY 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) : 3.230 REMARK 3 NUMBER OF PARTICLES : 348157 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 8QKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292133401. 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 : MONOMER STRUCTURE OF MMPL3 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 10004 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 4500.00 REMARK 245 ILLUMINATION MODE : OTHER 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 0 REMARK 465 THR A 376 REMARK 465 GLN A 377 REMARK 465 LYS A 378 REMARK 465 THR A 379 REMARK 465 LYS A 380 REMARK 465 THR A 381 REMARK 465 ARG A 382 REMARK 465 GLU A 383 REMARK 465 PRO A 739 REMARK 465 ARG A 740 REMARK 465 TRP A 741 REMARK 465 MET A 742 REMARK 465 LYS A 743 REMARK 465 ARG A 744 REMARK 465 VAL A 745 REMARK 465 GLN A 746 REMARK 465 GLU A 747 REMARK 465 LYS A 748 REMARK 465 LEU A 749 REMARK 465 GLY A 750 REMARK 465 LEU A 751 REMARK 465 GLY A 752 REMARK 465 GLU A 753 REMARK 465 THR A 754 REMARK 465 GLU A 755 REMARK 465 LEU A 756 REMARK 465 PRO A 757 REMARK 465 ASP A 758 REMARK 465 GLU A 759 REMARK 465 ARG A 760 REMARK 465 LYS A 761 REMARK 465 ARG A 762 REMARK 465 PRO A 763 REMARK 465 THR A 764 REMARK 465 VAL A 765 REMARK 465 ARG A 766 REMARK 465 GLU A 767 REMARK 465 SER A 768 REMARK 465 GLU A 769 REMARK 465 THR A 770 REMARK 465 ASP A 771 REMARK 465 GLN A 772 REMARK 465 ARG A 773 REMARK 465 GLU A 774 REMARK 465 ASN A 775 REMARK 465 LEU A 776 REMARK 465 TYR A 777 REMARK 465 PHE A 778 REMARK 465 GLN A 779 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 OG1 THR A 127 OD1 ASP A 129 2.13 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 THR A 118 52.29 -93.41 REMARK 500 LEU A 248 -65.33 -93.03 REMARK 500 THR A 285 -60.84 -93.68 REMARK 500 ILE A 356 81.76 -160.55 REMARK 500 THR A 717 -64.18 -96.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18464 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MMPL3 FROM MYCOBACTERIUM SMEGMATIS REMARK 900 RECONSTITUTED INTO PEPTIDISCS DBREF 8QKK A 2 773 UNP A0QP27 MMPL3_MYCS2 2 773 SEQADV 8QKK MET A 0 UNP A0QP27 INITIATING METHIONINE SEQADV 8QKK GLY A 1 UNP A0QP27 EXPRESSION TAG SEQADV 8QKK GLU A 774 UNP A0QP27 EXPRESSION TAG SEQADV 8QKK ASN A 775 UNP A0QP27 EXPRESSION TAG SEQADV 8QKK LEU A 776 UNP A0QP27 EXPRESSION TAG SEQADV 8QKK TYR A 777 UNP A0QP27 EXPRESSION TAG SEQADV 8QKK PHE A 778 UNP A0QP27 EXPRESSION TAG SEQADV 8QKK GLN A 779 UNP A0QP27 EXPRESSION TAG SEQRES 1 A 780 MET GLY PHE ALA TRP TRP GLY ARG THR VAL TYR GLN PHE SEQRES 2 A 780 ARG TYR ILE VAL ILE GLY VAL MET VAL ALA LEU CYS LEU SEQRES 3 A 780 GLY GLY GLY VAL TYR GLY ILE SER LEU GLY ASN HIS VAL SEQRES 4 A 780 THR GLN SER GLY PHE TYR ASP GLU GLY SER GLN SER VAL SEQRES 5 A 780 ALA ALA SER LEU ILE GLY ASP GLU VAL TYR GLY ARG ASP SEQRES 6 A 780 ARG THR SER HIS VAL VAL ALA ILE LEU THR PRO PRO ASP SEQRES 7 A 780 ASP LYS LYS VAL THR ASP LYS ALA TRP GLN LYS LYS VAL SEQRES 8 A 780 THR GLU GLU LEU ASP GLN VAL VAL LYS ASP HIS GLU ASP SEQRES 9 A 780 GLN ILE VAL GLY TRP VAL GLY TRP LEU LYS ALA PRO ASP SEQRES 10 A 780 THR THR ASP PRO THR VAL SER ALA MET LYS THR GLN ASP SEQRES 11 A 780 LEU ARG HIS THR PHE ILE SER ILE PRO LEU GLN GLY ASP SEQRES 12 A 780 ASP ASP ASP GLU ILE LEU LYS ASN TYR GLN VAL VAL GLU SEQRES 13 A 780 PRO GLU LEU GLN GLN VAL ASN GLY GLY ASP ILE ARG LEU SEQRES 14 A 780 ALA GLY LEU ASN PRO LEU ALA SER GLU LEU THR GLY THR SEQRES 15 A 780 ILE GLY GLU ASP GLN LYS ARG ALA GLU VAL ALA ALA ILE SEQRES 16 A 780 PRO LEU VAL ALA VAL VAL LEU PHE PHE VAL PHE GLY THR SEQRES 17 A 780 VAL ILE ALA ALA ALA LEU PRO ALA ILE ILE GLY GLY LEU SEQRES 18 A 780 ALA ILE ALA GLY ALA LEU GLY ILE MET ARG LEU VAL ALA SEQRES 19 A 780 GLU PHE THR PRO VAL HIS PHE PHE ALA GLN PRO VAL VAL SEQRES 20 A 780 THR LEU ILE GLY LEU GLY ILE ALA ILE ASP TYR GLY LEU SEQRES 21 A 780 PHE ILE VAL SER ARG PHE ARG GLU GLU ILE ALA GLU GLY SEQRES 22 A 780 TYR ASP THR GLU ALA ALA VAL ARG ARG THR VAL MET THR SEQRES 23 A 780 SER GLY ARG THR VAL VAL PHE SER ALA VAL ILE ILE VAL SEQRES 24 A 780 ALA SER SER VAL PRO LEU LEU LEU PHE PRO GLN GLY PHE SEQRES 25 A 780 LEU LYS SER ILE THR TYR ALA ILE ILE ALA SER VAL MET SEQRES 26 A 780 LEU ALA ALA ILE LEU SER ILE THR VAL LEU ALA ALA ALA SEQRES 27 A 780 LEU ALA ILE LEU GLY PRO ARG VAL ASP ALA LEU GLY VAL SEQRES 28 A 780 THR THR LEU LEU LYS ILE PRO PHE LEU ALA ASN TRP GLN SEQRES 29 A 780 PHE SER ARG ARG ILE ILE ASP TRP PHE ALA GLU LYS THR SEQRES 30 A 780 GLN LYS THR LYS THR ARG GLU GLU VAL GLU ARG GLY PHE SEQRES 31 A 780 TRP GLY ARG LEU VAL ASN VAL VAL MET LYS ARG PRO ILE SEQRES 32 A 780 ALA PHE ALA ALA PRO ILE LEU VAL VAL MET VAL LEU LEU SEQRES 33 A 780 ILE ILE PRO LEU GLY GLN LEU SER LEU GLY GLY ILE SER SEQRES 34 A 780 GLU LYS TYR LEU PRO PRO ASP ASN ALA VAL ARG GLN SER SEQRES 35 A 780 GLN GLU GLN PHE ASP LYS LEU PHE PRO GLY PHE ARG THR SEQRES 36 A 780 GLU PRO LEU THR LEU VAL MET LYS ARG GLU ASP GLY GLU SEQRES 37 A 780 PRO ILE THR ASP ALA GLN ILE ALA ASP MET ARG ALA LYS SEQRES 38 A 780 ALA LEU THR VAL SER GLY PHE THR ASP PRO ASP ASN ASP SEQRES 39 A 780 PRO GLU LYS MET TRP LYS GLU ARG PRO ALA ASN ASP SER SEQRES 40 A 780 GLY SER LYS ASP PRO SER VAL ARG VAL ILE GLN ASN GLY SEQRES 41 A 780 LEU GLU ASN ARG ASN ASP ALA ALA LYS LYS ILE ASP GLU SEQRES 42 A 780 LEU ARG ALA LEU GLN PRO PRO HIS GLY ILE GLU VAL PHE SEQRES 43 A 780 VAL GLY GLY THR PRO ALA LEU GLU GLN ASP SER ILE HIS SEQRES 44 A 780 SER LEU PHE ASP LYS LEU PRO LEU MET ALA LEU ILE LEU SEQRES 45 A 780 ILE VAL THR THR THR VAL LEU MET PHE LEU ALA PHE GLY SEQRES 46 A 780 SER VAL VAL LEU PRO ILE LYS ALA ALA LEU MET SER ALA SEQRES 47 A 780 LEU THR LEU GLY SER THR MET GLY ILE LEU THR TRP MET SEQRES 48 A 780 PHE VAL ASP GLY HIS GLY SER GLY LEU MET ASN TYR THR SEQRES 49 A 780 PRO GLN PRO LEU MET ALA PRO MET ILE GLY LEU ILE ILE SEQRES 50 A 780 ALA VAL ILE TRP GLY LEU SER THR ASP TYR GLU VAL PHE SEQRES 51 A 780 LEU VAL SER ARG MET VAL GLU ALA ARG GLU ARG GLY MET SEQRES 52 A 780 SER THR ALA GLU ALA ILE ARG ILE GLY THR ALA THR THR SEQRES 53 A 780 GLY ARG LEU ILE THR GLY ALA ALA LEU ILE LEU ALA VAL SEQRES 54 A 780 VAL ALA GLY ALA PHE VAL PHE SER ASP LEU VAL MET MET SEQRES 55 A 780 LYS TYR LEU ALA PHE GLY LEU LEU ILE ALA LEU LEU LEU SEQRES 56 A 780 ASP ALA THR ILE ILE ARG MET PHE LEU VAL PRO ALA VAL SEQRES 57 A 780 MET LYS LEU LEU GLY ASP ASP CYS TRP TRP ALA PRO ARG SEQRES 58 A 780 TRP MET LYS ARG VAL GLN GLU LYS LEU GLY LEU GLY GLU SEQRES 59 A 780 THR GLU LEU PRO ASP GLU ARG LYS ARG PRO THR VAL ARG SEQRES 60 A 780 GLU SER GLU THR ASP GLN ARG GLU ASN LEU TYR PHE GLN HELIX 1 AA1 GLY A 1 PHE A 12 1 12 HELIX 2 AA2 PHE A 12 ILE A 32 1 21 HELIX 3 AA3 SER A 33 ASN A 36 5 4 HELIX 4 AA4 SER A 48 GLY A 62 1 15 HELIX 5 AA5 ASP A 64 SER A 67 5 4 HELIX 6 AA6 PRO A 75 LYS A 79 5 5 HELIX 7 AA7 ASP A 83 HIS A 101 1 19 HELIX 8 AA8 LEU A 112 ALA A 114 5 3 HELIX 9 AA9 ASP A 119 ALA A 124 1 6 HELIX 10 AB1 ASP A 143 GLN A 159 1 17 HELIX 11 AB2 GLN A 160 GLY A 164 5 5 HELIX 12 AB3 LEU A 171 PHE A 205 1 35 HELIX 13 AB4 VAL A 208 ALA A 211 5 4 HELIX 14 AB5 ALA A 212 GLU A 234 1 23 HELIX 15 AB6 PHE A 241 GLY A 272 1 32 HELIX 16 AB7 ASP A 274 THR A 285 1 12 HELIX 17 AB8 THR A 285 VAL A 302 1 18 HELIX 18 AB9 PRO A 303 PHE A 307 5 5 HELIX 19 AC1 GLN A 309 THR A 332 1 24 HELIX 20 AC2 THR A 332 GLY A 342 1 11 HELIX 21 AC3 PRO A 343 ASP A 346 5 4 HELIX 22 AC4 VAL A 350 ILE A 356 1 7 HELIX 23 AC5 GLN A 363 GLU A 374 1 12 HELIX 24 AC6 VAL A 385 ARG A 400 1 16 HELIX 25 AC7 ARG A 400 ILE A 416 1 17 HELIX 26 AC8 ILE A 417 LEU A 422 5 6 HELIX 27 AC9 SER A 428 LEU A 432 5 5 HELIX 28 AD1 ASN A 436 PHE A 449 1 14 HELIX 29 AD2 THR A 470 VAL A 484 1 15 HELIX 30 AD3 ASP A 493 MET A 497 5 5 HELIX 31 AD4 ASP A 525 LEU A 536 1 12 HELIX 32 AD5 GLY A 548 GLY A 584 1 37 HELIX 33 AD6 VAL A 587 VAL A 612 1 26 HELIX 34 AD7 ALA A 629 ARG A 660 1 32 HELIX 35 AD8 SER A 663 PHE A 695 1 33 HELIX 36 AD9 LEU A 698 PHE A 722 1 25 HELIX 37 AE1 PHE A 722 GLY A 732 1 11 HELIX 38 AE2 ASP A 733 TRP A 737 5 5 SHEET 1 AA1 4 VAL A 109 GLY A 110 0 SHEET 2 AA1 4 THR A 133 SER A 136 -1 O SER A 136 N VAL A 109 SHEET 3 AA1 4 VAL A 69 LEU A 73 -1 N ALA A 71 O ILE A 135 SHEET 4 AA1 4 ILE A 166 GLY A 170 -1 O ARG A 167 N ILE A 72 SHEET 1 AA2 2 LEU A 424 GLY A 425 0 SHEET 2 AA2 2 LEU A 627 MET A 628 1 O LEU A 627 N GLY A 425 SHEET 1 AA3 4 LYS A 499 GLU A 500 0 SHEET 2 AA3 4 VAL A 513 ASN A 518 -1 O GLN A 517 N LYS A 499 SHEET 3 AA3 4 LEU A 457 ARG A 463 -1 N MET A 461 O ARG A 514 SHEET 4 AA3 4 ILE A 542 GLY A 547 -1 O PHE A 545 N VAL A 460 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