HEADER MEMBRANE PROTEIN 12-SEP-24 9DM7 TITLE MANNOSYLTRANSFERASE PIME IN COMPLEX WITH FAB_E6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB_E6 HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: FAB_E6 LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTEROIDES ABSCESSUS; SOURCE 3 ORGANISM_TAXID: 36809; SOURCE 4 GENE: D2E76_03800; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MANNOSYLTRANSFERASE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LIU REVDAT 1 25-JUN-25 9DM7 0 JRNL AUTH Y.LIU,C.M.BROWN,N.BORGES,R.N.NOBRE,S.ERRAMILLI, JRNL AUTH 2 M.BELCHER DUFRISNE,B.KLOSS,S.GIACOMETTI,A.M.ESTEVES, JRNL AUTH 3 C.G.TIMOTEO,P.TOKARZ,R.J.CATER,T.L.LOWARY,Y.S.MORITA, JRNL AUTH 4 A.A.KOSSIAKOFF,H.SANTOS,P.J.STANSFELD,R.NYGAARD,F.MANCIA JRNL TITL MECHANISTIC STUDIES OF MYCOBACTERIAL GLYCOLIPID BIOSYNTHESIS JRNL TITL 2 BY THE MANNOSYLTRANSFERASE PIME. JRNL REF NAT COMMUN V. 16 3974 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40301322 JRNL DOI 10.1038/S41467-025-57843-1 REMARK 2 REMARK 2 RESOLUTION. 3.02 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) : 3.020 REMARK 3 NUMBER OF PARTICLES : 145477 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9DM7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288398. 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 : MANNOSYLTRANSFERASE PIME 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 : 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 5800.00 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 THR A 6 REMARK 465 GLU A 7 REMARK 465 PRO A 8 REMARK 465 THR A 9 REMARK 465 ARG A 10 REMARK 465 ALA A 11 REMARK 465 ASN A 12 REMARK 465 VAL A 13 REMARK 465 GLU A 14 REMARK 465 PRO A 15 REMARK 465 PRO A 16 REMARK 465 MET A 17 REMARK 465 PRO A 18 REMARK 465 THR A 19 REMARK 465 ARG A 20 REMARK 465 ASP A 81 REMARK 465 LYS A 82 REMARK 465 THR A 83 REMARK 465 PRO A 84 REMARK 465 ASP A 85 REMARK 465 PHE A 86 REMARK 465 PRO A 87 REMARK 465 LEU A 88 REMARK 465 LYS A 246 REMARK 465 PRO A 247 REMARK 465 ASP A 248 REMARK 465 ARG A 249 REMARK 465 ILE A 250 REMARK 465 GLY A 251 REMARK 465 TRP A 371 REMARK 465 ARG A 372 REMARK 465 ILE A 373 REMARK 465 ASP A 374 REMARK 465 HIS A 406 REMARK 465 LEU A 407 REMARK 465 GLY A 408 REMARK 465 ARG A 409 REMARK 465 LEU A 410 REMARK 465 PRO A 411 REMARK 465 TRP A 412 REMARK 465 ARG A 413 REMARK 465 HIS A 414 REMARK 465 VAL A 415 REMARK 465 SER H 87 REMARK 465 ARG H 88 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 OE1 GLN L 6 O GLN L 100 1.68 REMARK 500 OD2 ASP A 58 NE2 GLN A 163 2.13 REMARK 500 OH TYR H 60 O ARG H 67 2.17 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 68 59.66 -91.82 REMARK 500 GLU A 76 52.00 -93.30 REMARK 500 PRO A 102 46.21 -78.51 REMARK 500 ASP A 138 115.14 -162.81 REMARK 500 PRO A 198 45.89 -84.20 REMARK 500 THR A 212 -13.73 73.63 REMARK 500 TRP A 323 34.25 -96.12 REMARK 500 PRO H 14 75.96 -68.85 REMARK 500 ALA H 61 -134.50 55.22 REMARK 500 ASP H 73 15.52 57.63 REMARK 500 SER L 12 -12.55 74.19 REMARK 500 ALA L 13 41.66 35.94 REMARK 500 GLN L 27 -128.59 50.25 REMARK 500 SER L 30 -132.55 59.16 REMARK 500 PRO L 44 -179.15 -69.55 REMARK 500 ALA L 51 -8.84 71.03 REMARK 500 TYR L 55 -168.53 -79.10 REMARK 500 GLU L 81 -10.36 73.82 REMARK 500 ASP L 82 40.80 36.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9DM5 RELATED DB: PDB REMARK 900 9DM5 IS THE MODEL FOR PRODUCT-BOUND PIME REMARK 900 RELATED ID: EMD-46999 RELATED DB: EMDB REMARK 900 MANNOSYLTRANSFERASE PIME IN COMPLEX WITH FAB_E6 DBREF1 9DM7 A 1 415 UNP A0A418LCK8_9MYCO DBREF2 9DM7 A A0A418LCK8 1 415 DBREF 9DM7 H 1 128 PDB 9DM7 9DM7 1 128 DBREF 9DM7 L 1 107 PDB 9DM7 9DM7 1 107 SEQRES 1 A 415 MET ALA THR GLU LYS THR GLU PRO THR ARG ALA ASN VAL SEQRES 2 A 415 GLU PRO PRO MET PRO THR ARG GLY ALA SER ALA TRP ARG SEQRES 3 A 415 ARG VAL ARG ALA TRP GLY PRO TRP LEU LEU GLY LEU SER SEQRES 4 A 415 VAL ALA VAL ARG LEU ALA TRP ALA TYR LEU THR PRO HIS SEQRES 5 A 415 GLY ALA ASP LEU VAL ASP LEU HIS VAL TYR VAL SER GLY SEQRES 6 A 415 PRO ALA THR LEU GLY HIS GLY ASN LEU TYR GLU PHE THR SEQRES 7 A 415 TYR PRO ASP LYS THR PRO ASP PHE PRO LEU PRO PHE THR SEQRES 8 A 415 TYR PRO PRO PHE ALA ALA VAL VAL PHE TRP PRO LEU HIS SEQRES 9 A 415 LEU ILE PRO PHE THR LEU LEU GLY LEU CYS TRP ILE LEU SEQRES 10 A 415 GLY THR ILE ALA ALA LEU TYR ALA VAL VAL ARG LEU SER SEQRES 11 A 415 GLN ARG LEU LEU GLY PHE ASP ASP ALA ARG ALA ALA ALA SEQRES 12 A 415 VAL TRP THR ALA VAL THR MET TRP THR GLU PRO VAL ARG SEQRES 13 A 415 SER THR LEU ASP TYR GLY GLN ILE ASN VAL LEU LEU MET SEQRES 14 A 415 LEU LEU ILE LEU LEU ALA VAL ALA SER SER ARG TRP TRP SEQRES 15 A 415 ILE SER GLY THR LEU ILE GLY LEU ALA GLY GLY VAL LYS SEQRES 16 A 415 LEU THR PRO LEU VAL SER GLY LEU TYR PHE LEU GLY ALA SEQRES 17 A 415 ARG ARG TRP THR THR ALA ILE TRP ALA GLY VAL VAL PHE SEQRES 18 A 415 LEU LEU THR VAL VAL VAL GLY ILE ALA VAL VAL GLY GLU SEQRES 19 A 415 GLN GLY ARG TYR TYR PHE THR ASP LEU LEU GLY LYS PRO SEQRES 20 A 415 ASP ARG ILE GLY PRO ILE ALA THR VAL PHE ASN GLN SER SEQRES 21 A 415 TRP ARG GLY GLY ILE SER ARG ILE LEU GLY HIS ASP ALA SEQRES 22 A 415 GLY SER GLY VAL LEU VAL LEU PHE ALA TYR ALA VAL THR SEQRES 23 A 415 ALA ILE LEU ALA PHE LEU ALA TRP ARG ALA VAL ASN ASP SEQRES 24 A 415 ARG LEU GLY GLN ILE CYS VAL VAL GLU MET PHE GLY LEU SEQRES 25 A 415 LEU ILE SER PRO ILE SER TRP THR HIS HIS TRP VAL TRP SEQRES 26 A 415 MET VAL PRO PHE MET VAL TRP LEU LEU HIS GLY PRO TRP SEQRES 27 A 415 ARG ASP LYS VAL GLY ALA LYS VAL PHE GLY CYS GLY TRP SEQRES 28 A 415 LEU VAL LEU LEU LEU ILE GLY VAL PRO TRP LEU LEU SER SEQRES 29 A 415 PHE ALA GLN PRO ASP ILE TRP ARG ILE ASP ARG PRO TRP SEQRES 30 A 415 PRO LEU ALA TRP ALA GLY LEU VAL ASP ILE VAL ALA ALA SEQRES 31 A 415 ILE ALA THR LEU THR TRP MET ALA VAL VAL GLY ARG ARG SEQRES 32 A 415 SER GLY HIS LEU GLY ARG LEU PRO TRP ARG HIS VAL SEQRES 1 H 126 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 126 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 126 PHE ASN PHE TYR TYR TYR SER ILE HIS TRP VAL ARG GLN SEQRES 4 H 126 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA SER ILE SER SEQRES 5 H 126 SER SER SER GLY SER THR SER TYR ALA ASP SER VAL LYS SEQRES 6 H 126 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 H 126 ALA TYR LEU GLN MET ASN SER ARG GLU ASP THR ALA VAL SEQRES 8 H 126 TYR TYR CYS ALA ARG SER GLN ALA VAL TYR TYR TRP ASP SEQRES 9 H 126 LEU TRP TRP SER MET TYR HIS THR GLY PHE ILE ASP TYR SEQRES 10 H 126 TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 1 L 107 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 107 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 107 GLN SER VAL SER SER ALA VAL ALA TRP TYR GLN GLN LYS SEQRES 4 L 107 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER ALA SER SEQRES 5 L 107 SER LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 107 ARG SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 107 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 L 107 SER SER SER LEU ILE THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 L 107 GLU ILE LYS HELIX 1 AA1 GLY A 21 ARG A 29 1 9 HELIX 2 AA2 TRP A 31 ALA A 47 1 17 HELIX 3 AA3 LEU A 56 SER A 64 1 9 HELIX 4 AA4 PRO A 93 TRP A 101 1 9 HELIX 5 AA5 PRO A 102 HIS A 104 5 3 HELIX 6 AA6 PRO A 107 GLY A 135 1 29 HELIX 7 AA7 ASP A 138 MET A 150 1 13 HELIX 8 AA8 THR A 152 GLY A 162 1 11 HELIX 9 AA9 ILE A 164 SER A 178 1 15 HELIX 10 AB1 ARG A 180 LYS A 195 1 16 HELIX 11 AB2 VAL A 200 ALA A 208 1 9 HELIX 12 AB3 THR A 212 VAL A 232 1 21 HELIX 13 AB4 GLU A 234 GLY A 245 1 12 HELIX 14 AB5 SER A 260 GLY A 270 1 11 HELIX 15 AB6 LEU A 278 VAL A 297 1 20 HELIX 16 AB7 ASP A 299 SER A 315 1 17 HELIX 17 AB8 TRP A 319 VAL A 324 5 6 HELIX 18 AB9 TRP A 325 GLY A 336 1 12 HELIX 19 AC1 PRO A 337 LYS A 341 5 5 HELIX 20 AC2 GLY A 343 GLY A 358 1 16 HELIX 21 AC3 GLY A 358 SER A 364 1 7 HELIX 22 AC4 PRO A 376 TRP A 381 1 6 HELIX 23 AC5 LEU A 384 SER A 404 1 21 HELIX 24 AC6 ASN H 28 TYR H 32 5 5 SHEET 1 AA1 4 GLN H 3 GLU H 6 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA1 4 ASN H 77 GLN H 82 -1 O THR H 78 N CYS H 22 SHEET 4 AA1 4 THR H 69 SER H 71 -1 N THR H 69 O ALA H 79 SHEET 1 AA2 4 SER H 57 THR H 58 0 SHEET 2 AA2 4 LEU H 45 ILE H 51 -1 N SER H 50 O THR H 58 SHEET 3 AA2 4 SER H 33 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AA2 4 VAL H 93 SER H 99 -1 O TYR H 95 N VAL H 37 SHEET 1 AA3 2 ALA H 101 TRP H 105 0 SHEET 2 AA3 2 TRP H 109 HIS H 113 -1 O SER H 110 N TYR H 104 SHEET 1 AA4 3 MET L 4 THR L 5 0 SHEET 2 AA4 3 CYS L 23 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA4 3 ASP L 70 PHE L 71 -1 O PHE L 71 N CYS L 23 SHEET 1 AA5 4 SER L 53 LEU L 54 0 SHEET 2 AA5 4 LYS L 45 TYR L 49 -1 N TYR L 49 O SER L 53 SHEET 3 AA5 4 VAL L 33 GLN L 38 -1 N TRP L 35 O ILE L 48 SHEET 4 AA5 4 THR L 85 GLN L 90 -1 O THR L 85 N GLN L 38 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 2 CYS L 23 CYS L 88 1555 1555 2.04 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