HEADER MEMBRANE PROTEIN 16-MAY-24 8ZKE TITLE CRYO-EM STRUCTURE OF INWARD-FACING ANHYDROMUROPEPTIDE PERMEASE (AMPG) TITLE 2 IN COMPLEX WITH GLCNAC-1,6-ANHMURNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUROPEPTIDE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YOKENELLA REGENSBURGEI; SOURCE 3 ORGANISM_TAXID: 158877; SOURCE 4 GENE: AMPG, NCTC11967_01129; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS AMPG, MFS, ANHYDROMUROPEPTIDE PERMEASE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR N.CHANG,U.KIM,Y.YOO,H.KIM,H.CHO REVDAT 3 16-JUL-25 8ZKE 1 JRNL REVDAT 2 11-JUN-25 8ZKE 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 HELIX ATOM REVDAT 1 21-MAY-25 8ZKE 0 JRNL AUTH N.CHANG,H.KIM,U.KIM,Y.CHO,Y.YOO,H.LEE,J.W.KIM,M.S.KIM,J.LEE, JRNL AUTH 2 Y.L.CHO,K.KIM,D.YONG,H.S.CHO JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS OF AMPG IN MUROPEPTIDE JRNL TITL 2 TRANSPORT AND MULTIPLE BETA-LACTAM ANTIBIOTICS RESISTANCE. JRNL REF NAT COMMUN V. 16 5744 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40593790 JRNL DOI 10.1038/S41467-025-61169-3 REMARK 2 REMARK 2 RESOLUTION. 3.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC 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) : 3.720 REMARK 3 NUMBER OF PARTICLES : 133506 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 8ZKE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300047966. 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 : CRYO-EM STRUCTURE REMARK 245 OFANHYDROMUROPEPTIDE PERMEASE REMARK 245 (AMPG) COMPLEX WITH GLCNAC-1,6- REMARK 245 ANHMURNAC REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 9.00 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 : 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 6700.00 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: MONOMERIC 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 1 REMARK 465 ALA A 2 REMARK 465 ASN A 3 REMARK 465 HIS A 4 REMARK 465 TYR A 5 REMARK 465 LEU A 6 REMARK 465 ARG A 7 REMARK 465 ILE A 8 REMARK 465 PHE A 9 REMARK 465 GLN A 10 REMARK 465 GLN A 11 REMARK 465 PRO A 195 REMARK 465 GLU A 196 REMARK 465 PRO A 197 REMARK 465 SER A 198 REMARK 465 ASP A 199 REMARK 465 VAL A 200 REMARK 465 VAL A 201 REMARK 465 PRO A 202 REMARK 465 VAL A 203 REMARK 465 PRO A 204 REMARK 465 ARG A 205 REMARK 465 THR A 206 REMARK 465 GLN A 410 REMARK 465 GLN A 411 REMARK 465 THR A 412 REMARK 465 GLU A 413 REMARK 465 SER A 414 REMARK 465 PHE A 415 REMARK 465 MET A 416 REMARK 465 MET A 417 REMARK 465 ARG A 418 REMARK 465 ARG A 419 REMARK 465 HIS A 420 REMARK 465 PHE A 421 REMARK 465 SER A 422 REMARK 465 GLY A 423 REMARK 465 ALA A 424 REMARK 465 TYR A 425 REMARK 465 GLN A 426 REMARK 465 PHE A 427 REMARK 465 ALA A 428 REMARK 465 LEU A 429 REMARK 465 TYR A 430 REMARK 465 LEU A 431 REMARK 465 LEU A 432 REMARK 465 LEU A 433 REMARK 465 LEU A 434 REMARK 465 GLY A 435 REMARK 465 CYS A 436 REMARK 465 LEU A 437 REMARK 465 LEU A 438 REMARK 465 LEU A 439 REMARK 465 ALA A 440 REMARK 465 LEU A 441 REMARK 465 TRP A 442 REMARK 465 LEU A 443 REMARK 465 ILE A 444 REMARK 465 MET A 445 REMARK 465 LEU A 446 REMARK 465 ALA A 447 REMARK 465 LEU A 448 REMARK 465 ASN A 449 REMARK 465 ALA A 450 REMARK 465 ILE A 451 REMARK 465 ASP A 452 REMARK 465 TYR A 453 REMARK 465 THR A 454 REMARK 465 SER A 455 REMARK 465 PHE A 456 REMARK 465 SER A 457 REMARK 465 PHE A 458 REMARK 465 LEU A 459 REMARK 465 ALA A 460 REMARK 465 GLY A 461 REMARK 465 LEU A 462 REMARK 465 LEU A 463 REMARK 465 GLU A 464 REMARK 465 VAL A 465 REMARK 465 ALA A 466 REMARK 465 ALA A 467 REMARK 465 LEU A 468 REMARK 465 ILE A 469 REMARK 465 ALA A 470 REMARK 465 ILE A 471 REMARK 465 ALA A 472 REMARK 465 GLY A 473 REMARK 465 VAL A 474 REMARK 465 LEU A 475 REMARK 465 LEU A 476 REMARK 465 GLY A 477 REMARK 465 ALA A 478 REMARK 465 ILE A 479 REMARK 465 LEU A 480 REMARK 465 ASP A 481 REMARK 465 TYR A 482 REMARK 465 LEU A 483 REMARK 465 ALA A 484 REMARK 465 LEU A 485 REMARK 465 ARG A 486 REMARK 465 ARG A 487 REMARK 465 THR A 488 REMARK 465 GLU A 489 REMARK 465 GLU A 490 REMARK 465 HIS A 491 REMARK 465 LYS A 492 REMARK 465 LEU A 493 REMARK 465 ALA A 494 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 SER A 32 -97.23 -113.27 REMARK 500 ILE A 44 51.74 33.98 REMARK 500 ASP A 45 -164.56 53.04 REMARK 500 ARG A 71 -62.76 83.49 REMARK 500 THR A 73 57.50 30.93 REMARK 500 ARG A 79 -11.06 91.50 REMARK 500 ARG A 108 -9.92 -55.80 REMARK 500 GLU A 139 -99.27 66.58 REMARK 500 ALA A 257 -122.32 -134.81 REMARK 500 ARG A 285 0.47 -66.82 REMARK 500 ALA A 291 -97.65 53.69 REMARK 500 HIS A 315 -166.59 62.57 REMARK 500 SER A 350 -146.45 62.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60190 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OFANHYDROMUROPEPTIDE PERMEASE (AMPG) COMPLEX WITH REMARK 900 GLCNAC-1,6-ANHMURNAC DBREF1 8ZKE A 1 494 UNP A0AB38FS76_9ENTR DBREF2 8ZKE A A0AB38FS76 1 494 SEQRES 1 A 494 MET ALA ASN HIS TYR LEU ARG ILE PHE GLN GLN PRO LYS SEQRES 2 A 494 SER ALA ILE LEU LEU ILE LEU GLY PHE ALA SER GLY LEU SEQRES 3 A 494 PRO LEU ALA LEU THR SER GLY THR LEU GLN ALA TRP MET SEQRES 4 A 494 THR VAL GLU ASN ILE ASP LEU LYS THR ILE GLY PHE PHE SEQRES 5 A 494 SER LEU VAL GLY GLN ALA TYR VAL PHE LYS PHE LEU TRP SEQRES 6 A 494 SER PRO VAL MET ASP ARG TYR THR PRO PRO PHE LEU GLY SEQRES 7 A 494 ARG ARG ARG GLY TRP LEU VAL THR THR GLN ILE LEU LEU SEQRES 8 A 494 LEU ILE ALA ILE ALA ALA MET GLY PHE LEU GLU PRO GLY SEQRES 9 A 494 THR GLN LEU ARG TRP MET ALA ALA LEU ALA VAL VAL ILE SEQRES 10 A 494 ALA PHE CYS SER ALA SER GLN ASP ILE VAL PHE ASP ALA SEQRES 11 A 494 TRP LYS THR ASP VAL LEU PRO ALA GLU GLU ARG GLY THR SEQRES 12 A 494 GLY ALA ALA ILE SER VAL LEU GLY TYR ARG LEU GLY MET SEQRES 13 A 494 LEU VAL SER GLY GLY LEU ALA LEU TRP MET ALA ASP LYS SEQRES 14 A 494 TRP LEU GLY TRP GLN GLY MET TYR TRP LEU MET ALA ALA SEQRES 15 A 494 LEU LEU VAL PRO CYS ILE ILE ALA THR LEU LEU ALA PRO SEQRES 16 A 494 GLU PRO SER ASP VAL VAL PRO VAL PRO ARG THR LEU GLU SEQRES 17 A 494 GLN ALA VAL VAL ALA PRO LEU ARG ASP PHE PHE GLY ARG SEQRES 18 A 494 ASN ASN ALA TRP LEU ILE LEU LEU LEU ILE VAL LEU TYR SEQRES 19 A 494 LYS LEU GLY ASP ALA PHE ALA MET SER LEU THR THR THR SEQRES 20 A 494 PHE LEU ILE ARG GLY VAL GLY PHE ASP ALA GLY GLU VAL SEQRES 21 A 494 GLY MET VAL ASN LYS THR LEU GLY LEU ILE ALA THR ILE SEQRES 22 A 494 ILE GLY ALA LEU TYR GLY GLY VAL LEU MET GLN ARG LEU SEQRES 23 A 494 SER LEU PHE ARG ALA LEU LEU ILE PHE GLY ILE LEU GLN SEQRES 24 A 494 GLY VAL SER ASN ALA GLY TYR TRP LEU LEU SER ILE THR SEQRES 25 A 494 ASP LYS HIS LEU MET SER MET ALA VAL ALA VAL PHE PHE SEQRES 26 A 494 GLU ASN LEU CYS GLY GLY MET GLY THR ALA ALA PHE VAL SEQRES 27 A 494 ALA LEU LEU MET THR LEU CYS ASN LYS SER PHE SER ALA SEQRES 28 A 494 THR GLN PHE ALA LEU LEU SER ALA LEU SER ALA VAL GLY SEQRES 29 A 494 ARG VAL TYR VAL GLY PRO ILE ALA GLY TRP PHE VAL GLU SEQRES 30 A 494 ALA HIS GLY TRP PRO THR PHE TYR LEU PHE SER VAL PHE SEQRES 31 A 494 ALA ALA VAL PRO GLY ILE LEU LEU LEU LEU ILE CYS ARG SEQRES 32 A 494 LYS THR LEU GLU TYR THR GLN GLN THR GLU SER PHE MET SEQRES 33 A 494 MET ARG ARG HIS PHE SER GLY ALA TYR GLN PHE ALA LEU SEQRES 34 A 494 TYR LEU LEU LEU LEU GLY CYS LEU LEU LEU ALA LEU TRP SEQRES 35 A 494 LEU ILE MET LEU ALA LEU ASN ALA ILE ASP TYR THR SER SEQRES 36 A 494 PHE SER PHE LEU ALA GLY LEU LEU GLU VAL ALA ALA LEU SEQRES 37 A 494 ILE ALA ILE ALA GLY VAL LEU LEU GLY ALA ILE LEU ASP SEQRES 38 A 494 TYR LEU ALA LEU ARG ARG THR GLU GLU HIS LYS LEU ALA HET 2YP A 501 33 HETNAM 2YP (2R)-2-[[(1R,2S,3R,4R,5R)-4-ACETAMIDO-2-[(2S,3R,4R,5S, HETNAM 2 2YP 6R)-3-ACETAMIDO-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL) HETNAM 3 2YP OXAN-2-YL]OXY-6,8-DIOXABICYCLO[3.2.1]OCTAN-3- HETNAM 4 2YP YL]OXY]PROPANOIC ACID FORMUL 2 2YP C19 H30 N2 O12 HELIX 1 AA1 SER A 14 SER A 24 1 11 HELIX 2 AA2 LEU A 26 THR A 31 1 6 HELIX 3 AA3 SER A 32 GLU A 42 1 11 HELIX 4 AA4 LEU A 46 PHE A 51 1 6 HELIX 5 AA5 SER A 53 VAL A 60 5 8 HELIX 6 AA6 TRP A 65 ASP A 70 1 6 HELIX 7 AA7 GLY A 82 LEU A 101 1 20 HELIX 8 AA8 ARG A 108 LEU A 113 1 6 HELIX 9 AA9 LEU A 113 TRP A 131 1 19 HELIX 10 AB1 ARG A 141 SER A 159 1 19 HELIX 11 AB2 GLY A 160 TRP A 170 1 11 HELIX 12 AB3 GLY A 172 LEU A 192 1 21 HELIX 13 AB4 LEU A 207 PHE A 218 5 12 HELIX 14 AB5 ASN A 223 LYS A 235 1 13 HELIX 15 AB6 LYS A 235 ALA A 241 1 7 HELIX 16 AB7 LEU A 244 ARG A 251 1 8 HELIX 17 AB8 VAL A 260 THR A 266 1 7 HELIX 18 AB9 THR A 266 ARG A 285 1 20 HELIX 19 AC1 ALA A 291 LEU A 298 1 8 HELIX 20 AC2 LEU A 298 ILE A 311 1 14 HELIX 21 AC3 MET A 317 CYS A 345 1 29 HELIX 22 AC4 SER A 350 HIS A 379 1 30 HELIX 23 AC5 TRP A 381 PHE A 387 1 7 HELIX 24 AC6 SER A 388 ALA A 391 5 4 HELIX 25 AC7 ALA A 392 GLU A 407 1 16 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 CONECT 2956 2957 2958 2970 CONECT 2957 2956 2971 CONECT 2958 2956 2959 2965 CONECT 2959 2958 2960 2961 CONECT 2960 2959 CONECT 2961 2959 2966 2967 CONECT 2962 2963 CONECT 2963 2962 2964 2965 CONECT 2964 2963 CONECT 2965 2958 2963 CONECT 2966 2961 CONECT 2967 2961 2968 2970 CONECT 2968 2967 2969 CONECT 2969 2968 CONECT 2970 2956 2967 CONECT 2971 2957 2972 2979 CONECT 2972 2971 2973 2984 CONECT 2973 2972 2974 CONECT 2974 2973 2975 2976 CONECT 2975 2974 CONECT 2976 2974 2977 2978 CONECT 2977 2976 CONECT 2978 2976 CONECT 2979 2971 2980 2981 CONECT 2980 2979 2983 CONECT 2981 2979 2982 CONECT 2982 2981 2983 CONECT 2983 2980 2982 2984 CONECT 2984 2972 2983 2985 CONECT 2985 2984 2986 CONECT 2986 2985 2987 2988 CONECT 2987 2986 CONECT 2988 2986 MASTER 247 0 1 25 0 0 0 6 2987 1 33 38 END