HEADER TRANSPORT PROTEIN 11-DEC-25 21FH TITLE CRYO-EM STRUCTURE OF DDDT G101D IN SUBSTRATE-FREE OUTWARD OPEN TITLE 2 CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DDDT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSYCHROBACTER SP. D2; SOURCE 3 ORGANISM_TAXID: 2759702; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRIMER, PSYCHROBACTER SP. D2, DIMETHYLSULFONIOPROPIONATE TRANSPORTER, KEYWDS 2 SUBSTRATE-FREE OUTWARD OPEN CONFORMATION, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.J.ZHU,P.WANG REVDAT 1 20-MAY-26 21FH 0 JRNL AUTH Y.Z.ZHANG,W.J.ZHU,K.LI,H.T.DING,M.HATTORI,S.LIU,C.GE, JRNL AUTH 2 Q.L.QIN,Z.J.TENG,N.H.LIU,H.Y.CAO,C.Y.LI,X.L.CHEN,Q.T.SHEN, JRNL AUTH 3 J.D.TODD,L.N.LIU,P.WANG JRNL TITL STRUCTURAL INSIGHTS INTO BACTERIAL JRNL TITL 2 DIMETHYLSULFONIOPROPIONATE IMPORT BY BCCT-FAMILY JRNL TITL 3 TRANSPORTERS. JRNL REF EMBO J. 2026 JRNL REFN ESSN 1460-2075 JRNL PMID 42104083 JRNL DOI 10.1038/S44318-026-00798-W REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, 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) : 2.660 REMARK 3 NUMBER OF PARTICLES : 255500 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 21FH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 17-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300066594. 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 : DDDT G101D IN SUBSTRATE-FREE REMARK 245 OUTWARD OPEN CONFORMATION 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 : 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 6000.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C3). 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 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 344.25669 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 92.24331 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 92.24330 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 344.25669 REMARK 350 BIOMT3 3 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 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 ASN A 4 REMARK 465 ASP A 505 REMARK 465 LEU A 506 REMARK 465 GLN A 507 REMARK 465 ASP A 508 REMARK 465 ASP A 509 REMARK 465 PRO A 510 REMARK 465 ILE A 511 REMARK 465 LYS A 512 REMARK 465 LEU A 513 REMARK 465 ALA A 514 REMARK 465 GLU A 515 REMARK 465 VAL A 516 REMARK 465 ASP A 517 REMARK 465 SER A 518 REMARK 465 LEU A 519 REMARK 465 GLU A 520 REMARK 465 GLU A 521 REMARK 465 ARG A 522 REMARK 465 GLN A 523 REMARK 465 LYS A 524 REMARK 465 PRO A 525 REMARK 465 ALA A 526 REMARK 465 ALA A 527 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA A 132 CB 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 100 -7.87 -59.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 95 O REMARK 620 2 VAL A 98 O 103.1 REMARK 620 3 PHE A 415 O 147.2 109.3 REMARK 620 4 THR A 418 OG1 80.5 163.9 69.8 REMARK 620 5 THR A 419 OG1 83.2 85.3 94.2 110.8 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-67625 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF DDDT G101D IN SUBSTRATE-FREE OUTWARD OPEN REMARK 900 CONFORMATION DBREF 21FH A 1 527 PDB 21FH 21FH 1 527 SEQRES 1 A 527 LEU LYS GLU ASN LYS ILE ASP TRP PHE ILE PHE ILE SER SEQRES 2 A 527 THR PHE VAL LEU ILE VAL ALA ILE CYS LEU PRO LEU VAL SEQRES 3 A 527 LEU TYR PRO GLU LYS GLY GLY GLU LEU VAL SER GLN ALA SEQRES 4 A 527 ASN SER PHE VAL THR SER ASN PHE GLY MET VAL PHE LEU SEQRES 5 A 527 TRP ALA GLY MET GLY GLY PHE ALA PHE LEU THR TYR LEU SEQRES 6 A 527 PHE PHE SER GLU HIS GLY LYS ILE LYS PHE GLY THR LYS SEQRES 7 A 527 ASP GLU LYS PRO GLU PHE SER ASN PHE SER TRP GLY ALA SEQRES 8 A 527 MET VAL PHE CYS ALA GLY VAL ALA SER ASP LEU VAL TYR SEQRES 9 A 527 TRP GLY THR ILE GLU TRP ALA TYR TYR PHE THR ALA PRO SEQRES 10 A 527 PRO TYR GLY ILE GLU PRO LYS SER THR ASP ALA ALA GLU SEQRES 11 A 527 ILE ALA ALA ALA TYR GLY ILE PHE HIS TRP GLY PRO SER SEQRES 12 A 527 ALA TRP ALA PHE PHE VAL LEU PRO SER LEU PRO ILE ALA SEQRES 13 A 527 TYR SER TYR TYR ILE LEU LYS VAL PRO VAL LEU ARG LEU SEQRES 14 A 527 SER GLU ILE CYS ARG ILE VAL ILE GLY LYS HIS SER ASP SEQRES 15 A 527 GLY VAL LEU GLY LYS VAL ILE ASP ILE ILE PHE MET PHE SEQRES 16 A 527 GLY ILE LEU GLY ALA ALA GLY THR SER LEU GLY LEU GLY SEQRES 17 A 527 THR PRO LEU VAL ALA ALA GLY ILE SER LYS ILE THR GLY SEQRES 18 A 527 ILE GLU SER SER THR SER MET THR VAL PHE VAL LEU VAL SEQRES 19 A 527 LEU CYS THR ALA LEU PHE THR TRP SER ALA TYR SER GLY SEQRES 20 A 527 LEU LYS ARG GLY LEU LYS LEU LEU SER ASP LEU ALA ILE SEQRES 21 A 527 ILE CYS SER VAL ILE LEU LEU THR TYR VAL LEU LEU VAL SEQRES 22 A 527 GLY PRO THR GLU PHE ILE LEU LYS MET GLY THR ASN SER SEQRES 23 A 527 VAL GLY LEU LEU PHE THR ASN PHE VAL ARG TRP ASN LEU SEQRES 24 A 527 TYR THR ASP PRO VAL SER GLY SER GLY PHE VAL GLU SER SEQRES 25 A 527 TRP THR VAL PHE TYR TRP ALA TRP TRP ILE VAL TYR THR SEQRES 26 A 527 PRO PHE MET GLY LEU PHE ILE ALA LYS ILE SER ARG GLY SEQRES 27 A 527 ARG THR ILE ARG GLN VAL ILE LEU GLY GLY ILE ALA TRP SEQRES 28 A 527 GLY THR LEU GLY CYS ALA ALA TYR PHE SER ILE LEU GLY SEQRES 29 A 527 ASN TYR ALA MET HIS LEU GLU LEU THR LYS GLU LEU SER SEQRES 30 A 527 VAL THR GLY LEU LEU GLU GLN ILE GLY ALA PRO ALA THR SEQRES 31 A 527 ILE MET GLU VAL ILE GLY THR LEU PRO LEU GLY SER VAL SEQRES 32 A 527 VAL VAL ILE VAL PHE SER PHE ILE ALA LEU ILE PHE LEU SEQRES 33 A 527 ALA THR THR PHE ASP SER ALA ALA TYR MET MET ALA SER SEQRES 34 A 527 SER THR THR PRO THR LEU GLY LEU ASN GLU GLU PRO ALA SEQRES 35 A 527 LYS TRP ASN ARG LEU PHE TRP ALA LEU THR LEU PHE ILE SEQRES 36 A 527 LEU PRO GLY THR LEU MET VAL LEU GLY GLY ASP LEU LYS SEQRES 37 A 527 THR LEU GLN THR ALA SER ILE LEU THR ALA ILE PRO PHE SEQRES 38 A 527 ILE PHE VAL ILE MET LEU LEU VAL VAL ALA LEU MET LYS SEQRES 39 A 527 MET LEU LYS THR GLY GLU HIS PHE ASN GLN ASP LEU GLN SEQRES 40 A 527 ASP ASP PRO ILE LYS LEU ALA GLU VAL ASP SER LEU GLU SEQRES 41 A 527 GLU ARG GLN LYS PRO ALA ALA HET NA A 601 1 HET NA A 602 1 HETNAM NA SODIUM ION FORMUL 2 NA 2(NA 1+) FORMUL 4 HOH *(H2 O) HELIX 1 AA1 ASP A 7 TYR A 28 1 22 HELIX 2 AA2 TYR A 28 PHE A 47 1 20 HELIX 3 AA3 GLY A 48 PHE A 67 1 20 HELIX 4 AA4 SER A 68 ILE A 73 5 6 HELIX 5 AA5 SER A 85 VAL A 98 1 14 HELIX 6 AA6 ASP A 101 GLU A 109 1 9 HELIX 7 AA7 GLU A 109 ALA A 116 1 8 HELIX 8 AA8 SER A 125 TRP A 140 1 16 HELIX 9 AA9 GLY A 141 LEU A 150 1 10 HELIX 10 AB1 PRO A 151 ILE A 161 1 11 HELIX 11 AB2 ARG A 168 CYS A 173 1 6 HELIX 12 AB3 CYS A 173 GLY A 178 1 6 HELIX 13 AB4 LYS A 179 ASP A 182 5 4 HELIX 14 AB5 GLY A 183 THR A 209 1 27 HELIX 15 AB6 THR A 209 THR A 220 1 12 HELIX 16 AB7 SER A 225 GLY A 247 1 23 HELIX 17 AB8 GLY A 251 GLY A 274 1 24 HELIX 18 AB9 PRO A 275 ASN A 293 1 19 HELIX 19 AC1 ASN A 293 LEU A 299 1 7 HELIX 20 AC2 GLY A 308 TYR A 324 1 17 HELIX 21 AC3 TYR A 324 ILE A 335 1 12 HELIX 22 AC4 THR A 340 THR A 373 1 34 HELIX 23 AC5 SER A 377 ILE A 385 1 9 HELIX 24 AC6 GLY A 386 GLY A 396 1 11 HELIX 25 AC7 LEU A 400 THR A 431 1 32 HELIX 26 AC8 ALA A 442 LEU A 463 1 22 HELIX 27 AC9 SER A 474 LEU A 476 5 3 HELIX 28 AD1 THR A 477 THR A 498 1 22 LINK O CYS A 95 NA NA A 602 1555 1555 2.45 LINK O VAL A 98 NA NA A 602 1555 1555 1.96 LINK O PHE A 415 NA NA A 602 1555 1555 2.49 LINK OG1 THR A 418 NA NA A 602 1555 1555 2.95 LINK OG1 THR A 419 NA NA A 602 1555 1555 2.81 LINK NA NA A 601 O HOH A 701 1555 1555 2.97 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 1432 7821 CONECT 1460 7821 CONECT 6395 7821 CONECT 6446 7821 CONECT 6460 7821 CONECT 7820 7822 CONECT 7821 1432 1460 6395 6446 CONECT 7821 6460 CONECT 7822 7820 MASTER 178 0 2 28 0 0 0 6 3870 1 9 41 END