HEADER TRANSPORT PROTEIN 11-DEC-25 21FK TITLE CRYO-EM STRUCTURE OF DDDT G101D IN SUBSTRATE-FREE INWARD 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 INWARD OPEN CONFORMATION, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.J.ZHU,P.WANG REVDAT 1 20-MAY-26 21FK 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. 3.29 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) : 3.290 REMARK 3 NUMBER OF PARTICLES : 115494 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 21FK 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_1300066609. 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 OF DDDT G101D REMARK 245 IN SUBSTRATE-FREE INWARD OPEN REMARK 245 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 293.76572 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 78.71429 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 78.71429 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 293.76572 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 LYS A 5 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 PHE A 47 31.63 -96.14 REMARK 500 ALA A 244 -61.96 -109.27 REMARK 500 ARG A 250 -174.23 78.46 REMARK 500 LEU A 435 146.06 -171.83 REMARK 500 LEU A 437 -134.46 52.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-67628 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF DDDT G101D IN SUBSTRATE-FREE INWARD OPEN REMARK 900 CONFORMATION DBREF 21FK A 1 504 PDB 21FK 21FK 1 504 SEQRES 1 A 504 LEU LYS GLU ASN LYS ILE ASP TRP PHE ILE PHE ILE SER SEQRES 2 A 504 THR PHE VAL LEU ILE VAL ALA ILE CYS LEU PRO LEU VAL SEQRES 3 A 504 LEU TYR PRO GLU LYS GLY GLY GLU LEU VAL SER GLN ALA SEQRES 4 A 504 ASN SER PHE VAL THR SER ASN PHE GLY MET VAL PHE LEU SEQRES 5 A 504 TRP ALA GLY MET GLY GLY PHE ALA PHE LEU THR TYR LEU SEQRES 6 A 504 PHE PHE SER GLU HIS GLY LYS ILE LYS PHE GLY THR LYS SEQRES 7 A 504 ASP GLU LYS PRO GLU PHE SER ASN PHE SER TRP GLY ALA SEQRES 8 A 504 MET VAL PHE CYS ALA GLY VAL ALA SER ASP LEU VAL TYR SEQRES 9 A 504 TRP GLY THR ILE GLU TRP ALA TYR TYR PHE THR ALA PRO SEQRES 10 A 504 PRO TYR GLY ILE GLU PRO LYS SER THR ASP ALA ALA GLU SEQRES 11 A 504 ILE ALA ALA ALA TYR GLY ILE PHE HIS TRP GLY PRO SER SEQRES 12 A 504 ALA TRP ALA PHE PHE VAL LEU PRO SER LEU PRO ILE ALA SEQRES 13 A 504 TYR SER TYR TYR ILE LEU LYS VAL PRO VAL LEU ARG LEU SEQRES 14 A 504 SER GLU ILE CYS ARG ILE VAL ILE GLY LYS HIS SER ASP SEQRES 15 A 504 GLY VAL LEU GLY LYS VAL ILE ASP ILE ILE PHE MET PHE SEQRES 16 A 504 GLY ILE LEU GLY ALA ALA GLY THR SER LEU GLY LEU GLY SEQRES 17 A 504 THR PRO LEU VAL ALA ALA GLY ILE SER LYS ILE THR GLY SEQRES 18 A 504 ILE GLU SER SER THR SER MET THR VAL PHE VAL LEU VAL SEQRES 19 A 504 LEU CYS THR ALA LEU PHE THR TRP SER ALA TYR SER GLY SEQRES 20 A 504 LEU LYS ARG GLY LEU LYS LEU LEU SER ASP LEU ALA ILE SEQRES 21 A 504 ILE CYS SER VAL ILE LEU LEU THR TYR VAL LEU LEU VAL SEQRES 22 A 504 GLY PRO THR GLU PHE ILE LEU LYS MET GLY THR ASN SER SEQRES 23 A 504 VAL GLY LEU LEU PHE THR ASN PHE VAL ARG TRP ASN LEU SEQRES 24 A 504 TYR THR ASP PRO VAL SER GLY SER GLY PHE VAL GLU SER SEQRES 25 A 504 TRP THR VAL PHE TYR TRP ALA TRP TRP ILE VAL TYR THR SEQRES 26 A 504 PRO PHE MET GLY LEU PHE ILE ALA LYS ILE SER ARG GLY SEQRES 27 A 504 ARG THR ILE ARG GLN VAL ILE LEU GLY GLY ILE ALA TRP SEQRES 28 A 504 GLY THR LEU GLY CYS ALA ALA TYR PHE SER ILE LEU GLY SEQRES 29 A 504 ASN TYR ALA MET HIS LEU GLU LEU THR LYS GLU LEU SER SEQRES 30 A 504 VAL THR GLY LEU LEU GLU GLN ILE GLY ALA PRO ALA THR SEQRES 31 A 504 ILE MET GLU VAL ILE GLY THR LEU PRO LEU GLY SER VAL SEQRES 32 A 504 VAL VAL ILE VAL PHE SER PHE ILE ALA LEU ILE PHE LEU SEQRES 33 A 504 ALA THR THR PHE ASP SER ALA ALA TYR MET MET ALA SER SEQRES 34 A 504 SER THR THR PRO THR LEU GLY LEU ASN GLU GLU PRO ALA SEQRES 35 A 504 LYS TRP ASN ARG LEU PHE TRP ALA LEU THR LEU PHE ILE SEQRES 36 A 504 LEU PRO GLY THR LEU MET VAL LEU GLY GLY ASP LEU LYS SEQRES 37 A 504 THR LEU GLN THR ALA SER ILE LEU THR ALA ILE PRO PHE SEQRES 38 A 504 ILE PHE VAL ILE MET LEU LEU VAL VAL ALA LEU MET LYS SEQRES 39 A 504 MET LEU LYS THR GLY GLU HIS PHE ASN GLN 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 PHE A 47 SER A 68 1 22 HELIX 4 AA4 GLU A 69 ILE A 73 5 5 HELIX 5 AA5 SER A 85 VAL A 98 1 14 HELIX 6 AA6 VAL A 98 GLU A 109 1 12 HELIX 7 AA7 GLU A 109 ALA A 116 1 8 HELIX 8 AA8 ALA A 128 TRP A 140 1 13 HELIX 9 AA9 TRP A 145 LEU A 150 1 6 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 220 1 38 HELIX 15 AB6 SER A 225 SER A 243 1 19 HELIX 16 AB7 LEU A 254 VAL A 273 1 20 HELIX 17 AB8 PRO A 275 ASN A 293 1 19 HELIX 18 AB9 ASN A 293 LEU A 299 1 7 HELIX 19 AC1 GLY A 308 TRP A 313 1 6 HELIX 20 AC2 TRP A 313 TYR A 324 1 12 HELIX 21 AC3 TYR A 324 SER A 336 1 13 HELIX 22 AC4 ILE A 341 THR A 373 1 33 HELIX 23 AC5 SER A 377 LEU A 382 1 6 HELIX 24 AC6 GLY A 386 THR A 397 1 12 HELIX 25 AC7 LEU A 400 THR A 432 1 33 HELIX 26 AC8 ALA A 442 LEU A 453 1 12 HELIX 27 AC9 PHE A 454 GLY A 464 1 11 HELIX 28 AD1 ASP A 466 ALA A 478 1 13 HELIX 29 AD2 PRO A 480 LYS A 497 1 18 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 MASTER 147 0 0 29 0 0 0 6 3858 1 0 39 END