HEADER TRANSPORT PROTEIN 11-DEC-25 21FI TITLE CRYO-EM STRUCTURE OF DDDT IN CLOSED DMSP-BOUND CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DDDT; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: 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 CLOSED DMSP-BOUND CONFORMATION, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.J.ZHU,P.WANG REVDAT 1 20-MAY-26 21FI 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. 2.52 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) : 2.520 REMARK 3 NUMBER OF PARTICLES : 446735 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 21FI 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_1300066573. 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 IN CLOSED DMSP-BOUND 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 : TFS FALCON 4I (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: D 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 344.25670 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 92.24330 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 92.24331 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 344.25670 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 ALA D 99 -154.49 -76.79 REMARK 500 ARG D 250 -76.23 -106.69 REMARK 500 LYS D 374 31.00 73.42 REMARK 500 ASN D 503 50.24 -90.14 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 D 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 95 O REMARK 620 2 VAL D 98 O 123.7 REMARK 620 3 PHE D 415 O 129.6 100.0 REMARK 620 4 THR D 418 OG1 61.7 136.5 69.6 REMARK 620 5 THR D 419 OG1 92.0 111.2 94.4 111.7 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-67626 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF DDDT IN CLOSED DMSP-BOUND CONFORMATION DBREF 21FI D 4 505 PDB 21FI 21FI 4 505 SEQRES 1 D 502 ASN LYS ILE ASP TRP PHE ILE PHE ILE SER THR PHE VAL SEQRES 2 D 502 LEU ILE VAL ALA ILE CYS LEU PRO LEU VAL LEU TYR PRO SEQRES 3 D 502 GLU LYS GLY GLY GLU LEU VAL SER GLN ALA ASN SER PHE SEQRES 4 D 502 VAL THR SER ASN PHE GLY MET VAL PHE LEU TRP ALA GLY SEQRES 5 D 502 MET GLY GLY PHE ALA PHE LEU THR TYR LEU PHE PHE SER SEQRES 6 D 502 GLU HIS GLY LYS ILE LYS PHE GLY THR LYS ASP GLU LYS SEQRES 7 D 502 PRO GLU PHE SER ASN PHE SER TRP GLY ALA MET VAL PHE SEQRES 8 D 502 CYS ALA GLY VAL ALA SER GLY LEU VAL TYR TRP GLY THR SEQRES 9 D 502 ILE GLU TRP ALA TYR TYR PHE THR ALA PRO PRO TYR GLY SEQRES 10 D 502 ILE GLU PRO LYS SER THR ASP ALA ALA GLU ILE ALA ALA SEQRES 11 D 502 ALA TYR GLY ILE PHE HIS TRP GLY PRO SER ALA TRP ALA SEQRES 12 D 502 PHE PHE VAL LEU PRO SER LEU PRO ILE ALA TYR SER TYR SEQRES 13 D 502 TYR ILE LEU LYS VAL PRO VAL LEU ARG LEU SER GLU ILE SEQRES 14 D 502 CYS ARG ILE VAL ILE GLY LYS HIS SER ASP GLY VAL LEU SEQRES 15 D 502 GLY LYS VAL ILE ASP ILE ILE PHE MET PHE GLY ILE LEU SEQRES 16 D 502 GLY ALA ALA GLY THR SER LEU GLY LEU GLY THR PRO LEU SEQRES 17 D 502 VAL ALA ALA GLY ILE SER LYS ILE THR GLY ILE GLU SER SEQRES 18 D 502 SER THR SER MET THR VAL PHE VAL LEU VAL LEU CYS THR SEQRES 19 D 502 ALA LEU PHE THR TRP SER ALA TYR SER GLY LEU LYS ARG SEQRES 20 D 502 GLY LEU LYS LEU LEU SER ASP LEU ALA ILE ILE CYS SER SEQRES 21 D 502 VAL ILE LEU LEU THR TYR VAL LEU LEU VAL GLY PRO THR SEQRES 22 D 502 GLU PHE ILE LEU LYS MET GLY THR ASN SER VAL GLY LEU SEQRES 23 D 502 LEU PHE THR ASN PHE VAL ARG TRP ASN LEU TYR THR ASP SEQRES 24 D 502 PRO VAL SER GLY SER GLY PHE VAL GLU SER TRP THR VAL SEQRES 25 D 502 PHE TYR TRP ALA TRP TRP ILE VAL TYR THR PRO PHE MET SEQRES 26 D 502 GLY LEU PHE ILE ALA LYS ILE SER ARG GLY ARG THR ILE SEQRES 27 D 502 ARG GLN VAL ILE LEU GLY GLY ILE ALA TRP GLY THR LEU SEQRES 28 D 502 GLY CYS ALA ALA TYR PHE SER ILE LEU GLY ASN TYR ALA SEQRES 29 D 502 MET HIS LEU GLU LEU THR LYS GLU LEU SER VAL THR GLY SEQRES 30 D 502 LEU LEU GLU GLN ILE GLY ALA PRO ALA THR ILE MET GLU SEQRES 31 D 502 VAL ILE GLY THR LEU PRO LEU GLY SER VAL VAL VAL ILE SEQRES 32 D 502 VAL PHE SER PHE ILE ALA LEU ILE PHE LEU ALA THR THR SEQRES 33 D 502 PHE ASP SER ALA ALA TYR MET MET ALA SER SER THR THR SEQRES 34 D 502 PRO THR LEU GLY LEU ASN GLU GLU PRO ALA LYS TRP ASN SEQRES 35 D 502 ARG LEU PHE TRP ALA LEU THR LEU PHE ILE LEU PRO GLY SEQRES 36 D 502 THR LEU MET VAL LEU GLY GLY ASP LEU LYS THR LEU GLN SEQRES 37 D 502 THR ALA SER ILE LEU THR ALA ILE PRO PHE ILE PHE VAL SEQRES 38 D 502 ILE MET LEU LEU VAL VAL ALA LEU MET LYS MET LEU LYS SEQRES 39 D 502 THR GLY GLU HIS PHE ASN GLN ASP HET DQY D 601 19 HET NA D 602 1 HET NA D 603 1 HETNAM DQY 3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC ACID HETNAM NA SODIUM ION FORMUL 2 DQY C5 H12 O2 S FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *3(H2 O) HELIX 1 AA1 TRP D 8 TYR D 28 1 21 HELIX 2 AA2 TYR D 28 SER D 68 1 41 HELIX 3 AA3 GLU D 69 ILE D 73 5 5 HELIX 4 AA4 SER D 85 VAL D 98 1 14 HELIX 5 AA5 SER D 100 ALA D 116 1 17 HELIX 6 AA6 SER D 125 HIS D 139 1 15 HELIX 7 AA7 GLY D 141 ILE D 161 1 21 HELIX 8 AA8 ARG D 168 CYS D 173 1 6 HELIX 9 AA9 CYS D 173 GLY D 178 1 6 HELIX 10 AB1 LYS D 179 ASP D 182 5 4 HELIX 11 AB2 GLY D 183 THR D 220 1 38 HELIX 12 AB3 SER D 225 GLY D 247 1 23 HELIX 13 AB4 ARG D 250 GLY D 274 1 25 HELIX 14 AB5 PRO D 275 ASN D 293 1 19 HELIX 15 AB6 ASN D 293 LEU D 299 1 7 HELIX 16 AB7 GLY D 308 TRP D 313 1 6 HELIX 17 AB8 TRP D 313 VAL D 323 1 11 HELIX 18 AB9 TYR D 324 ILE D 335 1 12 HELIX 19 AC1 THR D 340 THR D 373 1 34 HELIX 20 AC2 SER D 377 GLY D 386 1 10 HELIX 21 AC3 GLY D 386 GLY D 396 1 11 HELIX 22 AC4 LEU D 400 THR D 432 1 33 HELIX 23 AC5 ALA D 442 PHE D 454 1 13 HELIX 24 AC6 PHE D 454 LEU D 463 1 10 HELIX 25 AC7 ASP D 466 ILE D 479 1 14 HELIX 26 AC8 PRO D 480 THR D 498 1 19 LINK O MET D 92 NA NA D 602 1555 1555 3.06 LINK O CYS D 95 NA NA D 603 1555 1555 2.94 LINK O VAL D 98 NA NA D 603 1555 1555 2.99 LINK O PHE D 415 NA NA D 603 1555 1555 2.70 LINK OG1 THR D 418 NA NA D 603 1555 1555 2.99 LINK OG1 THR D 419 NA NA D 603 1555 1555 2.69 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 1393 7864 CONECT 1446 7865 CONECT 1474 7865 CONECT 6409 7865 CONECT 6460 7865 CONECT 6473 7865 CONECT 7845 7850 7851 7852 7863 CONECT 7846 7847 7848 7849 CONECT 7847 7846 CONECT 7848 7846 7850 7853 7854 CONECT 7849 7846 CONECT 7850 7845 7848 7855 7856 CONECT 7851 7845 7857 7858 7859 CONECT 7852 7845 7860 7861 7862 CONECT 7853 7848 CONECT 7854 7848 CONECT 7855 7850 CONECT 7856 7850 CONECT 7857 7851 CONECT 7858 7851 CONECT 7859 7851 CONECT 7860 7852 CONECT 7861 7852 CONECT 7862 7852 CONECT 7863 7845 CONECT 7864 1393 CONECT 7865 1446 1474 6409 6460 CONECT 7865 6473 MASTER 139 0 3 26 0 0 0 6 3893 1 28 39 END