HEADER TRANSPORT PROTEIN 10-JAN-25 9LGT TITLE CRYO-EM STRUCTURE OF THE GLUCOSE-SPECIFIC PTS TRANSPORTER IIC FROM V. TITLE 2 CHOLERAE IN THE INWARD-FACING CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PTS SYSTEM GLUCOSE-SPECIFIC EIICB COMPONENT; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EIICB-GLC; COMPND 5 EC: 2.7.1.199; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE M66-2; SOURCE 3 ORGANISM_TAXID: 579112; SOURCE 4 GENE: PTSG, VCM66_1937; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PTS TRANSPORTER, CRYO-EM, V. CHOLERAE, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.H.GUO,Q.S.ZHANG,Z.WANG,K.ZHANG,Y.FU REVDAT 1 14-JAN-26 9LGT 0 JRNL AUTH H.H.GUO JRNL TITL CRYO-EM STRUCTURE OF THE GLUCOSE-SPECIFIC PTS TRANSPORTER JRNL TITL 2 IIC FROM V. CHOLERAE IN THE INWARD-FACING CONFORMATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.68 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) : 3.680 REMARK 3 NUMBER OF PARTICLES : 87760 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 9LGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300054775. 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 : PTS SYSTEM GLUCOSE-SPECIFIC REMARK 245 EIIC COMPONENT 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 : 7.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ASP A 205 82.08 -157.32 REMARK 500 HIS A 355 138.60 -170.51 REMARK 500 PHE A 359 -55.77 -121.09 REMARK 500 SER A 360 29.69 -145.47 REMARK 500 HIS B 355 147.34 -173.70 REMARK 500 PHE B 359 -56.83 -122.76 REMARK 500 SER B 360 27.10 -145.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63072 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE GLUCOSE-SPECIFIC PTS TRANSPORTER IIC FROM REMARK 900 V. CHOLERAE IN THE INWARD-FACING CONFORMATION DBREF 9LGT A 29 410 UNP C3LNW4 C3LNW4_VIBCM 29 410 DBREF 9LGT B 29 410 UNP C3LNW4 C3LNW4_VIBCM 29 410 SEQRES 1 A 382 ALA PHE ALA ASN LEU GLN LYS VAL GLY LYS ALA LEU MET SEQRES 2 A 382 LEU PRO VAL SER VAL LEU PRO VAL ALA GLY ILE LEU LEU SEQRES 3 A 382 GLY VAL GLY ALA ALA ASN PHE SER TRP LEU PRO GLU VAL SEQRES 4 A 382 VAL SER HIS LEU MET GLU GLN ALA GLY GLY SER VAL PHE SEQRES 5 A 382 GLY GLN MET PRO LEU LEU PHE ALA VAL GLY VAL ALA LEU SEQRES 6 A 382 GLY PHE THR ASN ASN ASP GLY VAL SER GLY LEU SER ALA SEQRES 7 A 382 ILE VAL GLY TYR GLY ILE MET VAL ALA THR LEU LYS VAL SEQRES 8 A 382 MET ALA THR VAL MET GLY VAL SER GLY ILE ASP THR GLY SEQRES 9 A 382 VAL LEU GLY GLY ILE LEU ALA GLY GLY VAL ALA ALA TRP SEQRES 10 A 382 SER PHE ASN ARG PHE TYR LYS ILE GLN LEU PRO GLU TYR SEQRES 11 A 382 LEU GLY PHE PHE ALA GLY LYS ARG ALA VAL PRO ILE ILE SEQRES 12 A 382 THR GLY PHE ILE SER ILE ALA LEU GLY VAL VAL LEU SER SEQRES 13 A 382 PHE ILE TRP PRO PRO ILE GLY SER ALA ILE ALA THR PHE SEQRES 14 A 382 SER ASP TRP ALA ALA ASN GLN ASP PRO VAL THR ALA PHE SEQRES 15 A 382 GLY ILE TYR GLY ILE VAL GLU ARG SER LEU ILE PRO PHE SEQRES 16 A 382 GLY LEU HIS HIS ILE TRP ASN VAL PRO PHE PHE TYR GLN SEQRES 17 A 382 ALA GLY THR CYS VAL ASN GLY ALA GLY GLU THR VAL ASN SEQRES 18 A 382 GLY ILE MET THR CYS PHE LEU THR ALA ASP ASP ALA SER SEQRES 19 A 382 ARG ALA ALA GLY ASN GLY PHE GLY GLN LEU ALA GLY GLY SEQRES 20 A 382 TYR LEU PHE LYS MET PHE GLY LEU PRO ALA ALA ALA PHE SEQRES 21 A 382 ALA ILE ALA HIS CYS ALA LYS PRO GLU ASN ARG ALA LYS SEQRES 22 A 382 VAL MET GLY ILE MET ALA SER ALA ALA LEU THR SER PHE SEQRES 23 A 382 LEU THR GLY ILE THR GLU PRO ILE GLU PHE ALA PHE LEU SEQRES 24 A 382 PHE VAL ALA PRO VAL LEU TYR ALA ILE HIS ALA VAL LEU SEQRES 25 A 382 ALA GLY LEU ALA TYR VAL LEU THR ASN ALA LEU GLY VAL SEQRES 26 A 382 VAL HIS GLY HIS THR PHE SER ASN GLY PHE ILE ASP PHE SEQRES 27 A 382 VAL VAL GLN SER PRO ARG ALA ASP ASN MET LEU LEU LEU SEQRES 28 A 382 VAL GLY LEU GLY ILE GLY TYR ALA VAL LEU TYR TYR VAL SEQRES 29 A 382 VAL PHE THR PHE VAL ILE ARG ALA LEU ASN LEU LYS THR SEQRES 30 A 382 PRO GLY ARG GLU ASP SEQRES 1 B 382 ALA PHE ALA ASN LEU GLN LYS VAL GLY LYS ALA LEU MET SEQRES 2 B 382 LEU PRO VAL SER VAL LEU PRO VAL ALA GLY ILE LEU LEU SEQRES 3 B 382 GLY VAL GLY ALA ALA ASN PHE SER TRP LEU PRO GLU VAL SEQRES 4 B 382 VAL SER HIS LEU MET GLU GLN ALA GLY GLY SER VAL PHE SEQRES 5 B 382 GLY GLN MET PRO LEU LEU PHE ALA VAL GLY VAL ALA LEU SEQRES 6 B 382 GLY PHE THR ASN ASN ASP GLY VAL SER GLY LEU SER ALA SEQRES 7 B 382 ILE VAL GLY TYR GLY ILE MET VAL ALA THR LEU LYS VAL SEQRES 8 B 382 MET ALA THR VAL MET GLY VAL SER GLY ILE ASP THR GLY SEQRES 9 B 382 VAL LEU GLY GLY ILE LEU ALA GLY GLY VAL ALA ALA TRP SEQRES 10 B 382 SER PHE ASN ARG PHE TYR LYS ILE GLN LEU PRO GLU TYR SEQRES 11 B 382 LEU GLY PHE PHE ALA GLY LYS ARG ALA VAL PRO ILE ILE SEQRES 12 B 382 THR GLY PHE ILE SER ILE ALA LEU GLY VAL VAL LEU SER SEQRES 13 B 382 PHE ILE TRP PRO PRO ILE GLY SER ALA ILE ALA THR PHE SEQRES 14 B 382 SER ASP TRP ALA ALA ASN GLN ASP PRO VAL THR ALA PHE SEQRES 15 B 382 GLY ILE TYR GLY ILE VAL GLU ARG SER LEU ILE PRO PHE SEQRES 16 B 382 GLY LEU HIS HIS ILE TRP ASN VAL PRO PHE PHE TYR GLN SEQRES 17 B 382 ALA GLY THR CYS VAL ASN GLY ALA GLY GLU THR VAL ASN SEQRES 18 B 382 GLY ILE MET THR CYS PHE LEU THR ALA ASP ASP ALA SER SEQRES 19 B 382 ARG ALA ALA GLY ASN GLY PHE GLY GLN LEU ALA GLY GLY SEQRES 20 B 382 TYR LEU PHE LYS MET PHE GLY LEU PRO ALA ALA ALA PHE SEQRES 21 B 382 ALA ILE ALA HIS CYS ALA LYS PRO GLU ASN ARG ALA LYS SEQRES 22 B 382 VAL MET GLY ILE MET ALA SER ALA ALA LEU THR SER PHE SEQRES 23 B 382 LEU THR GLY ILE THR GLU PRO ILE GLU PHE ALA PHE LEU SEQRES 24 B 382 PHE VAL ALA PRO VAL LEU TYR ALA ILE HIS ALA VAL LEU SEQRES 25 B 382 ALA GLY LEU ALA TYR VAL LEU THR ASN ALA LEU GLY VAL SEQRES 26 B 382 VAL HIS GLY HIS THR PHE SER ASN GLY PHE ILE ASP PHE SEQRES 27 B 382 VAL VAL GLN SER PRO ARG ALA ASP ASN MET LEU LEU LEU SEQRES 28 B 382 VAL GLY LEU GLY ILE GLY TYR ALA VAL LEU TYR TYR VAL SEQRES 29 B 382 VAL PHE THR PHE VAL ILE ARG ALA LEU ASN LEU LYS THR SEQRES 30 B 382 PRO GLY ARG GLU ASP HELIX 1 AA1 ALA A 29 LEU A 40 1 12 HELIX 2 AA2 LEU A 40 VAL A 46 1 7 HELIX 3 AA3 VAL A 46 ALA A 58 1 13 HELIX 4 AA4 PRO A 65 GLY A 81 1 17 HELIX 5 AA5 GLN A 82 PHE A 95 1 14 HELIX 6 AA6 ASP A 99 GLY A 125 1 27 HELIX 7 AA7 THR A 131 PHE A 150 1 20 HELIX 8 AA8 PRO A 156 GLY A 160 5 5 HELIX 9 AA9 ALA A 167 THR A 172 1 6 HELIX 10 AB1 PHE A 174 GLN A 204 1 31 HELIX 11 AB2 ASP A 205 ILE A 221 1 17 HELIX 12 AB3 PRO A 222 GLY A 224 5 3 HELIX 13 AB4 LEU A 225 GLN A 236 1 12 HELIX 14 AB5 GLY A 250 ALA A 258 1 9 HELIX 15 AB6 ASP A 259 GLY A 266 1 8 HELIX 16 AB7 ASN A 267 ALA A 273 5 7 HELIX 17 AB8 GLY A 274 PHE A 281 1 8 HELIX 18 AB9 PHE A 281 ALA A 294 1 14 HELIX 19 AC1 LYS A 295 GLU A 297 5 3 HELIX 20 AC2 ASN A 298 GLY A 317 1 20 HELIX 21 AC3 THR A 319 PHE A 328 1 10 HELIX 22 AC4 ALA A 330 GLY A 352 1 23 HELIX 23 AC5 GLY A 362 GLN A 369 1 8 HELIX 24 AC6 SER A 370 ALA A 373 5 4 HELIX 25 AC7 ASN A 375 ASN A 402 1 28 HELIX 26 AC8 PHE B 30 LEU B 40 1 11 HELIX 27 AC9 LEU B 40 SER B 45 1 6 HELIX 28 AD1 VAL B 46 ALA B 59 1 14 HELIX 29 AD2 PRO B 65 GLN B 82 1 18 HELIX 30 AD3 GLN B 82 PHE B 95 1 14 HELIX 31 AD4 ASP B 99 MET B 124 1 26 HELIX 32 AD5 GLY B 132 PHE B 150 1 19 HELIX 33 AD6 PRO B 156 GLY B 160 5 5 HELIX 34 AD7 GLY B 164 ARG B 166 5 3 HELIX 35 AD8 ALA B 167 GLN B 204 1 38 HELIX 36 AD9 ASP B 205 ILE B 221 1 17 HELIX 37 AE1 LEU B 225 ALA B 237 1 13 HELIX 38 AE2 GLY B 250 ALA B 258 1 9 HELIX 39 AE3 ASP B 259 GLY B 266 1 8 HELIX 40 AE4 ASN B 267 ALA B 273 5 7 HELIX 41 AE5 GLY B 274 PHE B 281 1 8 HELIX 42 AE6 PHE B 281 ALA B 294 1 14 HELIX 43 AE7 LYS B 295 GLU B 297 5 3 HELIX 44 AE8 ASN B 298 THR B 316 1 19 HELIX 45 AE9 THR B 319 LEU B 327 1 9 HELIX 46 AF1 ALA B 330 GLY B 352 1 23 HELIX 47 AF2 GLY B 362 GLN B 369 1 8 HELIX 48 AF3 SER B 370 ALA B 373 5 4 HELIX 49 AF4 ASN B 375 ASN B 402 1 28 SHEET 1 AA1 2 CYS A 240 VAL A 241 0 SHEET 2 AA1 2 THR A 247 VAL A 248 -1 O VAL A 248 N CYS A 240 SHEET 1 AA2 2 CYS B 240 VAL B 241 0 SHEET 2 AA2 2 THR B 247 VAL B 248 -1 O VAL B 248 N CYS B 240 SSBOND 1 CYS A 240 CYS A 254 1555 1555 2.02 SSBOND 2 CYS B 240 CYS B 254 1555 1555 2.02 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 TER 2826 ASP A 410 TER 5652 ASP B 410 CONECT 1565 1657 CONECT 1657 1565 CONECT 4391 4483 CONECT 4483 4391 MASTER 123 0 0 49 4 0 0 6 5650 2 4 60 END