HEADER MEMBRANE PROTEIN 15-JUL-24 9G49 TITLE CRYO-EM RECONSTRUCTION OF THE FULL-LENGTH E. COLI TRANSMEMBRANE TITLE 2 FORMATE TRANSPORTER FOCA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMATE CHANNEL FOCA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FORMATE TRANSPORTER FOCA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: FOCA, YCAE, B0904, JW0887; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS FNT-TRANSPORTER, FOCA, FORMATE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR C.TUETING,K.JANSON,F.L.KYRILIS,F.HAMDI,P.L.KASTRITIS REVDAT 2 05-NOV-25 9G49 1 JRNL REVDAT 1 22-OCT-25 9G49 0 JRNL AUTH C.TUTING,K.JANSON,M.KAMMEL,C.IHLING,J.LORENZ,F.L.KYRILIS, JRNL AUTH 2 F.HAMDI,C.ERDMANN,A.SINZ,R.G.SAWERS,P.L.KASTRITIS JRNL TITL CONSERVED HYDROPHILIC CHECKPOINTS TUNE FOCA-MEDIATED JRNL TITL 2 FORMATE:H + SYMPORT. JRNL REF NAT COMMUN V. 16 9476 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41145500 JRNL DOI 10.1038/S41467-025-65159-3 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, COOT, REMARK 3 PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3KCV REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : THE INITAL MODEL WAS RIGID-FITTED USING REMARK 3 CHIMERAX, AND REFINED ITERATIVELY USING COOT AND PHENIX 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) : 2.560 REMARK 3 NUMBER OF PARTICLES : 302937 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 9G49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292140291. 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 : C5-SYMMETRIC COMPLEX OF THE REMARK 245 INNER MEMBRANE FORMATE REMARK 245 TRANSPORTER FOCA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : PLASMA TREATED, 25 S SAMPLE REMARK 245 NEGATIVE, 0.4 MBAR PRESSURE, 15 REMARK 245 MA CURRENT 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 : 3665 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA 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 0.308978 -0.951031 0.000000 124.38111 REMARK 350 BIOMT2 2 0.951031 0.308978 0.000000 -19.69621 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809008 -0.587806 0.000000 181.56156 REMARK 350 BIOMT2 3 0.587806 -0.809008 0.000000 92.50545 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809008 0.587806 0.000000 92.50508 REMARK 350 BIOMT2 4 -0.587806 -0.809008 0.000000 181.56191 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.308978 0.951031 0.000000 -19.69658 REMARK 350 BIOMT2 5 -0.951031 0.308978 0.000000 124.38162 REMARK 350 BIOMT3 5 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 LYS A 2 REMARK 465 ALA A 3 REMARK 465 ASP A 4 REMARK 465 ASN A 5 REMARK 465 ASN A 282 REMARK 465 ASP A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 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 7 -1.87 -140.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 104 0.15 SIDE CHAIN REMARK 500 ARG A 186 0.12 SIDE CHAIN REMARK 500 ARG A 280 0.26 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-51034 RELATED DB: EMDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE FULL-LENGTH E. COLI TRANSMEMBRANE REMARK 900 FORMATE TRANSPORTER FOCA DBREF 9G49 A 1 285 UNP P0AC23 FOCA_ECOLI 1 285 SEQRES 1 A 285 MET LYS ALA ASP ASN PRO PHE ASP LEU LEU LEU PRO ALA SEQRES 2 A 285 ALA MET ALA LYS VAL ALA GLU GLU ALA GLY VAL TYR LYS SEQRES 3 A 285 ALA THR LYS HIS PRO LEU LYS THR PHE TYR LEU ALA ILE SEQRES 4 A 285 THR ALA GLY VAL PHE ILE SER ILE ALA PHE VAL PHE TYR SEQRES 5 A 285 ILE THR ALA THR THR GLY THR GLY THR MET PRO PHE GLY SEQRES 6 A 285 MET ALA LYS LEU VAL GLY GLY ILE CYS PHE SER LEU GLY SEQRES 7 A 285 LEU ILE LEU CYS VAL VAL CYS GLY ALA ASP LEU PHE THR SEQRES 8 A 285 SER THR VAL LEU ILE VAL VAL ALA LYS ALA SER GLY ARG SEQRES 9 A 285 ILE THR TRP GLY GLN LEU ALA LYS ASN TRP LEU ASN VAL SEQRES 10 A 285 TYR PHE GLY ASN LEU VAL GLY ALA LEU LEU PHE VAL LEU SEQRES 11 A 285 LEU MET TRP LEU SER GLY GLU TYR MET THR ALA ASN GLY SEQRES 12 A 285 GLN TRP GLY LEU ASN VAL LEU GLN THR ALA ASP HIS LYS SEQRES 13 A 285 VAL HIS HIS THR PHE ILE GLU ALA VAL CYS LEU GLY ILE SEQRES 14 A 285 LEU ALA ASN LEU MET VAL CYS LEU ALA VAL TRP MET SER SEQRES 15 A 285 TYR SER GLY ARG SER LEU MET ASP LYS ALA PHE ILE MET SEQRES 16 A 285 VAL LEU PRO VAL ALA MET PHE VAL ALA SER GLY PHE GLU SEQRES 17 A 285 HIS SER ILE ALA ASN MET PHE MET ILE PRO MET GLY ILE SEQRES 18 A 285 VAL ILE ARG ASP PHE ALA SER PRO GLU PHE TRP THR ALA SEQRES 19 A 285 VAL GLY SER ALA PRO GLU ASN PHE SER HIS LEU THR VAL SEQRES 20 A 285 MET ASN PHE ILE THR ASP ASN LEU ILE PRO VAL THR ILE SEQRES 21 A 285 GLY ASN ILE ILE GLY GLY GLY LEU LEU VAL GLY LEU THR SEQRES 22 A 285 TYR TRP VAL ILE TYR LEU ARG GLU ASN ASP HIS HIS FORMUL 2 HOH *(H2 O) HELIX 1 AA1 LEU A 11 THR A 28 1 18 HELIX 2 AA2 HIS A 30 THR A 56 1 27 HELIX 3 AA3 PRO A 63 CYS A 85 1 23 HELIX 4 AA4 LEU A 89 VAL A 94 1 6 HELIX 5 AA5 ILE A 96 SER A 102 1 7 HELIX 6 AA6 THR A 106 SER A 135 1 30 HELIX 7 AA7 GLY A 136 THR A 140 5 5 HELIX 8 AA8 GLY A 143 LYS A 156 1 14 HELIX 9 AA9 THR A 160 GLY A 185 1 26 HELIX 10 AB1 SER A 187 ILE A 194 1 8 HELIX 11 AB2 MET A 195 SER A 205 1 11 HELIX 12 AB3 HIS A 209 ALA A 227 1 19 HELIX 13 AB4 SER A 228 GLY A 236 1 9 HELIX 14 AB5 ALA A 238 SER A 243 5 6 HELIX 15 AB6 THR A 246 ASN A 254 1 9 HELIX 16 AB7 ASN A 254 LEU A 268 1 15 HELIX 17 AB8 LEU A 269 LEU A 279 1 11 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 2105 GLU A 281 HETATM 2106 O HOH A 301 46.246 57.683 96.403 1.00 20.00 O MASTER 170 0 0 17 0 0 0 6 2105 1 0 22 END