HEADER ELECTRON TRANSPORT, PROTEIN FIBRIL 07-JAN-22 7TFS TITLE CRYO-EM OF THE OMCE NANOWIRES FROM GEOBACTER SULFURREDUCENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER SULFURREDUCENS; SOURCE 3 ORGANISM_TAXID: 35554; SOURCE 4 STRAIN: ATCC 51573 / DSM 12127 / PCA KEYWDS HELICAL SYMMETRY, CYTOCHROME NANOWIRE, FILAMENT, ELECTRON TRANSPORT, KEYWDS 2 PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR F.WANG,K.MUSTAFA,C.H.CHAN,K.JOSHI,A.I.HOCHBAUM,D.R.BOND,E.H.EGELMAN REVDAT 2 16-NOV-22 7TFS 1 JRNL REVDAT 1 04-MAY-22 7TFS 0 JRNL AUTH F.WANG,K.MUSTAFA,V.SUCIU,K.JOSHI,C.H.CHAN,S.CHOI,Z.SU,D.SI, JRNL AUTH 2 A.I.HOCHBAUM,E.H.EGELMAN,D.R.BOND JRNL TITL CRYO-EM STRUCTURE OF AN EXTRACELLULAR GEOBACTER OMCE JRNL TITL 2 CYTOCHROME FILAMENT REVEALS TETRAHAEM PACKING. JRNL REF NAT MICROBIOL V. 7 1291 2022 JRNL REFN ESSN 2058-5276 JRNL PMID 35798889 JRNL DOI 10.1038/S41564-022-01159-Z REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 4.300 REMARK 3 NUMBER OF PARTICLES : 346826 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 7TFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262237. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : FILAMENT OF OMCE PROTEIN 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 : 6.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 58.81 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 33.90 ANGSTROMS 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 -0.998066 0.062163 0.000000 0.00000 REMARK 350 BIOMT2 1 -0.062163 -0.998066 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -101.70000 REMARK 350 BIOMT1 2 -0.463667 0.886009 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.886009 -0.463667 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -67.80000 REMARK 350 BIOMT1 3 0.517848 0.855473 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.855473 0.517848 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -33.90000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.517848 -0.855473 0.000000 0.00000 REMARK 350 BIOMT2 5 0.855473 0.517848 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 33.90000 REMARK 350 BIOMT1 6 -0.463667 -0.886009 0.000000 0.00000 REMARK 350 BIOMT2 6 0.886009 -0.463667 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 67.80000 REMARK 350 BIOMT1 7 -0.998066 -0.062163 0.000000 0.00000 REMARK 350 BIOMT2 7 0.062163 -0.998066 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 101.70000 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 ARG A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 VAL A 5 REMARK 465 LYS A 6 REMARK 465 ILE A 7 REMARK 465 GLY A 8 REMARK 465 LEU A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 THR A 12 REMARK 465 ALA A 13 REMARK 465 LEU A 14 REMARK 465 LEU A 15 REMARK 465 VAL A 16 REMARK 465 ALA A 17 REMARK 465 VAL A 18 REMARK 465 THR A 19 REMARK 465 ALA A 20 REMARK 465 ALA A 21 REMARK 465 GLY A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 SER A 25 REMARK 465 ILE A 26 REMARK 465 LYS A 27 REMARK 465 ASN A 28 REMARK 465 THR A 29 REMARK 465 LYS A 232 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CD2 LEU A 166 O1D HEC A 304 1.37 REMARK 500 SG CYS A 204 CAC HEC A 303 2.05 REMARK 500 CD1 LEU A 187 CAC HEC A 304 2.08 REMARK 500 SG CYS A 106 CAC HEC A 302 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 214 C - N - CD ANGL. DEV. = -16.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 63 48.71 -87.92 REMARK 500 PRO A 65 109.65 -50.08 REMARK 500 LEU A 166 50.61 -91.76 REMARK 500 ASN A 185 -5.56 70.22 REMARK 500 ASN A 210 31.11 -99.47 REMARK 500 PHE A 215 42.40 73.63 REMARK 500 SER A 223 17.79 59.62 REMARK 500 HIS A 230 59.78 -94.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 64 PRO A 65 -143.18 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 HEC A 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 31 NE2 REMARK 620 2 HEC A 302 NA 94.2 REMARK 620 3 HEC A 302 NB 85.9 89.3 REMARK 620 4 HEC A 302 NC 83.4 177.2 89.0 REMARK 620 5 HEC A 302 ND 92.2 91.1 178.1 90.5 REMARK 620 6 HIS A 107 NE2 175.1 90.5 95.4 91.9 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HEC A 301 NA 89.4 REMARK 620 3 HEC A 301 NB 108.2 91.1 REMARK 620 4 HEC A 301 NC 90.1 178.2 87.4 REMARK 620 5 HEC A 301 ND 70.4 89.5 178.4 91.9 REMARK 620 6 HIS A 208 NE2 150.8 95.5 100.5 85.7 80.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 304 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 149 NE2 REMARK 620 2 HEC A 304 NA 69.7 REMARK 620 3 HEC A 304 NB 85.9 90.0 REMARK 620 4 HEC A 304 NC 106.8 176.0 87.9 REMARK 620 5 HEC A 304 ND 91.5 91.6 176.3 90.3 REMARK 620 6 HIS A 230 NE2 154.1 85.3 101.2 98.4 82.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 303 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 205 NE2 REMARK 620 2 HEC A 303 NA 82.4 REMARK 620 3 HEC A 303 NB 91.1 89.6 REMARK 620 4 HEC A 303 NC 98.5 178.7 89.4 REMARK 620 5 HEC A 303 ND 90.1 90.7 178.8 90.3 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25879 RELATED DB: EMDB REMARK 900 CRYO-EM OF THE OMCE NANOWIRES FROM GEOBACTER SULFURREDUCENS DBREF 7TFS A 1 232 UNP Q74FJ0 Q74FJ0_GEOSL 1 232 SEQRES 1 A 232 MET ARG SER GLU VAL LYS ILE GLY LEU ALA LEU THR ALA SEQRES 2 A 232 LEU LEU VAL ALA VAL THR ALA ALA GLY ALA ALA SER ILE SEQRES 3 A 232 LYS ASN THR LYS HIS ASP LEU SER SER GLY SER THR GLY SEQRES 4 A 232 ALA THR PHE LYS ALA THR ASN THR ASP GLN ILE CYS VAL SEQRES 5 A 232 PHE CYS HIS THR PRO HIS ASN ALA GLN GLN ASP ILE PRO SEQRES 6 A 232 LEU TRP ASN ARG GLY ASN PRO THR ALA SER THR PHE THR SEQRES 7 A 232 LEU TYR SER SER SER SER MET ASN ASN VAL PRO VAL LYS SEQRES 8 A 232 GLN GLY PHE THR ALA ASP SER ILE SER LEU PHE CYS MET SEQRES 9 A 232 SER CYS HIS ASP GLY ALA THR GLY LEU GLY GLY ALA VAL SEQRES 10 A 232 HIS ASN ASP PRO ASN GLY ALA ALA ILE ALA MET VAL GLY SEQRES 11 A 232 GLY ASN ASP LEU ILE THR GLY GLU ALA ASN LEU GLY THR SEQRES 12 A 232 ASP LEU SER ASN ASP HIS PRO VAL ASN PHE GLU VAL THR SEQRES 13 A 232 PRO ALA GLY ILE ALA ALA ASP GLY ASN LEU GLY ALA LEU SEQRES 14 A 232 ASP THR GLY THR ASN PRO PRO THR MET LYS THR GLY ASP SEQRES 15 A 232 VAL THR ASN GLY LEU PRO LEU PHE LYS SER ALA ARG GLY SEQRES 16 A 232 ALA THR THR LEU GLU CYS GLY SER CYS HIS LYS VAL HIS SEQRES 17 A 232 ASP ASN THR ASP ALA PRO PHE LEU ARG THR THR MET ALA SEQRES 18 A 232 GLY SER LYS LEU CYS LEU GLY CYS HIS LYS LYS HET HEC A 301 43 HET HEC A 302 43 HET HEC A 303 43 HET HEC A 304 43 HETNAM HEC HEME C FORMUL 2 HEC 4(C34 H34 FE N4 O4) HELIX 1 AA1 ILE A 50 CYS A 54 5 5 HELIX 2 AA2 THR A 73 PHE A 77 5 5 HELIX 3 AA3 ASN A 87 LYS A 91 5 5 HELIX 4 AA4 SER A 98 HIS A 107 1 10 HELIX 5 AA5 MET A 128 ASN A 132 5 5 HELIX 6 AA6 THR A 156 GLY A 164 1 9 HELIX 7 AA7 SER A 223 HIS A 230 1 8 SHEET 1 AA1 2 PHE A 153 GLU A 154 0 SHEET 2 AA1 2 THR A 198 LEU A 199 -1 O LEU A 199 N PHE A 153 SHEET 1 AA2 3 ALA A 168 ASP A 170 0 SHEET 2 AA2 3 THR A 177 LYS A 179 -1 O THR A 177 N ASP A 170 SHEET 3 AA2 3 LEU A 187 PRO A 188 -1 O LEU A 187 N MET A 178 LINK SG CYS A 54 CAC HEC A 301 1555 1555 1.85 LINK SG CYS A 54 C3C HEC A 301 1555 1555 1.98 LINK SG CYS A 103 CAB HEC A 302 1555 1555 1.86 LINK SG CYS A 201 CAB HEC A 303 1555 1555 1.87 LINK SG CYS A 226 CAB HEC A 304 1555 1555 1.88 LINK SG CYS A 229 CAC HEC A 304 1555 1555 1.95 LINK NE2 HIS A 31 FE HEC A 302 1555 1555 2.08 LINK NE2 HIS A 55 FE HEC A 301 1555 1555 2.00 LINK NE2 HIS A 107 FE HEC A 302 1555 1555 2.01 LINK NE2 HIS A 149 FE HEC A 304 1555 1555 2.06 LINK NE2 HIS A 205 FE HEC A 303 1555 1555 2.05 LINK NE2 HIS A 208 FE HEC A 301 1555 1555 1.97 LINK NE2 HIS A 230 FE HEC A 304 1555 1555 2.09 CISPEP 1 ASN A 174 PRO A 175 0 -3.32 CISPEP 2 ALA A 213 PRO A 214 0 3.61 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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