HEADER ELECTRON TRANSPORT 22-AUG-22 8E5G TITLE CRYO-EM OF A. VENEFICUS CYTOCHROME FILAMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TYPE CYTOCHROME; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS VENEFICUS; SOURCE 3 ORGANISM_TAXID: 58290 KEYWDS HELICAL SYMMETRY, CYTOCHROME FILMANET, CONDUCTIVE NANOWIRES, KEYWDS 2 MICROBIAL NANOWIRES, ELECTRON TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR F.WANG,D.P.BAQUERO,M.KRUPOVIC,E.H.EGELMAN REVDAT 2 26-JUL-23 8E5G 1 JRNL REVDAT 1 10-MAY-23 8E5G 0 JRNL AUTH D.P.BAQUERO,V.CVIRKAITE-KRUPOVIC,S.S.HU,J.L.FIELDS,X.LIU, JRNL AUTH 2 C.RENSING,E.H.EGELMAN,M.KRUPOVIC,F.WANG JRNL TITL EXTRACELLULAR CYTOCHROME NANOWIRES APPEAR TO BE UBIQUITOUS JRNL TITL 2 IN PROKARYOTES. JRNL REF CELL V. 186 2853 2023 JRNL REFN ISSN 1097-4172 JRNL PMID 37290436 JRNL DOI 10.1016/J.CELL.2023.05.012 REMARK 2 REMARK 2 RESOLUTION. 3.90 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 92602 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 8E5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267882. 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 : EXTRACELLULAR CYTOCHROME REMARK 245 FILAMENT 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) : 4500.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: UCSF CHIMERA 1.14_B42059. 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 0.390121 0.920764 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.920764 0.390121 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -65.47400 REMARK 350 BIOMT1 3 0.833703 0.552213 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.552213 0.833703 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -32.73700 REMARK 350 BIOMT1 4 0.833703 -0.552213 0.000000 0.00000 REMARK 350 BIOMT2 4 0.552213 0.833703 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 32.73700 REMARK 350 BIOMT1 5 0.390121 -0.920764 0.000000 0.00000 REMARK 350 BIOMT2 5 0.920764 0.390121 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 65.47400 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 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 ALA A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 MET A 10 REMARK 465 VAL A 11 REMARK 465 THR A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 MET A 16 REMARK 465 GLY A 17 REMARK 465 THR A 18 REMARK 465 LEU A 19 REMARK 465 VAL A 20 REMARK 465 LEU A 21 REMARK 465 PRO A 22 REMARK 465 SER A 23 REMARK 465 THR A 24 REMARK 465 THR A 25 REMARK 465 SER A 26 REMARK 465 LEU A 27 REMARK 465 PHE A 28 REMARK 465 LEU A 29 REMARK 465 GLY A 30 REMARK 465 ALA A 251 REMARK 465 SER A 252 REMARK 465 ASN A 253 REMARK 465 TRP A 254 REMARK 465 PRO A 255 REMARK 465 GLY A 256 REMARK 465 TRP A 257 REMARK 465 TYR A 258 REMARK 465 PRO A 259 REMARK 465 TYR A 260 REMARK 465 SER A 261 REMARK 465 TRP A 262 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 GLN A 31 CG CD OE1 NE2 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 SG CYS A 84 CAC HEC A 302 2.03 REMARK 500 SG CYS A 188 CAC HEC A 304 2.09 REMARK 500 OG SER A 203 O ASN A 231 2.19 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 HIS A 64 42.24 -102.27 REMARK 500 ASP A 97 31.51 -140.28 REMARK 500 THR A 161 -13.87 -140.36 REMARK 500 LYS A 162 32.20 -95.52 REMARK 500 GLN A 166 -73.52 18.49 REMARK 500 ASP A 180 -109.34 56.27 REMARK 500 ASN A 207 -149.52 -114.80 REMARK 500 TYR A 212 -4.39 68.20 REMARK 500 ASN A 227 149.08 70.23 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 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 50 NE2 REMARK 620 2 HEC A 301 NA 92.4 REMARK 620 3 HEC A 301 NB 92.2 89.8 REMARK 620 4 HEC A 301 NC 88.3 178.4 88.6 REMARK 620 5 HEC A 301 ND 87.3 90.5 179.4 91.0 REMARK 620 N 1 2 3 4 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 64 NE2 REMARK 620 2 HEC A 303 NA 95.1 REMARK 620 3 HEC A 303 NB 108.8 87.9 REMARK 620 4 HEC A 303 NC 91.6 173.2 90.9 REMARK 620 5 HEC A 303 ND 78.6 91.8 172.6 88.5 REMARK 620 6 HIS A 119 NE2 156.3 90.4 94.4 83.0 78.2 REMARK 620 N 1 2 3 4 5 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 85 NE2 REMARK 620 2 HEC A 302 NA 86.0 REMARK 620 3 HEC A 302 NB 95.2 88.3 REMARK 620 4 HEC A 302 NC 92.8 178.3 90.6 REMARK 620 5 HEC A 302 ND 83.8 91.4 179.0 89.7 REMARK 620 N 1 2 3 4 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 189 NE2 REMARK 620 2 HEC A 304 NA 99.7 REMARK 620 3 HEC A 304 NB 100.6 91.1 REMARK 620 4 HEC A 304 NC 81.4 178.9 88.4 REMARK 620 5 HEC A 304 ND 79.7 88.3 179.4 92.2 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27912 RELATED DB: EMDB REMARK 900 CRYO-EM OF A. VENEFICUS CYTOCHROME FILAMENT DBREF 8E5G A 1 262 UNP F2KMU8 F2KMU8_ARCVS 1 262 SEQRES 1 A 262 MET ASN GLY GLY LYS LEU ALA LEU LEU MET VAL THR LEU SEQRES 2 A 262 ALA ALA MET GLY THR LEU VAL LEU PRO SER THR THR SER SEQRES 3 A 262 LEU PHE LEU GLY GLN HIS MET TRP TYR ASN ILE SER GLY SEQRES 4 A 262 THR GLY ASN ASN LEU PRO CYS GLU LYS CYS HIS ALA ASP SEQRES 5 A 262 VAL PHE ALA GLU PHE LYS ASN ASN PRO GLY ALA HIS LYS SEQRES 6 A 262 THR ILE GLY GLY GLY THR ASP THR VAL GLU HIS ILE ARG SEQRES 7 A 262 ALA ALA CYS GLY GLU CYS HIS ARG THR SER VAL VAL GLY SEQRES 8 A 262 THR PHE ALA SER GLY ASP GLY THR SER ALA THR PRO GLY SEQRES 9 A 262 GLN GLU ALA HIS ALA ALA ALA THR ILE ALA CYS MET ALA SEQRES 10 A 262 CYS HIS GLU PHE GLY PRO ASN GLY ASN ALA PRO TYR SER SEQRES 11 A 262 GLY ALA PRO VAL ALA GLY GLY PHE ASP ASN VAL THR THR SEQRES 12 A 262 ASP THR ALA SER SER PRO TYR ASN TYR ASP ASN GLY ASP SEQRES 13 A 262 THR THR TYR GLY THR LYS GLU ALA HIS GLN THR PHE ILE SEQRES 14 A 262 GLU ARG ALA VAL GLU ASP LYS THR LEU ILE ASP SER ASN SEQRES 15 A 262 GLU ALA CYS ILE ALA CYS HIS THR TYR VAL PRO VAL LYS SEQRES 16 A 262 ILE ASN TRP THR HIS LYS VAL SER LEU GLU PHE ASN CYS SEQRES 17 A 262 THR TYR GLU TYR ASN THR GLY THR SER GLY VAL THR THR SEQRES 18 A 262 HIS TYR ASN VAL THR ASN TRP THR VAL ASN GLY THR ARG SEQRES 19 A 262 TYR THR THR VAL PHE GLY ASN THR THR GLY ASN GLY SER SEQRES 20 A 262 VAL ASN ASP ALA SER ASN TRP PRO GLY TRP TYR PRO TYR SEQRES 21 A 262 SER TRP 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 PRO A 45 CYS A 49 5 5 HELIX 2 AA2 HIS A 50 ASN A 59 1 10 HELIX 3 AA3 THR A 73 ARG A 86 1 14 HELIX 4 AA4 GLN A 166 ASP A 175 1 10 HELIX 5 AA5 SER A 181 ILE A 186 1 6 SHEET 1 AA1 2 SER A 95 GLY A 96 0 SHEET 2 AA1 2 ALA A 101 THR A 102 -1 O THR A 102 N SER A 95 SHEET 1 AA2 3 VAL A 194 TYR A 210 0 SHEET 2 AA2 3 TYR A 223 GLY A 240 -1 O ASN A 224 N THR A 209 SHEET 3 AA2 3 GLY A 246 VAL A 248 -1 O SER A 247 N PHE A 239 LINK SG CYS A 46 CAB HEC A 301 1555 1555 1.79 LINK SG CYS A 49 CAC HEC A 301 1555 1555 1.91 LINK SG CYS A 81 CAB HEC A 302 1555 1555 1.80 LINK SG CYS A 115 CAB HEC A 303 1555 1555 1.73 LINK SG CYS A 118 CAC HEC A 303 1555 1555 1.99 LINK SG CYS A 185 CAB HEC A 304 1555 1555 1.84 LINK NE2 HIS A 50 FE HEC A 301 1555 1555 2.04 LINK NE2 HIS A 64 FE HEC A 303 1555 1555 2.09 LINK NE2 HIS A 85 FE HEC A 302 1555 1555 2.05 LINK NE2 HIS A 119 FE HEC A 303 1555 1555 2.01 LINK NE2 HIS A 189 FE HEC A 304 1555 1555 2.04 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