HEADER MOTOR PROTEIN 13-MAR-23 8GI2 TITLE CRYO-EM STRUCTURE OF NATRINEMA SP. J7-2 TYPE IV PILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NATRINEMA PILIN, ORF10; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NATRINEMA SP. J7-2; SOURCE 3 ORGANISM_TAXID: 406552 KEYWDS HELICAL, PILI, NATRINEMA, PROTEIN FIBRIL, MOTOR PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.R.SONANI,M.A.B.KREUTZBERGER,Y.LIU,M.KRUPOVIC,E.H.EGELMAN REVDAT 1 16-AUG-23 8GI2 0 JRNL AUTH M.A.B.KREUTZBERGER,V.CVIRKAITE-KRUPOVIC,Y.LIU,D.P.BAQUERO, JRNL AUTH 2 J.LIU,R.R.SONANI,C.R.CALLADINE,F.WANG,M.KRUPOVIC,E.H.EGELMAN JRNL TITL THE EVOLUTION OF ARCHAEAL FLAGELLAR FILAMENTS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 56120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37399404 JRNL DOI 10.1073/PNAS.2304256120 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 261069 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 8GI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272973. 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 : TYPE IV PILI 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 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 : 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) = 108.72 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 4.95 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 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 0.992115 0.125333 0.000000 -16.23610 REMARK 350 BIOMT2 2 -0.125333 0.992115 0.000000 18.41480 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -49.54000 REMARK 350 BIOMT1 3 -0.199710 -0.979855 0.000000 301.29000 REMARK 350 BIOMT2 3 0.979855 -0.199710 0.000000 30.40330 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -44.58600 REMARK 350 BIOMT1 4 -0.863923 0.503623 0.000000 188.02800 REMARK 350 BIOMT2 4 -0.503623 -0.863923 0.000000 327.28400 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -39.63200 REMARK 350 BIOMT1 5 0.754251 0.656586 0.000000 -56.79680 REMARK 350 BIOMT2 5 -0.656586 0.754251 0.000000 124.73200 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -34.67800 REMARK 350 BIOMT1 6 0.379779 -0.925077 0.000000 213.61500 REMARK 350 BIOMT2 6 0.925077 0.379779 0.000000 -42.13330 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -29.72400 REMARK 350 BIOMT1 7 -0.998027 -0.062790 0.000000 284.86600 REMARK 350 BIOMT2 7 0.062790 -0.998027 0.000000 267.52800 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -24.77000 REMARK 350 BIOMT1 8 0.260842 0.965382 0.000000 -31.28110 REMARK 350 BIOMT2 8 -0.965382 0.260842 0.000000 235.62500 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -19.81600 REMARK 350 BIOMT1 9 0.830596 -0.556876 0.000000 100.39900 REMARK 350 BIOMT2 9 0.556876 0.830596 0.000000 -53.55810 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -14.86200 REMARK 350 BIOMT1 10 -0.793990 -0.607930 0.000000 332.02200 REMARK 350 BIOMT2 10 0.607930 -0.793990 0.000000 163.96800 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -9.90800 REMARK 350 BIOMT1 11 -0.320944 0.947098 0.000000 51.66610 REMARK 350 BIOMT2 11 -0.947098 -0.320944 0.000000 313.52400 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -4.95400 REMARK 350 BIOMT1 12 -0.320944 -0.947098 0.000000 313.52000 REMARK 350 BIOMT2 12 0.947098 -0.320944 0.000000 51.69060 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 4.95400 REMARK 350 BIOMT1 13 -0.793990 0.607930 0.000000 163.94200 REMARK 350 BIOMT2 13 -0.607930 -0.793990 0.000000 332.03500 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 9.90800 REMARK 350 BIOMT1 14 0.830596 0.556876 0.000000 -53.56590 REMARK 350 BIOMT2 14 -0.556876 0.830596 0.000000 100.39500 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 14.86200 REMARK 350 BIOMT1 15 0.260842 -0.965382 0.000000 235.62800 REMARK 350 BIOMT2 15 0.965382 0.260842 0.000000 -31.26270 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 19.81600 REMARK 350 BIOMT1 16 -0.998027 0.062790 0.000000 267.50500 REMARK 350 BIOMT2 16 -0.062790 -0.998027 0.000000 284.88700 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 24.77000 REMARK 350 BIOMT1 17 0.379779 0.925077 0.000000 -42.15000 REMARK 350 BIOMT2 17 -0.925077 0.379779 0.000000 213.61200 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 29.72400 REMARK 350 BIOMT1 18 0.754251 -0.656586 0.000000 124.73600 REMARK 350 BIOMT2 18 0.656586 0.754251 0.000000 -56.78700 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 34.67800 REMARK 350 BIOMT1 19 -0.863923 -0.503623 0.000000 327.27000 REMARK 350 BIOMT2 19 0.503623 -0.863923 0.000000 188.05300 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 39.63200 REMARK 350 BIOMT1 20 -0.199710 0.979855 0.000000 30.37980 REMARK 350 BIOMT2 20 -0.979855 -0.199710 0.000000 301.29200 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 44.58600 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 ASP A 2 REMARK 465 LEU A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 TYR A 6 REMARK 465 LYS A 7 REMARK 465 GLN A 8 REMARK 465 LYS A 9 REMARK 465 LEU A 10 REMARK 465 ILE A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 REMARK 465 ASP A 14 REMARK 465 GLU A 15 REMARK 465 GLU A 16 REMARK 465 ARG A 17 REMARK 465 ALA A 18 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 ASN A 102 -61.75 -120.19 REMARK 500 THR A 103 -170.64 -172.39 REMARK 500 ALA A 118 -75.88 -105.20 REMARK 500 ASN A 120 -177.51 -59.87 REMARK 500 ASP A 121 92.11 -160.46 REMARK 500 VAL A 124 -22.15 -38.07 REMARK 500 ALA A 125 -154.89 60.21 REMARK 500 ASN A 126 126.84 -28.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40060 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF NATRINEMA SP. J7-2 TYPE IV PILUS DBREF 8GI2 A 1 165 PDB 8GI2 8GI2 1 165 SEQRES 1 A 165 MET ASP LEU LYS LYS TYR LYS GLN LYS LEU ILE GLY SER SEQRES 2 A 165 ASP GLU GLU ARG ALA VAL SER PRO VAL ILE GLY VAL ILE SEQRES 3 A 165 LEU MET VAL ALA ILE THR VAL ILE LEU ALA ALA VAL ILE SEQRES 4 A 165 ALA ALA PHE VAL LEU ASP LEU GLY GLY SER VAL GLY ASN SEQRES 5 A 165 GLU ALA GLN ALA GLY VAL ASN MET GLU VAL ASP GLU SER SEQRES 6 A 165 GLN GLY GLY ASN ILE THR VAL GLU VAL THR SER MET GLY SEQRES 7 A 165 ASN ALA ASP HIS VAL VAL LEU GLY GLY SER ILE ASP SER SEQRES 8 A 165 ASP GLN THR PRO TYR GLN GLY SER SER LYS ASN THR GLY SEQRES 9 A 165 LYS LEU LYS LEU THR VAL GLY ASP SER VAL THR ILE ASN SEQRES 10 A 165 ALA ASN ASN ASP GLY SER VAL ALA ASN TYR GLY LEU SER SEQRES 11 A 165 SER THR GLU GLY THR VAL THR ALA ILE ALA VAL ILE GLU SEQRES 12 A 165 GLU ASP GLU THR ARG THR GLN VAL ALA SER VAL ASP TYR SEQRES 13 A 165 SER GLY PHE THR ALA LYS ASP ILE SER HELIX 1 AA1 VAL A 19 LEU A 46 1 28 SHEET 1 AA1 3 VAL A 58 ASP A 63 0 SHEET 2 AA1 3 ASN A 69 VAL A 74 -1 O GLU A 73 N ASN A 59 SHEET 3 AA1 3 VAL A 114 ASN A 117 -1 O VAL A 114 N VAL A 72 SHEET 1 AA2 3 HIS A 82 GLY A 87 0 SHEET 2 AA2 3 GLY A 134 ILE A 142 -1 O THR A 137 N GLY A 86 SHEET 3 AA2 3 THR A 147 TYR A 156 -1 O VAL A 154 N VAL A 136 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