HEADER PROTEIN FIBRIL 21-JAN-25 9MYG TITLE CRYO-EM STRUCTURE OF NATRINEMA SP. J7-2 TYPE IV PILUS, PILA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARCHAEAL TYPE IV PILIN N-TERMINAL DOMAIN-CONTAINING COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NATRINEMA SP. J7-2; SOURCE 3 ORGANISM_TAXID: 406552; SOURCE 4 GENE: NJ7G_0728; SOURCE 5 EXPRESSION_SYSTEM: NATRINEMA SP. J7-2; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 406552 KEYWDS TYPE IV PILUS, PILIN, BIOFILM, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR R.R.SONANI,E.H.EGELMAN REVDAT 1 26-NOV-25 9MYG 0 JRNL AUTH J.XIANG,R.R.SONANI,Y.WANG,Z.CHEN,W.XIONG,J.CHEN,S.LI,K.AN, JRNL AUTH 2 Y.WANG,Y.LIU,M.A.B.KREUTZBERGER,M.KRUPOVIC,E.H.EGELMAN,S.DU, JRNL AUTH 3 X.CHEN JRNL TITL A TYPE IV PILI-MEDIATED MUTUALISM BETWEEN TWO CO-RESIDENT JRNL TITL 2 TEMPERATE ARCHAEAL VIRUSES AND THEIR HOST. JRNL REF CELL REP V. 44 15873 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 40544455 JRNL DOI 10.1016/J.CELREP.2025.115873 REMARK 2 REMARK 2 RESOLUTION. 3.80 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 35647 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 9MYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000292088. 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 PILUS 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 : 7.00 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) = 108.81 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 0.388481 -0.921457 0.000000 211.93200 REMARK 350 BIOMT2 2 0.921457 0.388481 0.000000 -42.82260 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -29.70000 REMARK 350 BIOMT1 3 -0.997503 -0.070627 0.000000 285.87800 REMARK 350 BIOMT2 3 0.070627 -0.997503 0.000000 266.41500 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -24.75000 REMARK 350 BIOMT1 4 0.254771 0.967001 0.000000 -30.68670 REMARK 350 BIOMT2 4 -0.967001 0.254771 0.000000 236.70400 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -19.80000 REMARK 350 BIOMT1 5 0.833211 -0.552955 0.000000 99.50760 REMARK 350 BIOMT2 5 0.552955 0.833211 0.000000 -53.37400 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -14.85000 REMARK 350 BIOMT1 6 -0.792077 -0.610422 0.000000 332.11500 REMARK 350 BIOMT2 6 0.610422 -0.792077 0.000000 163.39700 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -9.90000 REMARK 350 BIOMT1 7 -0.322431 0.946593 0.000000 51.92110 REMARK 350 BIOMT2 7 -0.946593 -0.322431 0.000000 313.68800 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -4.95000 REMARK 350 BIOMT1 8 -0.322431 -0.946593 0.000000 313.67600 REMARK 350 BIOMT2 8 0.946593 -0.322431 0.000000 51.99460 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 4.95000 REMARK 350 BIOMT1 9 -0.792077 0.610422 0.000000 163.31900 REMARK 350 BIOMT2 9 -0.610422 -0.792077 0.000000 332.15300 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 9.90000 REMARK 350 BIOMT1 10 0.833211 0.552955 0.000000 -53.39740 REMARK 350 BIOMT2 10 -0.552955 0.833211 0.000000 99.49510 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 14.85000 REMARK 350 BIOMT1 11 0.254771 -0.967001 0.000000 236.71200 REMARK 350 BIOMT2 11 0.967001 0.254771 0.000000 -30.63130 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 19.80000 REMARK 350 BIOMT1 12 -0.997503 0.070627 0.000000 266.34800 REMARK 350 BIOMT2 12 -0.070627 -0.997503 0.000000 285.94100 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 24.75000 REMARK 350 BIOMT1 13 0.388481 0.921457 0.000000 -42.87230 REMARK 350 BIOMT2 13 -0.921457 0.388481 0.000000 211.92200 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 29.70000 REMARK 350 BIOMT1 14 0.746986 -0.664839 0.000000 126.89600 REMARK 350 BIOMT2 14 0.664839 0.746986 0.000000 -56.91810 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 34.65000 REMARK 350 BIOMT1 15 -0.870184 -0.492727 0.000000 326.63900 REMARK 350 BIOMT2 15 0.492727 -0.870184 0.000000 190.46500 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 39.60000 REMARK 350 BIOMT1 16 -0.185838 0.982580 0.000000 28.06430 REMARK 350 BIOMT2 16 -0.982580 -0.185838 0.000000 299.77700 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 44.55000 REMARK 350 BIOMT1 17 0.990024 -0.140901 0.000000 20.86030 REMARK 350 BIOMT2 17 0.140901 0.990024 0.000000 -18.09730 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 49.50000 REMARK 350 BIOMT1 18 -0.452590 -0.891719 0.000000 324.08100 REMARK 350 BIOMT2 18 0.891719 -0.452590 0.000000 77.57590 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 54.45000 REMARK 350 BIOMT1 19 -0.698165 0.715936 0.000000 135.75000 REMARK 350 BIOMT2 19 -0.715936 -0.698165 0.000000 333.75400 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 59.40000 REMARK 350 BIOMT1 20 0.902811 0.430038 0.000000 -46.02340 REMARK 350 BIOMT2 20 -0.430038 0.902811 0.000000 72.88140 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 64.35000 REMARK 350 BIOMT1 21 0.115977 -0.993252 0.000000 259.52600 REMARK 350 BIOMT2 21 0.993252 0.115977 0.000000 -15.07000 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 69.30000 REMARK 350 BIOMT1 22 -0.977600 0.210472 0.000000 244.26200 REMARK 350 BIOMT2 22 -0.210472 -0.977600 0.000000 302.51900 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 74.25000 REMARK 350 BIOMT1 23 0.514440 0.857527 0.000000 -51.44440 REMARK 350 BIOMT2 23 -0.857527 0.514440 0.000000 185.67000 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 79.20000 REMARK 350 BIOMT1 24 0.645858 -0.763458 0.000000 154.51000 REMARK 350 BIOMT2 24 0.763458 0.645858 0.000000 -56.56790 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 84.15000 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 ALA A 5 REMARK 465 LEU A 6 REMARK 465 LYS A 7 REMARK 465 PRO A 8 REMARK 465 LYS A 9 REMARK 465 LEU A 10 REMARK 465 VAL A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 REMARK 465 ASP A 14 REMARK 465 ASN 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: 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 OD1 ASP A 140 OG1 THR A 142 2.12 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 SER A 97 4.45 -69.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48737 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF NATRINEMA SP. J7-2 TYPE IV PILUS, PILA1 DBREF 9MYG A 1 154 UNP I7CEX0 I7CEX0_NATSJ 1 154 SEQRES 1 A 154 MET ASP LEU LYS ALA LEU LYS PRO LYS LEU VAL GLY SER SEQRES 2 A 154 ASP ASN GLU ARG ALA VAL SER PRO VAL ILE GLY VAL ILE SEQRES 3 A 154 LEU MET VAL ALA ILE THR VAL ILE LEU ALA ALA VAL ILE SEQRES 4 A 154 ALA ALA PHE VAL LEU ASP LEU GLY GLY SER VAL GLY GLN SEQRES 5 A 154 GLU ALA GLN ALA GLY VAL THR ILE GLU VAL ASP GLU SER SEQRES 6 A 154 SER GLN GLU ILE GLN VAL GLU VAL THR SER MET GLY ASN SEQRES 7 A 154 SER ASP LEU VAL LYS LEU GLY GLY ALA THR ASP GLY ILE SEQRES 8 A 154 ALA SER ASN ALA GLY SER THR ILE SER GLY ASP HIS THR SEQRES 9 A 154 ASP MET GLN THR GLY ASP VAL VAL THR MET ASP GLY SER SEQRES 10 A 154 SER TRP SER SER THR SER GLY ALA SER ALA SER GLY THR SEQRES 11 A 154 ILE THR ALA ILE ALA VAL ILE GLU GLU ASP GLU THR GLU SEQRES 12 A 154 THR GLN VAL ALA SER GLU GLU TYR ASP PHE SER HELIX 1 AA1 VAL A 19 SER A 49 1 31 HELIX 2 AA2 ALA A 87 ALA A 95 1 9 HELIX 3 AA3 SER A 117 SER A 121 5 5 SHEET 1 AA1 4 GLY A 57 ASP A 63 0 SHEET 2 AA1 4 GLU A 68 SER A 75 -1 O GLU A 68 N ASP A 63 SHEET 3 AA1 4 VAL A 111 ASP A 115 -1 O MET A 114 N ILE A 69 SHEET 4 AA1 4 ILE A 99 SER A 100 -1 N SER A 100 O THR A 113 SHEET 1 AA2 3 LEU A 81 GLY A 86 0 SHEET 2 AA2 3 SER A 128 ILE A 137 -1 O THR A 132 N GLY A 85 SHEET 3 AA2 3 THR A 142 ASP A 152 -1 O THR A 144 N ALA A 135 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 1872 SER A 154 MASTER 222 0 0 3 7 0 0 6 953 1 0 12 END