HEADER PROTEIN FIBRIL 21-NOV-24 9EGP TITLE CRYO-EM OF TYPE IV PILUS FROM GEOBACTER METALLIREDUCENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GEOPILIN DOMAIN 2 PROTEIN; COMPND 3 CHAIN: B; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: GEOPILIN DOMAIN 1 PROTEIN; COMPND 6 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER METALLIREDUCENS; SOURCE 3 ORGANISM_TAXID: 28232; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: GEOBACTER METALLIREDUCENS; SOURCE 6 ORGANISM_TAXID: 28232 KEYWDS PILUS, TYPE IV PILUS, HELICAL SYMMETRY, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR M.EGOROVA,H.A.PETERSEN,C.H.CHAN,D.R.BOND,F.WANG REVDAT 1 26-NOV-25 9EGP 0 JRNL AUTH M.EGOROVA,H.A.PETERSEN,C.H.CHAN,D.R.BOND,F.WANG JRNL TITL CRYO-EM OF TYPE IV PILUS FROM GEOBACTER METALLIREDUCENS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.60 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 193496 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 9EGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1000290024. 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 : 7.40 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) : 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 : 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) = 91.75 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 10.09 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: B, A REMARK 350 BIOMT1 1 0.933355 0.358954 0.000000 0.00000 REMARK 350 BIOMT2 1 -0.358954 0.933355 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -121.12800 REMARK 350 BIOMT1 2 0.330234 -0.943899 0.000000 0.00000 REMARK 350 BIOMT2 2 0.943899 0.330234 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -111.03400 REMARK 350 BIOMT1 3 -0.953559 -0.301205 0.000000 0.00000 REMARK 350 BIOMT2 3 0.301205 -0.953559 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -100.94000 REMARK 350 BIOMT1 4 -0.271894 0.962327 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.962327 -0.271894 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -90.84600 REMARK 350 BIOMT1 5 0.970194 0.242328 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.242328 0.970194 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -80.75200 REMARK 350 BIOMT1 6 0.212536 -0.977153 0.000000 0.00000 REMARK 350 BIOMT2 6 0.977153 0.212536 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -70.65800 REMARK 350 BIOMT1 7 -0.983198 -0.182544 0.000000 0.00000 REMARK 350 BIOMT2 7 0.182544 -0.983198 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -60.56400 REMARK 350 BIOMT1 8 -0.152382 0.988322 0.000000 0.00000 REMARK 350 BIOMT2 8 -0.988322 -0.152382 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -50.47000 REMARK 350 BIOMT1 9 0.992521 0.122077 0.000000 0.00000 REMARK 350 BIOMT2 9 -0.122077 0.992521 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -40.37600 REMARK 350 BIOMT1 10 0.091658 -0.995791 0.000000 0.00000 REMARK 350 BIOMT2 10 0.995791 0.091658 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -30.28200 REMARK 350 BIOMT1 11 -0.998128 -0.061153 0.000000 0.00000 REMARK 350 BIOMT2 11 0.061153 -0.998128 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -20.18800 REMARK 350 BIOMT1 12 -0.030591 0.999532 0.000000 0.00000 REMARK 350 BIOMT2 12 -0.999532 -0.030591 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -10.09400 REMARK 350 BIOMT1 13 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 13 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 14 -0.030591 -0.999532 0.000000 0.00000 REMARK 350 BIOMT2 14 0.999532 -0.030591 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 10.09400 REMARK 350 BIOMT1 15 -0.998128 0.061153 0.000000 0.00000 REMARK 350 BIOMT2 15 -0.061153 -0.998128 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 20.18800 REMARK 350 BIOMT1 16 0.091658 0.995791 0.000000 0.00000 REMARK 350 BIOMT2 16 -0.995791 0.091658 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 30.28200 REMARK 350 BIOMT1 17 0.992521 -0.122077 0.000000 0.00000 REMARK 350 BIOMT2 17 0.122077 0.992521 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 40.37600 REMARK 350 BIOMT1 18 -0.152382 -0.988322 0.000000 0.00000 REMARK 350 BIOMT2 18 0.988322 -0.152382 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 50.47000 REMARK 350 BIOMT1 19 -0.983198 0.182544 0.000000 0.00000 REMARK 350 BIOMT2 19 -0.182544 -0.983198 0.000000 0.00000 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 60.56400 REMARK 350 BIOMT1 20 0.212536 0.977153 0.000000 0.00000 REMARK 350 BIOMT2 20 -0.977153 0.212536 0.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 70.65800 REMARK 350 BIOMT1 21 0.970194 -0.242328 0.000000 0.00000 REMARK 350 BIOMT2 21 0.242328 0.970194 0.000000 0.00000 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 80.75200 REMARK 350 BIOMT1 22 -0.271894 -0.962327 0.000000 0.00000 REMARK 350 BIOMT2 22 0.962327 -0.271894 0.000000 0.00000 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 90.84600 REMARK 350 BIOMT1 23 -0.953559 0.301205 0.000000 0.00000 REMARK 350 BIOMT2 23 -0.301205 -0.953559 0.000000 0.00000 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 100.94000 REMARK 350 BIOMT1 24 0.330234 0.943899 0.000000 0.00000 REMARK 350 BIOMT2 24 -0.943899 0.330234 0.000000 0.00000 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 111.03400 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 B 1 REMARK 465 LYS B 2 REMARK 465 LYS B 3 REMARK 465 LYS B 4 REMARK 465 ILE B 5 REMARK 465 PHE B 6 REMARK 465 LEU B 7 REMARK 465 THR B 8 REMARK 465 GLY B 9 REMARK 465 LEU B 10 REMARK 465 CYS B 11 REMARK 465 PHE B 12 REMARK 465 LEU B 13 REMARK 465 SER B 14 REMARK 465 ILE B 15 REMARK 465 GLY B 16 REMARK 465 SER B 17 REMARK 465 VAL B 18 REMARK 465 ALA B 19 REMARK 465 PHE B 20 REMARK 465 ALA B 21 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 GLN A 3 REMARK 465 LYS A 4 REMARK 465 LEU A 5 REMARK 465 ARG A 6 REMARK 465 ASN A 7 REMARK 465 LYS A 8 REMARK 465 LYS A 9 REMARK 465 GLY A 10 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 OE2 GLU A 58 OH TYR A 67 2.15 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 B 46 -164.64 -79.11 REMARK 500 LYS B 69 57.16 -98.43 REMARK 500 THR B 89 15.39 55.30 REMARK 500 ALA B 90 17.16 -140.93 REMARK 500 ALA B 92 -129.72 51.76 REMARK 500 THR B 100 41.06 38.58 REMARK 500 TRP B 109 -157.79 -147.88 REMARK 500 LYS B 110 -0.62 83.79 REMARK 500 TYR A 61 1.71 -63.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47993 RELATED DB: EMDB REMARK 900 CRYO-EM OF TYPE IV PILUS FROM GEOBACTER METALLIREDUCENS DBREF 9EGP B 1 113 UNP Q39VU0 Q39VU0_GEOMG 1 113 DBREF 9EGP A 1 69 UNP Q39VU1 Q39VU1_GEOMG 1 69 SEQRES 1 B 113 MET LYS LYS LYS ILE PHE LEU THR GLY LEU CYS PHE LEU SEQRES 2 B 113 SER ILE GLY SER VAL ALA PHE ALA ALA SER LYS ASP VAL SEQRES 3 B 113 THR GLY SER GLY GLU ILE GLY GLY SER ASN SER THR PRO SEQRES 4 B 113 LYS LEU ALA ILE GLN THR SER ASN GLN VAL THR LEU THR SEQRES 5 B 113 TYR ASP GLY GLY THR GLY HIS THR TYR GLY ILE ALA THR SEQRES 6 B 113 LEU HIS ALA LYS GLY THR ARG LYS TYR ALA SER THR SER SEQRES 7 B 113 ASN ASP THR LYS ILE TYR TYR ASN ASP ASN THR ALA THR SEQRES 8 B 113 ALA ALA PRO SER ALA PRO VAL GLY THR ALA THR ILE GLY SEQRES 9 B 113 GLY SER THR ASN TRP LYS ASN ALA LEU SEQRES 1 A 69 MET LEU GLN LYS LEU ARG ASN LYS LYS GLY PHE THR LEU SEQRES 2 A 69 ILE GLU LEU LEU ILE VAL VAL ALA ILE ILE GLY ILE LEU SEQRES 3 A 69 ALA ALA ILE ALA ILE PRO GLN PHE ALA ALA TYR ARG GLN SEQRES 4 A 69 LYS ALA PHE ASN SER ALA ALA GLU SER ASP LEU LYS ASN SEQRES 5 A 69 THR LYS THR ASN LEU GLU SER TYR TYR SER GLU HIS GLN SEQRES 6 A 69 PHE TYR PRO ASN HELIX 1 AA1 GLY B 34 THR B 38 5 5 HELIX 2 AA2 THR A 12 ALA A 27 1 16 HELIX 3 AA3 PHE A 34 HIS A 64 1 31 SHEET 1 AA1 4 VAL B 26 THR B 27 0 SHEET 2 AA1 4 VAL B 49 ASP B 54 -1 O LEU B 51 N VAL B 26 SHEET 3 AA1 4 GLY B 62 HIS B 67 -1 O GLY B 62 N ASP B 54 SHEET 4 AA1 4 LYS B 73 THR B 77 -1 O TYR B 74 N THR B 65 SHEET 1 AA2 2 SER B 29 ILE B 32 0 SHEET 2 AA2 2 LEU B 41 GLN B 44 -1 O LEU B 41 N ILE B 32 SHEET 1 AA3 2 TYR B 84 TYR B 85 0 SHEET 2 AA3 2 ASN B 111 ALA B 112 -1 O ASN B 111 N TYR B 85 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 658 LEU B 113 TER 1129 ASN A 69 MASTER 243 0 0 3 8 0 0 6 1127 2 0 15 END