HEADER PROTEIN FIBRIL 16-MAY-23 8P2V TITLE NEISSERIA MENINGITIDIS TYPE IV PILUS SB-GATDH VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEISSERIA MENINGITIDIS PILE VARIANT SB-GATDH; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS 8013; SOURCE 3 ORGANISM_TAXID: 604162 KEYWDS PILIN, EXTRACELLULAR, ADHESION, AGGREGATION, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR D.FERNANDEZ-MARTINEZ,G.DUMENIL REVDAT 2 13-NOV-24 8P2V 1 REMARK REVDAT 1 03-APR-24 8P2V 0 JRNL AUTH D.FERNANDEZ-MARTINEZ,Y.KONG,S.GOUSSARD,A.ZAVALA,P.GASTINEAU, JRNL AUTH 2 M.REY,G.AYME,J.CHAMOT-ROOKE,P.LAFAYE,M.VOS,A.MECHALY, JRNL AUTH 3 G.DUMENIL JRNL TITL CRYO-EM STRUCTURES OF TYPE IV PILI COMPLEXED WITH NANOBODIES JRNL TITL 2 REVEAL IMMUNE ESCAPE MECHANISMS. JRNL REF NAT COMMUN V. 15 2414 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38499587 JRNL DOI 10.1038/S41467-024-46677-Y REMARK 2 REMARK 2 RESOLUTION. 2.99 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 271827 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 8P2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130421. 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 : PILE VARIANT SB CONTAINING REMARK 245 GATDH AND G3P PTMS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.01 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 CYS A 154 58.16 -95.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17375 RELATED DB: EMDB REMARK 900 NEISSERIA MENINGITIDIS TYPE IV PILUS SB-GATDH VARIANT DBREF 8P2V A 1 161 PDB 8P2V 8P2V 1 161 SEQRES 1 A 161 PHE THR LEU ILE GLU LEU MET ILE VAL ILE ALA ILE VAL SEQRES 2 A 161 GLY ILE LEU ALA ALA VAL ALA LEU PRO ALA TYR GLN ASP SEQRES 3 A 161 TYR THR ALA ARG ALA GLN VAL SER GLU ALA ILE LEU LEU SEQRES 4 A 161 ALA GLU GLY GLN LYS SER ALA VAL THR GLU TYR TYR LEU SEQRES 5 A 161 ASN HIS GLY GLU TRP PRO GLY ASP ASN SER SER ALA GLY SEQRES 6 A 161 VAL ALA THR SER ALA ASP ILE LYS GLY LYS TYR VAL GLN SEQRES 7 A 161 SER VAL THR VAL ALA ASN GLY VAL ILE THR ALA GLN MET SEQRES 8 A 161 ALA SER SER ASN VAL ASN ASN GLU ILE LYS SER LYS LYS SEQRES 9 A 161 LEU SER LEU TRP ALA LYS ARG GLN ASN GLY SER VAL LYS SEQRES 10 A 161 TRP PHE CYS GLY GLN PRO VAL THR ARG THR THR ALA THR SEQRES 11 A 161 ALA THR ASP VAL ALA ALA ALA ASN GLY LYS THR ASP ASP SEQRES 12 A 161 LYS ILE ASN THR LYS HIS LEU PRO SER THR CYS ARG ASP SEQRES 13 A 161 ASP SER SER ALA SER HET G3P A 201 10 HET WKE A 202 19 HETNAM G3P SN-GLYCEROL-3-PHOSPHATE HETNAM WKE (2~{R})-~{N}-[(2~{R},3~{S},4~{S},5~{R},6~{R})-5- HETNAM 2 WKE ACETAMIDO-2-METHYL-4,6-BIS(OXIDANYL)OXAN-3-YL]-2,3- HETNAM 3 WKE BIS(OXIDANYL)PROPANAMIDE FORMUL 2 G3P C3 H9 O6 P FORMUL 3 WKE C11 H20 N2 O7 HELIX 1 AA1 THR A 2 ALA A 18 1 17 HELIX 2 AA2 ALA A 23 GLY A 42 1 20 HELIX 3 AA3 GLN A 43 GLY A 55 1 13 HELIX 4 AA4 ASP A 60 GLY A 65 1 6 HELIX 5 AA5 THR A 68 ILE A 72 5 5 HELIX 6 AA6 ASN A 146 LEU A 150 5 5 SHEET 1 AA1 4 VAL A 77 ALA A 83 0 SHEET 2 AA1 4 VAL A 86 MET A 91 -1 O THR A 88 N THR A 81 SHEET 3 AA1 4 LYS A 104 ARG A 111 -1 O LEU A 105 N ALA A 89 SHEET 4 AA1 4 VAL A 116 GLY A 121 -1 O PHE A 119 N TRP A 108 SHEET 1 AA2 2 VAL A 124 THR A 125 0 SHEET 2 AA2 2 ALA A 135 ALA A 136 -1 O ALA A 135 N THR A 125 SSBOND 1 CYS A 120 CYS A 154 1555 1555 2.03 LINK OG SER A 63 C2 WKE A 202 1555 1555 1.43 LINK CB SER A 69 O4P G3P A 201 1555 1555 1.40 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 1198 SER A 161 HETATM 1199 O1 G3P A 201 194.725 172.289 155.786 1.00 76.02 O HETATM 1200 C1 G3P A 201 194.813 171.020 155.178 1.00 76.18 C HETATM 1201 C2 G3P A 201 194.307 169.949 156.137 1.00 76.89 C HETATM 1202 O2 G3P A 201 195.233 168.887 156.187 1.00 74.41 O HETATM 1203 C3 G3P A 201 194.136 170.539 157.532 1.00 74.66 C HETATM 1204 O1P G3P A 201 193.006 169.963 158.148 1.00 74.43 O HETATM 1205 O4P G3P A 201 191.627 169.397 160.215 1.00 68.72 O HETATM 1206 O2P G3P A 201 191.811 171.745 159.481 1.00 71.80 O HETATM 1207 O3P G3P A 201 193.754 170.613 160.497 1.00 69.18 O HETATM 1208 P G3P A 201 192.544 170.434 159.614 1.00 68.52 P HETATM 1209 C1 WKE A 202 188.325 176.882 173.999 1.00 72.74 C HETATM 1210 C2 WKE A 202 188.512 174.524 173.814 1.00 72.42 C HETATM 1211 C3 WKE A 202 189.950 174.531 174.337 1.00 71.62 C HETATM 1212 C4 WKE A 202 191.140 172.428 174.723 1.00 75.35 C HETATM 1213 C5 WKE A 202 191.909 172.727 173.469 1.00 73.92 C HETATM 1214 C6 WKE A 202 190.188 175.748 175.221 1.00 71.21 C HETATM 1215 C7 WKE A 202 189.744 177.028 174.530 1.00 69.61 C HETATM 1216 C8 WKE A 202 190.685 179.132 175.288 1.00 79.87 C HETATM 1217 C9 WKE A 202 190.829 180.100 176.425 1.00 77.76 C HETATM 1218 C10 WKE A 202 191.835 181.181 176.046 1.00 76.73 C HETATM 1219 N1 WKE A 202 189.825 178.133 175.464 1.00 74.55 N HETATM 1220 O1 WKE A 202 191.318 171.401 175.357 1.00 72.00 O HETATM 1221 O6 WKE A 202 191.580 175.840 175.543 1.00 78.08 O HETATM 1222 O3 WKE A 202 191.334 179.278 174.266 1.00 79.72 O HETATM 1223 O4 WKE A 202 189.563 180.704 176.706 1.00 74.84 O HETATM 1224 O5 WKE A 202 191.373 181.874 174.882 1.00 76.14 O HETATM 1225 N WKE A 202 190.253 173.342 175.111 1.00 75.81 N HETATM 1226 C WKE A 202 187.902 178.137 173.246 1.00 73.42 C HETATM 1227 O WKE A 202 188.255 175.751 173.129 1.00 77.16 O CONECT 479 1210 CONECT 512 1205 CONECT 904 1146 CONECT 1146 904 CONECT 1199 1200 CONECT 1200 1199 1201 CONECT 1201 1200 1202 1203 CONECT 1202 1201 CONECT 1203 1201 1204 CONECT 1204 1203 1208 CONECT 1205 512 1208 CONECT 1206 1208 CONECT 1207 1208 CONECT 1208 1204 1205 1206 1207 CONECT 1209 1215 1226 1227 CONECT 1210 479 1211 1227 CONECT 1211 1210 1214 1225 CONECT 1212 1213 1220 1225 CONECT 1213 1212 CONECT 1214 1211 1215 1221 CONECT 1215 1209 1214 1219 CONECT 1216 1217 1219 1222 CONECT 1217 1216 1218 1223 CONECT 1218 1217 1224 CONECT 1219 1215 1216 CONECT 1220 1212 CONECT 1221 1214 CONECT 1222 1216 CONECT 1223 1217 CONECT 1224 1218 CONECT 1225 1211 1212 CONECT 1226 1209 CONECT 1227 1209 1210 MASTER 116 0 2 6 6 0 0 6 1226 1 33 13 END