HEADER PROTEIN FIBRIL 22-JUN-23 8PIZ TITLE NEISSERIA MENINGITIDIS TYPE IV PILUS SB-DATDH VARIANT BOUND TO THE C24 TITLE 2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PILIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: C24 NANOBODY; COMPND 6 CHAIN: B; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS 8013; SOURCE 3 ORGANISM_TAXID: 604162; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 6 ORGANISM_TAXID: 30538; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PILIN, EXTRACELLULAR, ADHESION, AGGREGATION, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR D.FERNANDEZ-MARTINEZ,G.DUMENIL REVDAT 2 09-OCT-24 8PIZ 1 REMARK REVDAT 1 03-APR-24 8PIZ 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. 2.75 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 : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 2.750 REMARK 3 NUMBER OF PARTICLES : 249060 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 8PIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131425. 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 : NEISSERIA MENINGITIDIS PILE, SB REMARK 245 -DATDH VARIANT, BOUND TO THE REMARK 245 C24 NANOBODY 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 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) : 4000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 SER B 129 REMARK 465 GLU B 130 REMARK 465 PRO B 131 REMARK 465 LYS B 132 REMARK 465 THR B 133 REMARK 465 PRO B 134 REMARK 465 LYS B 135 REMARK 465 PRO B 136 REMARK 465 GLN B 137 REMARK 465 PRO B 138 REMARK 465 ALA B 139 REMARK 465 ALA B 140 REMARK 465 ALA B 141 REMARK 465 LEU B 142 REMARK 465 GLU B 143 REMARK 465 HIS B 144 REMARK 465 HIS B 145 REMARK 465 HIS B 146 REMARK 465 HIS B 147 REMARK 465 HIS B 148 REMARK 465 HIS B 149 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 ALA A 18 30.97 -96.31 REMARK 500 LYS A 140 -118.34 48.12 REMARK 500 ALA B 94 -169.39 -161.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17384 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17695 RELATED DB: EMDB REMARK 900 NEISSERIA MENINGITIDIS TYPE IV PILUS SB-DATDH VARIANT DBREF1 8PIZ A 1 161 UNP A0A1I9GEU1_NEIME DBREF2 8PIZ A A0A1I9GEU1 1 161 DBREF 8PIZ B 1 149 PDB 8PIZ 8PIZ 1 149 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 SEQRES 1 B 149 MET ALA GLN LEU GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 B 149 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SER SEQRES 3 B 149 SER GLY PHE ARG SER ASP TYR TYR ALA ILE VAL TRP PHE SEQRES 4 B 149 ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS SEQRES 5 B 149 ILE SER THR SER GLY LYS THR THR ILE TYR ALA ASP SER SEQRES 6 B 149 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 7 B 149 ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 B 149 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP PHE ARG GLY SEQRES 9 B 149 SER ARG LEU SER ASP VAL CYS SER TYR SER SER MET ASP SEQRES 10 B 149 TYR TRP GLY LYS GLY THR LEU ALA THR VAL SER SER GLU SEQRES 11 B 149 PRO LYS THR PRO LYS PRO GLN PRO ALA ALA ALA LEU GLU SEQRES 12 B 149 HIS HIS HIS HIS HIS HIS HET G3P A 201 10 HET B6D A 202 16 HETNAM G3P SN-GLYCEROL-3-PHOSPHATE HETNAM B6D 2,4-BISACETAMIDO-2,4,6-TRIDEOXY-BETA-D-GLUCOPYRANOSE HETSYN B6D 2,4-BIS(ACETYLAMINO)-2,4,6-TRIDEOXY-BETA-D- HETSYN 2 B6D GLUCOPYRANOSE; 2,4-DIACETAMIDO-2,4,6-TRIDEOXY-BETA-D- HETSYN 3 B6D GLUCOPYRANOSE; BACILLOSAMINE; 2,4-BISACETAMIDO-2,4,6- HETSYN 4 B6D TRIDEOXY-BETA-D-GLUCOSE; 2,4-BISACETAMIDO-2,4,6- HETSYN 5 B6D TRIDEOXY-D-GLUCOSE; 2,4-BISACETAMIDO-2,4,6-TRIDEOXY- HETSYN 6 B6D GLUCOSE FORMUL 3 G3P C3 H9 O6 P FORMUL 4 B6D C10 H18 N2 O5 HELIX 1 AA1 THR A 2 ALA A 18 1 17 HELIX 2 AA2 ALA A 23 GLN A 43 1 21 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 97 LYS A 101 5 5 HELIX 7 AA7 ASN A 146 LEU A 150 5 5 HELIX 8 AA8 ARG B 30 ASP B 32 5 3 HELIX 9 AA9 LYS B 89 THR B 93 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 107 N ILE A 87 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 SHEET 1 AA3 4 LEU B 4 SER B 9 0 SHEET 2 AA3 4 SER B 19 GLY B 28 -1 O SER B 27 N GLN B 5 SHEET 3 AA3 4 THR B 80 ASN B 86 -1 O VAL B 81 N CYS B 24 SHEET 4 AA3 4 PHE B 70 ASP B 75 -1 N THR B 71 O GLN B 84 SHEET 1 AA4 6 LEU B 13 VAL B 14 0 SHEET 2 AA4 6 THR B 123 VAL B 127 1 O THR B 126 N VAL B 14 SHEET 3 AA4 6 ALA B 94 PHE B 102 -1 N TYR B 96 O THR B 123 SHEET 4 AA4 6 TYR B 34 GLN B 41 -1 N PHE B 39 O TYR B 97 SHEET 5 AA4 6 GLU B 48 ILE B 53 -1 O GLU B 48 N ARG B 40 SHEET 6 AA4 6 THR B 60 TYR B 62 -1 O ILE B 61 N CYS B 52 SHEET 1 AA5 4 LEU B 13 VAL B 14 0 SHEET 2 AA5 4 THR B 123 VAL B 127 1 O THR B 126 N VAL B 14 SHEET 3 AA5 4 ALA B 94 PHE B 102 -1 N TYR B 96 O THR B 123 SHEET 4 AA5 4 TYR B 118 TRP B 119 -1 O TYR B 118 N ALA B 100 SSBOND 1 CYS A 120 CYS A 154 1555 1555 2.03 SSBOND 2 CYS B 24 CYS B 98 1555 1555 2.03 SSBOND 3 CYS B 52 CYS B 111 1555 1555 2.03 LINK OG SER A 63 C1 B6D A 202 1555 1555 1.44 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 TER 2164 SER B 128 HETATM 2165 O1 G3P A 201 168.617 165.608 147.333 1.00 64.56 O HETATM 2166 C1 G3P A 201 167.856 164.671 146.605 1.00 65.14 C HETATM 2167 C2 G3P A 201 168.324 163.251 146.911 1.00 65.73 C HETATM 2168 O2 G3P A 201 168.700 162.612 145.712 1.00 68.25 O HETATM 2169 C3 G3P A 201 169.508 163.265 147.871 1.00 59.64 C HETATM 2170 O1P G3P A 201 169.303 164.230 148.878 1.00 57.61 O HETATM 2171 O4P G3P A 201 169.992 165.540 150.957 1.00 53.49 O HETATM 2172 O2P G3P A 201 171.553 165.348 149.063 1.00 64.54 O HETATM 2173 O3P G3P A 201 171.092 163.382 150.488 1.00 60.55 O HETATM 2174 P G3P A 201 170.503 164.627 149.871 1.00 58.02 P HETATM 2175 C1 B6D A 202 175.895 164.270 164.266 1.00 55.64 C HETATM 2176 N2 B6D A 202 174.248 164.305 166.131 1.00 52.55 N HETATM 2177 C3 B6D A 202 175.595 162.357 165.904 1.00 49.83 C HETATM 2178 C4 B6D A 202 176.554 161.556 165.039 1.00 45.88 C HETATM 2179 C5 B6D A 202 177.471 162.496 164.276 1.00 48.09 C HETATM 2180 C6 B6D A 202 178.433 161.703 163.402 1.00 51.96 C HETATM 2181 C7 B6D A 202 172.939 164.528 166.119 1.00 55.90 C HETATM 2182 C8 B6D A 202 172.431 165.458 167.180 1.00 53.77 C HETATM 2183 C9 B6D A 202 178.107 158.570 166.727 1.00 50.33 C HETATM 2184 C2 B6D A 202 174.904 163.479 165.134 1.00 50.63 C HETATM 2185 O7 B6D A 202 172.201 164.015 165.296 1.00 60.58 O HETATM 2186 N4 B6D A 202 177.339 160.671 165.873 1.00 51.95 N HETATM 2187 C10 B6D A 202 177.257 159.348 165.769 1.00 54.63 C HETATM 2188 O10 B6D A 202 176.537 158.804 164.949 1.00 58.87 O HETATM 2189 O5 B6D A 202 176.673 163.367 163.477 1.00 57.32 O HETATM 2190 O3 B6D A 202 174.603 161.478 166.447 1.00 57.64 O CONECT 479 2175 CONECT 512 2171 CONECT 904 1146 CONECT 1146 904 CONECT 1355 1938 CONECT 1578 2034 CONECT 1938 1355 CONECT 2034 1578 CONECT 2165 2166 CONECT 2166 2165 2167 CONECT 2167 2166 2168 2169 CONECT 2168 2167 CONECT 2169 2167 2170 CONECT 2170 2169 2174 CONECT 2171 512 2174 CONECT 2172 2174 CONECT 2173 2174 CONECT 2174 2170 2171 2172 2173 CONECT 2175 479 2184 2189 CONECT 2176 2181 2184 CONECT 2177 2178 2184 2190 CONECT 2178 2177 2179 2186 CONECT 2179 2178 2180 2189 CONECT 2180 2179 CONECT 2181 2176 2182 2185 CONECT 2182 2181 CONECT 2183 2187 CONECT 2184 2175 2176 2177 CONECT 2185 2181 CONECT 2186 2178 2187 CONECT 2187 2183 2186 2188 CONECT 2188 2187 CONECT 2189 2175 2179 CONECT 2190 2177 MASTER 149 0 2 9 20 0 0 6 2188 2 34 25 END