HEADER PROTEIN FIBRIL 21-JUN-23 8PIJ TITLE NEISSERIA MENINGITIDIS TYPE IV PILUS SB-GATDH VARIANT BOUND TO THE C24 TITLE 2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PILIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: C24 NANOBODY; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS 8013; SOURCE 3 ORGANISM_TAXID: 604162; SOURCE 4 EXPRESSION_SYSTEM: NEISSERIA MENINGITIDIS 8013; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 604162; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 8 ORGANISM_TAXID: 30538; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PILIN, EXTRACELLULAR, ADHESION, AGGREGATION, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR D.FERNANDEZ-MARTINEZ,G.DUMENIL REVDAT 2 20-NOV-24 8PIJ 1 REMARK REVDAT 1 03-APR-24 8PIJ 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. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 434690 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 8PIJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131246. 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 : COMPLEX OF NEISSERIA REMARK 245 MENINGITIDIS PILE SB-GATDH AND REMARK 245 THE 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 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 95 73.23 -101.85 REMARK 500 PHE B 29 -144.50 54.19 REMARK 500 VAL B 50 -59.94 -122.83 REMARK 500 SER B 115 62.89 65.22 REMARK 500 ASP B 117 -74.57 -101.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17375 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17683 RELATED DB: EMDB REMARK 900 NEISSERIA MENINGITIDIS TYPE IV PILUS SB-GATDH VARIANT BOUND TO THE REMARK 900 C24 NANOBODY DBREF1 8PIJ A 1 161 UNP A0A1I9GEU1_NEIME DBREF2 8PIJ A A0A1I9GEU1 1 161 DBREF 8PIJ B 1 128 PDB 8PIJ 8PIJ 1 128 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 128 MET ALA GLN LEU GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 B 128 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SER SEQRES 3 B 128 SER GLY PHE ARG SER ASP TYR TYR ALA ILE VAL TRP PHE SEQRES 4 B 128 ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS SEQRES 5 B 128 ILE SER THR SER GLY LYS THR THR ILE TYR ALA ASP SER SEQRES 6 B 128 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 7 B 128 ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 B 128 ASP THR ALA VAL TYR TYR CYS ALA ALA ASP PHE ARG GLY SEQRES 9 B 128 SER ARG LEU SER ASP VAL CYS SER TYR SER SER MET ASP SEQRES 10 B 128 TYR TRP GLY LYS GLY THR LEU ALA THR VAL 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 3 G3P C3 H9 O6 P FORMUL 4 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 ALA A 46 GLY A 55 1 10 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 HELIX 7 AA7 ARG B 30 ASP B 32 5 3 HELIX 8 AA8 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 GLN B 5 SER B 9 0 SHEET 2 AA3 4 LEU B 20 SER B 27 -1 O ALA B 25 N VAL B 7 SHEET 3 AA3 4 THR B 80 MET B 85 -1 O LEU B 83 N LEU B 22 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 VAL B 37 O ALA B 99 SHEET 5 AA4 6 ARG B 47 ILE B 53 -1 O SER B 51 N TRP B 38 SHEET 6 AA4 6 THR B 60 TYR B 62 -1 O ILE B 61 N CYS B 52 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 2.04 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 TER 2164 SER B 128 HETATM 2165 O1 G3P A 201 209.076 169.435 208.135 1.00 71.36 O HETATM 2166 C1 G3P A 201 209.571 168.196 207.679 1.00 71.27 C HETATM 2167 C2 G3P A 201 208.406 167.309 207.255 1.00 71.90 C HETATM 2168 O2 G3P A 201 207.190 167.906 207.644 1.00 75.92 O HETATM 2169 C3 G3P A 201 208.426 167.132 205.742 1.00 62.92 C HETATM 2170 O1P G3P A 201 207.706 168.179 205.134 1.00 59.09 O HETATM 2171 O4P G3P A 201 207.281 169.534 203.013 1.00 69.75 O HETATM 2172 O2P G3P A 201 208.498 167.395 202.847 1.00 71.09 O HETATM 2173 O3P G3P A 201 206.087 167.400 203.356 1.00 65.20 O HETATM 2174 P G3P A 201 207.390 168.131 203.558 1.00 63.95 P HETATM 2175 C1 WKE A 202 200.543 164.013 189.157 1.00 51.03 C HETATM 2176 C2 WKE A 202 201.741 166.060 189.257 1.00 58.91 C HETATM 2177 C3 WKE A 202 202.738 165.604 188.196 1.00 52.76 C HETATM 2178 C4 WKE A 202 204.363 167.185 187.324 1.00 58.11 C HETATM 2179 C5 WKE A 202 204.586 168.388 186.458 1.00 55.48 C HETATM 2180 C6 WKE A 202 202.164 164.496 187.322 1.00 53.32 C HETATM 2181 C7 WKE A 202 201.517 163.403 188.160 1.00 48.22 C HETATM 2182 C8 WKE A 202 201.083 161.156 187.333 1.00 59.28 C HETATM 2183 C9 WKE A 202 200.402 160.315 186.296 1.00 59.68 C HETATM 2184 C10 WKE A 202 200.335 158.873 186.780 1.00 57.21 C HETATM 2185 N1 WKE A 202 200.834 162.462 187.295 1.00 56.45 N HETATM 2186 O1 WKE A 202 205.267 166.658 187.949 1.00 63.70 O HETATM 2187 O6 WKE A 202 203.212 163.927 186.532 1.00 61.58 O HETATM 2188 O3 WKE A 202 201.822 160.643 188.156 1.00 59.20 O HETATM 2189 O4 WKE A 202 199.076 160.806 186.075 1.00 61.25 O HETATM 2190 O5 WKE A 202 199.529 158.811 187.961 1.00 57.18 O HETATM 2191 N WKE A 202 203.115 166.730 187.366 1.00 55.95 N HETATM 2192 C WKE A 202 199.905 162.940 190.030 1.00 54.92 C HETATM 2193 O WKE A 202 201.243 164.938 189.985 1.00 61.70 O CONECT 479 2176 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 2181 2192 2193 CONECT 2176 479 2177 2193 CONECT 2177 2176 2180 2191 CONECT 2178 2179 2186 2191 CONECT 2179 2178 CONECT 2180 2177 2181 2187 CONECT 2181 2175 2180 2185 CONECT 2182 2183 2185 2188 CONECT 2183 2182 2184 2189 CONECT 2184 2183 2190 CONECT 2185 2181 2182 CONECT 2186 2178 CONECT 2187 2180 CONECT 2188 2182 CONECT 2189 2183 CONECT 2190 2184 CONECT 2191 2177 2178 CONECT 2192 2175 CONECT 2193 2175 2176 MASTER 131 0 2 8 16 0 0 6 2191 2 37 23 END