HEADER PROTEIN FIBRIL 23-JUN-23 8PJP TITLE NEISSERIA MENINGITIDIS PILE, SB-GATDH VARIANT, BOUND TO THE F10 TITLE 2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PILIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: NANOBODY F10; COMPND 6 CHAIN: C; 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 PILUS, AGGREGATION, ADHESION, EXTRACELLULAR, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR D.FERNANDEZ-MARTINEZ,G.DUMENIL REVDAT 2 16-OCT-24 8PJP 1 REMARK REVDAT 1 03-APR-24 8PJP 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. 2.92 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) : 2.920 REMARK 3 NUMBER OF PARTICLES : 158939 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 8PJP 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_1292130590. 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, REMARK 245 VARIANT SA-GATDH COMPLEXED WITH REMARK 245 THE F10 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 : 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) : 6100.00 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, C 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 C 1 REMARK 465 ALA C 2 REMARK 465 SER C 128 REMARK 465 GLU C 129 REMARK 465 PRO C 130 REMARK 465 LYS C 131 REMARK 465 THR C 132 REMARK 465 PRO C 133 REMARK 465 LYS C 134 REMARK 465 PRO C 135 REMARK 465 GLN C 136 REMARK 465 PRO C 137 REMARK 465 ALA C 138 REMARK 465 ALA C 139 REMARK 465 ALA C 140 REMARK 465 LEU C 141 REMARK 465 GLU C 142 REMARK 465 HIS C 143 REMARK 465 HIS C 144 REMARK 465 HIS C 145 REMARK 465 HIS C 146 REMARK 465 HIS C 147 REMARK 465 HIS C 148 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 56.81 -94.72 REMARK 500 VAL C 50 -60.94 -121.87 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-17718 RELATED DB: EMDB REMARK 900 NEISSERIA MENINGITIDIS PILE, SB-GATDH VARIANT, BOUND TO THE F10 REMARK 900 NANOBODY DBREF1 8PJP A 1 161 UNP A0A1I9GEU1_NEIME DBREF2 8PJP A A0A1I9GEU1 1 161 DBREF 8PJP C 1 148 PDB 8PJP 8PJP 1 148 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 C 148 MET ALA GLN LEU GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 C 148 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 C 148 SER GLY PHE THR LEU ASP GLN TYR ALA ILE GLY TRP PHE SEQRES 4 C 148 ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS SEQRES 5 C 148 ILE SER SER ARG GLY GLY ALA THR ASN TYR ALA HIS SER SEQRES 6 C 148 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 7 C 148 ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 C 148 ASP THR ALA VAL TYR TYR CYS ALA ALA GLY VAL TYR THR SEQRES 9 C 148 ILE VAL THR GLY THR GLY PRO GLU ASP GLY MET ASP TYR SEQRES 10 C 148 TRP GLY LYS GLY THR LEU VAL THR VAL SER SER GLU PRO SEQRES 11 C 148 LYS THR PRO LYS PRO GLN PRO ALA ALA ALA LEU GLU HIS SEQRES 12 C 148 HIS HIS HIS HIS HIS 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 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 HELIX 7 AA7 LYS C 89 THR C 93 5 5 HELIX 8 AA8 GLY C 110 ASP C 113 5 4 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 SHEET 1 AA3 4 LEU C 6 SER C 9 0 SHEET 2 AA3 4 SER C 19 ALA C 26 -1 O ALA C 25 N VAL C 7 SHEET 3 AA3 4 THR C 80 ASN C 86 -1 O MET C 85 N LEU C 20 SHEET 4 AA3 4 PHE C 70 ASP C 75 -1 N THR C 71 O GLN C 84 SHEET 1 AA4 6 LEU C 13 VAL C 14 0 SHEET 2 AA4 6 THR C 122 VAL C 126 1 O THR C 125 N VAL C 14 SHEET 3 AA4 6 ALA C 94 GLY C 101 -1 N TYR C 96 O THR C 122 SHEET 4 AA4 6 ALA C 35 GLN C 41 -1 N PHE C 39 O TYR C 97 SHEET 5 AA4 6 ARG C 47 ILE C 53 -1 O GLU C 48 N ARG C 40 SHEET 6 AA4 6 THR C 60 TYR C 62 -1 O ASN C 61 N CYS C 52 SHEET 1 AA5 4 LEU C 13 VAL C 14 0 SHEET 2 AA5 4 THR C 122 VAL C 126 1 O THR C 125 N VAL C 14 SHEET 3 AA5 4 ALA C 94 GLY C 101 -1 N TYR C 96 O THR C 122 SHEET 4 AA5 4 MET C 115 TYR C 117 -1 O ASP C 116 N ALA C 100 SSBOND 1 CYS A 120 CYS A 154 1555 1555 2.03 SSBOND 2 CYS C 24 CYS C 98 1555 1555 2.03 LINK OG SER A 63 C2 WKE 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 2130 SER C 127 HETATM 2131 O1 G3P A 201 150.559 191.065 154.248 1.00 82.36 O HETATM 2132 C1 G3P A 201 151.690 191.861 153.972 1.00 82.71 C HETATM 2133 C2 G3P A 201 152.600 191.910 155.195 1.00 81.92 C HETATM 2134 O2 G3P A 201 152.964 193.246 155.456 1.00 79.00 O HETATM 2135 C3 G3P A 201 151.874 191.335 156.406 1.00 80.42 C HETATM 2136 O1P G3P A 201 152.783 190.589 157.184 1.00 80.11 O HETATM 2137 O4P G3P A 201 153.449 189.351 159.311 1.00 74.83 O HETATM 2138 O2P G3P A 201 151.570 188.510 157.953 1.00 77.88 O HETATM 2139 O3P G3P A 201 151.313 190.582 159.268 1.00 74.29 O HETATM 2140 P G3P A 201 152.272 189.747 158.456 1.00 75.00 P HETATM 2141 C1 WKE A 202 147.224 183.717 172.900 1.00 55.87 C HETATM 2142 C2 WKE A 202 149.444 184.609 172.717 1.00 59.59 C HETATM 2143 C3 WKE A 202 149.002 185.936 173.354 1.00 54.04 C HETATM 2144 C4 WKE A 202 150.526 187.743 173.975 1.00 58.58 C HETATM 2145 C5 WKE A 202 149.989 188.468 172.778 1.00 57.04 C HETATM 2146 C6 WKE A 202 147.773 185.741 174.231 1.00 55.31 C HETATM 2147 C7 WKE A 202 146.668 184.995 173.507 1.00 49.29 C HETATM 2148 C8 WKE A 202 144.516 185.452 174.523 1.00 61.38 C HETATM 2149 C9 WKE A 202 143.571 185.166 175.652 1.00 55.37 C HETATM 2150 C10 WKE A 202 142.823 183.869 175.381 1.00 57.85 C HETATM 2151 N1 WKE A 202 145.606 184.695 174.446 1.00 52.84 N HETATM 2152 O1 WKE A 202 151.395 188.221 174.684 1.00 59.21 O HETATM 2153 O6 WKE A 202 147.285 187.020 174.653 1.00 66.60 O HETATM 2154 O3 WKE A 202 144.272 186.342 173.726 1.00 68.15 O HETATM 2155 O4 WKE A 202 144.312 185.036 176.869 1.00 58.44 O HETATM 2156 O5 WKE A 202 141.900 183.625 176.448 1.00 58.59 O HETATM 2157 N WKE A 202 150.001 186.544 174.217 1.00 59.34 N HETATM 2158 C WKE A 202 146.145 183.001 172.099 1.00 59.30 C HETATM 2159 O WKE A 202 148.322 184.032 172.043 1.00 63.43 O CONECT 479 2142 CONECT 512 2137 CONECT 904 1146 CONECT 1146 904 CONECT 1350 1923 CONECT 1923 1350 CONECT 2131 2132 CONECT 2132 2131 2133 CONECT 2133 2132 2134 2135 CONECT 2134 2133 CONECT 2135 2133 2136 CONECT 2136 2135 2140 CONECT 2137 512 2140 CONECT 2138 2140 CONECT 2139 2140 CONECT 2140 2136 2137 2138 2139 CONECT 2141 2147 2158 2159 CONECT 2142 479 2143 2159 CONECT 2143 2142 2146 2157 CONECT 2144 2145 2152 2157 CONECT 2145 2144 CONECT 2146 2143 2147 2153 CONECT 2147 2141 2146 2151 CONECT 2148 2149 2151 2154 CONECT 2149 2148 2150 2155 CONECT 2150 2149 2156 CONECT 2151 2147 2148 CONECT 2152 2144 CONECT 2153 2146 CONECT 2154 2148 CONECT 2155 2149 CONECT 2156 2150 CONECT 2157 2143 2144 CONECT 2158 2141 CONECT 2159 2141 2142 MASTER 150 0 2 8 20 0 0 6 2157 2 35 25 END