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 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