HEADER PROTEIN FIBRIL 04-MAR-26 11ME TITLE CRYO-EM OF T2SS OUTG PILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE II SECRETION SYSTEM CORE PROTEIN G; COMPND 3 CHAIN: B, C, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICKEYA DADANTII; SOURCE 3 ORGANISM_TAXID: 204038; SOURCE 4 GENE: OUTG, DDA3937_02418; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDOPILUS, T2SS, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR R.R.SONANI,M.LEJEUNE,S.IVASHCHENKO,B.BARDIAUX,M.VOS,O.FRANCETIC, AUTHOR 2 V.E.SHEVCHIK,N.IZADI-PRUNEYRE,E.H.EGELMAN REVDAT 1 23-SEP-26 11ME 0 JRNL AUTH M.LEJEUNE,S.IVASHCHENKO,R.DAZZONI,B.BARDIAUX,R.R.SONANI, JRNL AUTH 2 M.VOS,T.JACOBSEN,E.H.EGELMAN,M.NILGES,O.FRANCETIC, JRNL AUTH 3 V.E.SHEVCHIK,N.IZADI-PRUNEYRE JRNL TITL STRUCTURAL DETERMINANTS OF ENDOPILUS ASSEMBLY, STABILITY, JRNL TITL 2 AND FUNCTIONAL SPECIFICITY IN BACTERIAL TYPE II SECRETION. JRNL REF STRUCTURE 2026 JRNL REFN ISSN 0969-2126 JRNL PMID 42624105 JRNL DOI 10.1016/J.STR.2026.07.013 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 139840 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 11ME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305691. 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 : OUTG T2SS FILAMENT 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 : 7.00 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) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, E 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 HIS B 106 -7.34 62.96 REMARK 500 HIS C 106 0.98 57.98 REMARK 500 PRO E 103 2.05 -65.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 117 OD1 REMARK 620 2 ASP B 117 OD2 53.8 REMARK 620 3 MET B 119 O 87.1 127.7 REMARK 620 4 THR B 122 OG1 116.7 69.4 110.6 REMARK 620 5 ASP B 124 OD1 98.2 74.7 152.6 91.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR C 114 O REMARK 620 2 ASP C 117 OD1 102.9 REMARK 620 3 ASP C 117 OD2 125.6 52.0 REMARK 620 4 THR C 122 OG1 154.8 99.5 62.2 REMARK 620 5 ASP C 124 O 92.6 93.8 130.7 97.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR D 114 O REMARK 620 2 ASP D 117 OD1 79.3 REMARK 620 3 MET D 119 O 95.0 94.8 REMARK 620 4 THR D 122 OG1 158.7 113.7 100.3 REMARK 620 5 ASP D 125 OD1 86.6 157.7 103.7 75.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR E 114 O REMARK 620 2 ASP E 117 OD1 77.0 REMARK 620 3 ASP E 117 OD2 117.6 45.7 REMARK 620 4 THR E 122 OG1 174.9 106.6 67.1 REMARK 620 5 ASP E 125 OD1 72.0 148.3 152.5 104.8 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-75832 RELATED DB: EMDB REMARK 900 CRYO-EM OF T2SS OUTG PILUS DBREF 11ME B 1 132 UNP E0SM38 E0SM38_DICD3 8 139 DBREF 11ME C 1 132 UNP E0SM38 E0SM38_DICD3 8 139 DBREF 11ME D 1 132 UNP E0SM38 E0SM38_DICD3 8 139 DBREF 11ME E 1 132 UNP E0SM38 E0SM38_DICD3 8 139 SEQRES 1 B 132 PHE THR LEU LEU GLU ILE MET VAL VAL ILE VAL ILE LEU SEQRES 2 B 132 GLY VAL LEU ALA SER LEU VAL VAL PRO ASN LEU MET GLY SEQRES 3 B 132 ASN LYS GLU LYS ALA ASP ARG GLN LYS ALA ILE SER ASP SEQRES 4 B 132 ILE VAL ALA LEU GLU SER ALA LEU ASP MET TYR LYS LEU SEQRES 5 B 132 ASP ASN SER ARG TYR PRO THR THR GLU GLN GLY LEU GLY SEQRES 6 B 132 ALA LEU VAL LYS LYS PRO THR THR PRO PRO GLU PRO ARG SEQRES 7 B 132 SER TYR PRO GLN ASP GLY TYR ILE ARG ARG LEU PRO GLN SEQRES 8 B 132 ASP PRO TRP GLY ALA GLU TYR GLN LEU VAL SER PRO GLY SEQRES 9 B 132 ARG HIS GLY LYS VAL ASP VAL PHE SER TYR GLY PRO ASP SEQRES 10 B 132 GLY MET PRO ASP THR ASP ASP ASP ILE GLY ASN TRP ASN SEQRES 11 B 132 VAL GLY SEQRES 1 C 132 PHE THR LEU LEU GLU ILE MET VAL VAL ILE VAL ILE LEU SEQRES 2 C 132 GLY VAL LEU ALA SER LEU VAL VAL PRO ASN LEU MET GLY SEQRES 3 C 132 ASN LYS GLU LYS ALA ASP ARG GLN LYS ALA ILE SER ASP SEQRES 4 C 132 ILE VAL ALA LEU GLU SER ALA LEU ASP MET TYR LYS LEU SEQRES 5 C 132 ASP ASN SER ARG TYR PRO THR THR GLU GLN GLY LEU GLY SEQRES 6 C 132 ALA LEU VAL LYS LYS PRO THR THR PRO PRO GLU PRO ARG SEQRES 7 C 132 SER TYR PRO GLN ASP GLY TYR ILE ARG ARG LEU PRO GLN SEQRES 8 C 132 ASP PRO TRP GLY ALA GLU TYR GLN LEU VAL SER PRO GLY SEQRES 9 C 132 ARG HIS GLY LYS VAL ASP VAL PHE SER TYR GLY PRO ASP SEQRES 10 C 132 GLY MET PRO ASP THR ASP ASP ASP ILE GLY ASN TRP ASN SEQRES 11 C 132 VAL GLY SEQRES 1 D 132 PHE THR LEU LEU GLU ILE MET VAL VAL ILE VAL ILE LEU SEQRES 2 D 132 GLY VAL LEU ALA SER LEU VAL VAL PRO ASN LEU MET GLY SEQRES 3 D 132 ASN LYS GLU LYS ALA ASP ARG GLN LYS ALA ILE SER ASP SEQRES 4 D 132 ILE VAL ALA LEU GLU SER ALA LEU ASP MET TYR LYS LEU SEQRES 5 D 132 ASP ASN SER ARG TYR PRO THR THR GLU GLN GLY LEU GLY SEQRES 6 D 132 ALA LEU VAL LYS LYS PRO THR THR PRO PRO GLU PRO ARG SEQRES 7 D 132 SER TYR PRO GLN ASP GLY TYR ILE ARG ARG LEU PRO GLN SEQRES 8 D 132 ASP PRO TRP GLY ALA GLU TYR GLN LEU VAL SER PRO GLY SEQRES 9 D 132 ARG HIS GLY LYS VAL ASP VAL PHE SER TYR GLY PRO ASP SEQRES 10 D 132 GLY MET PRO ASP THR ASP ASP ASP ILE GLY ASN TRP ASN SEQRES 11 D 132 VAL GLY SEQRES 1 E 132 PHE THR LEU LEU GLU ILE MET VAL VAL ILE VAL ILE LEU SEQRES 2 E 132 GLY VAL LEU ALA SER LEU VAL VAL PRO ASN LEU MET GLY SEQRES 3 E 132 ASN LYS GLU LYS ALA ASP ARG GLN LYS ALA ILE SER ASP SEQRES 4 E 132 ILE VAL ALA LEU GLU SER ALA LEU ASP MET TYR LYS LEU SEQRES 5 E 132 ASP ASN SER ARG TYR PRO THR THR GLU GLN GLY LEU GLY SEQRES 6 E 132 ALA LEU VAL LYS LYS PRO THR THR PRO PRO GLU PRO ARG SEQRES 7 E 132 SER TYR PRO GLN ASP GLY TYR ILE ARG ARG LEU PRO GLN SEQRES 8 E 132 ASP PRO TRP GLY ALA GLU TYR GLN LEU VAL SER PRO GLY SEQRES 9 E 132 ARG HIS GLY LYS VAL ASP VAL PHE SER TYR GLY PRO ASP SEQRES 10 E 132 GLY MET PRO ASP THR ASP ASP ASP ILE GLY ASN TRP ASN SEQRES 11 E 132 VAL GLY HET CA B 200 1 HET CA C 200 1 HET CA D 200 1 HET CA E 200 1 HETNAM CA CALCIUM ION FORMUL 5 CA 4(CA 2+) HELIX 1 AA1 THR B 2 ALA B 17 1 16 HELIX 2 AA2 MET B 25 SER B 55 1 31 HELIX 3 AA3 GLY B 63 VAL B 68 5 6 HELIX 4 AA4 TRP B 129 VAL B 131 5 3 HELIX 5 AA5 THR C 2 ALA C 17 1 16 HELIX 6 AA6 GLY C 26 SER C 55 1 30 HELIX 7 AA7 GLY C 63 VAL C 68 5 6 HELIX 8 AA8 TRP C 129 VAL C 131 5 3 HELIX 9 AA9 THR D 2 ALA D 17 1 16 HELIX 10 AB1 GLY D 26 SER D 55 1 30 HELIX 11 AB2 GLY D 63 VAL D 68 5 6 HELIX 12 AB3 TRP D 129 VAL D 131 5 3 HELIX 13 AB4 THR E 2 ALA E 17 1 16 HELIX 14 AB5 GLY E 26 SER E 55 1 30 HELIX 15 AB6 GLY E 63 VAL E 68 5 6 HELIX 16 AB7 TRP E 129 VAL E 131 5 3 SHEET 1 AA1 3 GLN B 99 VAL B 101 0 SHEET 2 AA1 3 ASP B 110 SER B 113 -1 O PHE B 112 N GLN B 99 SHEET 3 AA1 3 ILE B 126 GLY B 127 -1 O ILE B 126 N SER B 113 SHEET 1 AA2 3 GLN C 99 VAL C 101 0 SHEET 2 AA2 3 ASP C 110 SER C 113 -1 O ASP C 110 N VAL C 101 SHEET 3 AA2 3 ILE C 126 GLY C 127 -1 O ILE C 126 N SER C 113 SHEET 1 AA3 3 GLN D 99 VAL D 101 0 SHEET 2 AA3 3 ASP D 110 SER D 113 -1 O PHE D 112 N GLN D 99 SHEET 3 AA3 3 ILE D 126 GLY D 127 -1 O ILE D 126 N SER D 113 SHEET 1 AA4 3 GLN E 99 VAL E 101 0 SHEET 2 AA4 3 ASP E 110 SER E 113 -1 O PHE E 112 N GLN E 99 SHEET 3 AA4 3 ILE E 126 GLY E 127 -1 O ILE E 126 N SER E 113 LINK OD1 ASP B 117 CA CA B 200 1555 1555 2.28 LINK OD2 ASP B 117 CA CA B 200 1555 1555 2.54 LINK O MET B 119 CA CA B 200 1555 1555 2.23 LINK OG1 THR B 122 CA CA B 200 1555 1555 2.40 LINK OD1 ASP B 124 CA CA B 200 1555 1555 2.77 LINK O TYR C 114 CA CA C 200 1555 1555 2.58 LINK OD1 ASP C 117 CA CA C 200 1555 1555 2.37 LINK OD2 ASP C 117 CA CA C 200 1555 1555 2.52 LINK OG1 THR C 122 CA CA C 200 1555 1555 2.59 LINK O ASP C 124 CA CA C 200 1555 1555 2.37 LINK O TYR D 114 CA CA D 200 1555 1555 2.62 LINK OD1 ASP D 117 CA CA D 200 1555 1555 2.71 LINK O MET D 119 CA CA D 200 1555 1555 2.30 LINK OG1 THR D 122 CA CA D 200 1555 1555 2.39 LINK OD1 ASP D 125 CA CA D 200 1555 1555 2.96 LINK O TYR E 114 CA CA E 200 1555 1555 3.02 LINK OD1 ASP E 117 CA CA E 200 1555 1555 2.54 LINK OD2 ASP E 117 CA CA E 200 1555 1555 2.99 LINK OG1 THR E 122 CA CA E 200 1555 1555 2.75 LINK OD1 ASP E 125 CA CA E 200 1555 1555 2.77 CISPEP 1 PRO B 74 PRO B 75 0 -1.93 CISPEP 2 SER B 102 PRO B 103 0 -9.42 CISPEP 3 PRO C 74 PRO C 75 0 -10.91 CISPEP 4 SER C 102 PRO C 103 0 -19.79 CISPEP 5 PRO D 74 PRO D 75 0 -11.92 CISPEP 6 SER D 102 PRO D 103 0 -4.72 CISPEP 7 PRO E 74 PRO E 75 0 -3.10 CISPEP 8 SER E 102 PRO E 103 0 -11.70 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 CONECT 911 4101 CONECT 912 4101 CONECT 920 4101 CONECT 945 4101 CONECT 961 4101 CONECT 1910 4102 CONECT 1936 4102 CONECT 1937 4102 CONECT 1970 4102 CONECT 1983 4102 CONECT 2935 4103 CONECT 2961 4103 CONECT 2970 4103 CONECT 2995 4103 CONECT 3019 4103 CONECT 3960 4104 CONECT 3986 4104 CONECT 3987 4104 CONECT 4020 4104 CONECT 4044 4104 CONECT 4101 911 912 920 945 CONECT 4101 961 CONECT 4102 1910 1936 1937 1970 CONECT 4102 1983 CONECT 4103 2935 2961 2970 2995 CONECT 4103 3019 CONECT 4104 3960 3986 3987 4020 CONECT 4104 4044 MASTER 163 0 4 16 12 0 0 6 4100 4 28 44 END