HEADER CELL INVASION 21-OCT-14 4D3E TITLE TETRAMER OF IPAD, MODIFIED FROM 2J0O, FITTED INTO NEGATIVE STAIN TITLE 2 ELECTRON MICROSCOPY RECONSTRUCTION OF THE WILD TYPE TIP COMPLEX FROM TITLE 3 THE TYPE III SECRETION SYSTEM OF SHIGELLA FLEXNERI COMPND MOL_ID: 1; COMPND 2 MOLECULE: INVASIN IPAD; COMPND 3 CHAIN: D; COMPND 4 FRAGMENT: COILDED-COIL AND GLOBULAR DOMAIN, UNP RESIDUES 125-332; COMPND 5 SYNONYM: 36 KDA MEMBRANE ANTIGEN; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: YES [LACKING FIRST 124 AA AND WITH LAST 10 AA MODELLED COMPND 8 INTO HELIX] SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI 5A STR. M90T; SOURCE 3 ORGANISM_TAXID: 1086030; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL INVASION, TIP COMPLEX, TYPE III SECRETION SYSTEM, SHIGELLA KEYWDS 2 FLEXNERI, WILD TYPE, IPAD EXPDTA ELECTRON MICROSCOPY NUMMDL 4 AUTHOR M.CHEUNG,D.-K.SHEN,F.MAKINO,T.KATO,D.ROEHRICH,I.MARTINEZ-ARGUDO, AUTHOR 2 M.L.WALKER,I.MURILLO,X.LIU,M.PAIN,J.BROWN,G.FRAZER,J.MANTELL,P.MINA, AUTHOR 3 T.TODD,R.B.SESSIONS,K.NAMBA,A.J.BLOCKER REVDAT 5 29-APR-20 4D3E 1 REMARK REVDAT 4 31-JAN-18 4D3E 1 REMARK REVDAT 3 30-AUG-17 4D3E 1 REMARK REVDAT 2 14-JAN-15 4D3E 1 JRNL REVDAT 1 10-DEC-14 4D3E 0 JRNL AUTH M.CHEUNG,D.SHEN,F.MAKINO,T.KATO,A.D.ROEHRICH, JRNL AUTH 2 I.MARTINEZ-ARGUDO,M.L.WALKER,I.MURILLO,X.LIU,M.PAIN,J.BROWN, JRNL AUTH 3 G.FRAZER,J.MANTELL,P.MINA,T.TODD,R.B.SESSIONS,K.NAMBA, JRNL AUTH 4 A.J.BLOCKER JRNL TITL THREE-DIMENSIONAL ELECTRON MICROSCOPY RECONSTRUCTION AND JRNL TITL 2 CYSTEINE-MEDIATED CROSSLINKING PROVIDE A MODEL OF THE T3SS JRNL TITL 3 NEEDLE TIP COMPLEX. JRNL REF MOL.MICROBIOL. V. 95 31 2015 JRNL REFN ISSN 0950-382X JRNL PMID 25353930 JRNL DOI 10.1111/MMI.12843 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.JOHNSON,P.ROVERSI,M.ESPINA,A.OLIVE,J.E.DEANE,S.BIRKET, REMARK 1 AUTH 2 T.FIELD,W.D.PICKING,A.J.BLOCKER,E.E.GALYOV,W.L.PICKING, REMARK 1 AUTH 3 S.M.LEA REMARK 1 TITL SELF-CHAPERONING OF THE TYPE III SECRETION SYSTEM NEEDLE TIP REMARK 1 TITL 2 PROTEINS IPAD AND BIPD REMARK 1 REF J.BIOL.CHEM. V. 282 4035 2007 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 17077085 REMARK 1 DOI 10.1074/JBC.M607945200 REMARK 2 REMARK 2 RESOLUTION. 2.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, EMAN, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2J0O REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--SEE PUBLICATION REFINEMENT PROTOCOL--X REMARK 3 -RAY 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) : 24.00 REMARK 3 NUMBER OF PARTICLES : 2963 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THIS MODEL IS RESULT OF RIGID-BODY TRANSFORMATION REMARK 3 OF AN EXISTING PDB MODEL, CONSTRAINED BY A 24 A RESOLUTION EM REMARK 3 MAP AND SOME CYSTEINE-MEDIATED CROSSLINKING DATA. THEREFORE, IT REMARK 3 DOES NOT SUPPORT ATOMISTIC INTERPRETATIONS BECAUSE OF LACK OF REMARK 3 RESOLUTION. REMARK 4 REMARK 4 4D3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290062074. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NEGATIVE STAIN REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : WILD-TYPE T3SS NEEDLE COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.10 REMARK 245 SAMPLE SUPPORT DETAILS : CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : 0.1% (W/V) DDM, 150 MM NACL, 25 REMARK 245 MM TRIS PH 8, 5 MM EDTA REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : FIRST ZERO OF CTF SET TO 19A REMARK 245 FOR ALL MICROGRAPHS REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 31-AUG-11 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI 20 REMARK 245 DETECTOR TYPE : FEI EAGLE (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 90.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 70754 REMARK 245 SOURCE : LAB6 REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE D 329 CD1 PHE D 332 1.33 REMARK 500 CE MET D 128 CD2 PHE D 329 1.34 REMARK 500 CA LEU D 230 CE LYS D 300 1.42 REMARK 500 CA THR D 323 OD2 ASP D 326 1.49 REMARK 500 O PHE D 329 CE1 PHE D 332 1.67 REMARK 500 CB LEU D 230 CE LYS D 300 1.73 REMARK 500 CD1 ILE D 138 CD1 ILE D 319 1.73 REMARK 500 O GLU D 229 NZ LYS D 300 1.79 REMARK 500 SD MET D 128 CE2 PHE D 329 1.86 REMARK 500 CE MET D 128 CG PHE D 329 1.90 REMARK 500 CA LEU D 230 NZ LYS D 300 1.98 REMARK 500 O THR D 325 CD1 PHE D 329 1.99 REMARK 500 C THR D 323 OD2 ASP D 326 2.03 REMARK 500 O CYS D 322 N ASP D 326 2.06 REMARK 500 CG MET D 128 CE2 PHE D 329 2.07 REMARK 500 C PHE D 329 CD1 PHE D 332 2.09 REMARK 500 CE2 TYR D 149 CG2 ILE D 307 2.09 REMARK 500 OG SER D 141 CD2 LEU D 315 2.11 REMARK 500 N THR D 323 OD2 ASP D 326 2.13 REMARK 500 SD MET D 128 CD2 PHE D 329 2.13 REMARK 500 O CYS D 322 OD2 ASP D 326 2.15 REMARK 500 O THR D 325 CE1 PHE D 329 2.17 REMARK 500 O THR D 323 OD2 ASP D 326 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 SER D 321 C CYS D 322 N -0.143 REMARK 500 2 SER D 321 C CYS D 322 N -0.144 REMARK 500 3 SER D 321 C CYS D 322 N -0.143 REMARK 500 4 SER D 321 C CYS D 322 N -0.144 REMARK 500 REMARK 500 REMARK: NULL 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 1 ASP D 126 136.69 156.44 REMARK 500 1 GLN D 127 0.64 -155.65 REMARK 500 1 SER D 130 155.09 -48.15 REMARK 500 1 LEU D 150 -71.05 -54.05 REMARK 500 1 ASN D 215 48.66 -146.98 REMARK 500 1 LYS D 240 -77.54 -97.85 REMARK 500 1 ASN D 241 125.91 162.68 REMARK 500 2 ASP D 126 136.65 156.40 REMARK 500 2 GLN D 127 0.77 -155.71 REMARK 500 2 SER D 130 155.12 -48.08 REMARK 500 2 LEU D 150 -71.04 -53.99 REMARK 500 2 ASN D 215 48.70 -147.02 REMARK 500 2 LYS D 240 -77.61 -97.84 REMARK 500 2 ASN D 241 125.91 162.67 REMARK 500 3 ASP D 126 136.62 156.41 REMARK 500 3 GLN D 127 0.73 -155.67 REMARK 500 3 SER D 130 155.08 -48.10 REMARK 500 3 LEU D 150 -71.06 -53.98 REMARK 500 3 ASN D 215 48.66 -147.00 REMARK 500 3 LYS D 240 -77.59 -97.79 REMARK 500 3 ASN D 241 125.93 162.66 REMARK 500 4 ASP D 126 136.68 156.43 REMARK 500 4 GLN D 127 0.72 -155.71 REMARK 500 4 SER D 130 155.05 -48.10 REMARK 500 4 LEU D 150 -70.98 -54.10 REMARK 500 4 ASN D 215 48.69 -147.01 REMARK 500 4 LYS D 240 -77.57 -97.85 REMARK 500 4 ASN D 241 125.96 162.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-2801 RELATED DB: EMDB DBREF 4D3E D 125 332 UNP P18013 IPAD_SHIFL 125 332 SEQRES 1 D 208 GLY ASP GLN MET ILE SER HIS ARG GLU LEU TRP ALA LYS SEQRES 2 D 208 ILE ALA ASN SER ILE ASN ASP ILE ASN GLU GLN TYR LEU SEQRES 3 D 208 LYS VAL TYR GLU HIS ALA VAL SER SER TYR THR GLN MET SEQRES 4 D 208 TYR GLN ASP PHE SER ALA VAL LEU SER SER LEU ALA GLY SEQRES 5 D 208 TRP ILE SER PRO GLY GLY ASN ASP GLY ASN SER VAL LYS SEQRES 6 D 208 LEU GLN VAL ASN SER LEU LYS LYS ALA LEU GLU GLU LEU SEQRES 7 D 208 LYS GLU LYS TYR LYS ASP LYS PRO LEU TYR PRO ALA ASN SEQRES 8 D 208 ASN THR VAL SER GLN GLU GLN ALA ASN LYS TRP LEU THR SEQRES 9 D 208 GLU LEU GLY GLY THR ILE GLY LYS VAL SER GLN LYS ASN SEQRES 10 D 208 GLY GLY TYR VAL VAL SER ILE ASN MET THR PRO ILE ASP SEQRES 11 D 208 ASN MET LEU LYS SER LEU ASP ASN LEU GLY GLY ASN GLY SEQRES 12 D 208 GLU VAL VAL LEU ASP ASN ALA LYS TYR GLN ALA TRP ASN SEQRES 13 D 208 ALA GLY PHE SER ALA GLU ASP GLU THR MET LYS ASN ASN SEQRES 14 D 208 LEU GLN THR LEU VAL GLN LYS TYR SER ASN ALA ASN SER SEQRES 15 D 208 ILE PHE ASP ASN LEU VAL LYS VAL LEU SER SER THR ILE SEQRES 16 D 208 SER SER CYS THR ASP THR ASP LYS LEU PHE LEU HIS PHE HELIX 1 1 SER D 130 TYR D 149 1 20 HELIX 2 2 TYR D 149 GLY D 176 1 28 HELIX 3 3 GLN D 191 LYS D 207 1 17 HELIX 4 4 SER D 219 LEU D 230 1 12 HELIX 5 5 MET D 250 GLY D 264 1 15 HELIX 6 6 ASP D 272 PHE D 332 1 61 SHEET 1 DA 3 ILE D 178 PRO D 180 0 SHEET 2 DA 3 VAL D 188 LEU D 190 -1 O LYS D 189 N SER D 179 SHEET 3 DA 3 VAL D 269 LEU D 271 -1 O VAL D 269 N LEU D 190 SHEET 1 DB 3 PRO D 210 TYR D 212 0 SHEET 2 DB 3 TYR D 244 ILE D 248 -1 O VAL D 246 N LEU D 211 SHEET 3 DB 3 GLY D 235 GLN D 239 -1 O LYS D 236 N SER D 247 CISPEP 1 GLY D 182 ASN D 183 1 12.75 CISPEP 2 ASN D 183 ASP D 184 1 -3.74 CISPEP 3 GLY D 185 ASN D 186 1 3.64 CISPEP 4 TYR D 212 PRO D 213 1 0.76 CISPEP 5 ASN D 266 GLY D 267 1 -1.53 CISPEP 6 GLY D 182 ASN D 183 2 12.82 CISPEP 7 ASN D 183 ASP D 184 2 -3.70 CISPEP 8 GLY D 185 ASN D 186 2 3.68 CISPEP 9 TYR D 212 PRO D 213 2 0.72 CISPEP 10 ASN D 266 GLY D 267 2 -1.49 CISPEP 11 GLY D 182 ASN D 183 3 12.74 CISPEP 12 ASN D 183 ASP D 184 3 -3.70 CISPEP 13 GLY D 185 ASN D 186 3 3.69 CISPEP 14 TYR D 212 PRO D 213 3 0.69 CISPEP 15 ASN D 266 GLY D 267 3 -1.46 CISPEP 16 GLY D 182 ASN D 183 4 12.76 CISPEP 17 ASN D 183 ASP D 184 4 -3.79 CISPEP 18 GLY D 185 ASN D 186 4 3.67 CISPEP 19 TYR D 212 PRO D 213 4 0.66 CISPEP 20 ASN D 266 GLY D 267 4 -1.56 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1