PDB Short entry for 5FNA HEADER HYDROLASE 11-NOV-15 5FNA TITLE CRYO-EM RECONSTRUCTION OF CASPASE-1 CARD COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-1; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 FRAGMENT: CARD DOMAIN; COMPND 5 SYNONYM: CASP-1,INTERLEUKIN-1 BETA CONVERTASE,IL-1BC,INTERLEUKIN-1 COMPND 6 BETA-CONVERTING ENZYME,IL-1 BETA-CONVERTING ENZYME,P45; COMPND 7 EC: 3.4.22.36; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CASP1, IL1BC, IL1BCE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDB-HIS-MBP KEYWDS HYDROLASE, CARD, INFLAMMASOME, FILAMENT, SIGNALOSOME, HELICAL KEYWDS 2 RECONSTRUCTION, DEATH DOMAIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LI,A.LU,F.I.SCHMIDT,Q.YIN,S.CHEN,T.M.FU,A.B.TONG,H.L.PLOEGH,Y.MAO, AUTHOR 2 H.WU REVDAT 6 11-SEP-19 5FNA 1 COMPND SOURCE DBREF REVDAT 5 30-AUG-17 5FNA 1 REMARK REVDAT 4 18-MAY-16 5FNA 1 JRNL REVDAT 3 13-APR-16 5FNA 1 JRNL REVDAT 2 06-APR-16 5FNA 1 JRNL REVDAT 1 30-MAR-16 5FNA 0 JRNL AUTH Y.LI,A.LU,F.I.SCHMIDT,Q.YIN,S.CHEN,T.M.FU,A.B.TONG, JRNL AUTH 2 H.L.PLOEGH,Y.MAO,H.WU JRNL TITL MOLECULAR BASIS OF CASPASE-1 POLYMERIZATION AND ITS JRNL TITL 2 INHIBITION BY A NOVEL CAPPING MECHANISM JRNL REF NAT.STRUCT.MOL.BIOL. V. 23 416 2016 JRNL REFN ISSN 1545-9993 JRNL PMID 27043298 JRNL DOI 10.1038/NSMB.3199 REMARK 2 REMARK 2 RESOLUTION. 4.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : IHRSR, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL 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 : REFINEMENT PROTOCOL--EM 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) : 4.800 REMARK 3 NUMBER OF PARTICLES : 69222 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD REMARK 3 -3241. (DEPOSITION ID: 14034). REMARK 4 REMARK 4 5FNA 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_1290065503. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : CASPASE-1 CARD REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.20 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 20 MM SODIUM HEPES, 150 MM REMARK 245 NACL, 2 MM DTT REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 02-FEB-15 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI ARCTICA REMARK 245 DETECTOR TYPE : DIRECT ELECTRON DE-16 (4K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 6000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 28736 REMARK 245 SOURCE : FIELD EMISSION GUN 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 ASP A 2 -131.17 58.32 REMARK 500 ALA A 47 -132.16 58.87 REMARK 500 ASP B 2 -131.15 58.32 REMARK 500 ALA B 47 -132.18 58.88 REMARK 500 ASP C 2 -131.13 58.37 REMARK 500 ALA C 47 -132.15 58.91 REMARK 500 ASP D 2 -131.12 58.27 REMARK 500 ALA D 47 -132.20 58.94 REMARK 500 ASP E 2 -131.15 58.33 REMARK 500 ALA E 47 -132.14 58.84 REMARK 500 ASP F 2 -131.15 58.28 REMARK 500 ALA F 47 -132.15 58.88 REMARK 500 ASP G 2 -131.12 58.34 REMARK 500 ALA G 47 -132.15 58.86 REMARK 500 ASP H 2 -131.16 58.37 REMARK 500 ALA H 47 -132.18 58.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3241 RELATED DB: EMDB DBREF 5FNA A 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA B 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA C 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA D 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA E 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA F 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA G 1 85 UNP P29466 CASP1_HUMAN 2 86 DBREF 5FNA H 1 85 UNP P29466 CASP1_HUMAN 2 86 SEQRES 1 A 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 A 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 A 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 A 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 A 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 A 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 A 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 B 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 B 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 B 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 B 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 B 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 B 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 B 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 C 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 C 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 C 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 C 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 C 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 C 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 C 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 D 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 D 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 D 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 D 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 D 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 D 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 D 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 E 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 E 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 E 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 E 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 E 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 E 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 E 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 F 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 F 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 F 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 F 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 F 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 F 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 F 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 G 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 G 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 G 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 G 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 G 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 G 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 G 85 ASP SER TYR LEU ALA GLY THR SEQRES 1 H 85 ALA ASP LYS VAL LEU LYS GLU LYS ARG LYS LEU PHE ILE SEQRES 2 H 85 ARG SER MET GLY GLU GLY THR ILE ASN GLY LEU LEU ASP SEQRES 3 H 85 GLU LEU LEU GLN THR ARG VAL LEU ASN LYS GLU GLU MET SEQRES 4 H 85 GLU LYS VAL LYS ARG GLU ASN ALA THR VAL MET ASP LYS SEQRES 5 H 85 THR ARG ALA LEU ILE ASP SER VAL ILE PRO LYS GLY ALA SEQRES 6 H 85 GLN ALA CYS GLN ILE CYS ILE THR TYR ILE CYS GLU GLU SEQRES 7 H 85 ASP SER TYR LEU ALA GLY THR HELIX 1 1 ALA A 1 LYS A 8 5 8 HELIX 2 2 ARG A 9 MET A 16 5 8 HELIX 3 3 GLY A 17 THR A 31 1 15 HELIX 4 4 ASN A 35 LYS A 41 1 7 HELIX 5 5 VAL A 42 GLU A 45 5 4 HELIX 6 6 THR A 48 MET A 50 5 3 HELIX 7 7 ASP A 51 SER A 59 1 9 HELIX 8 8 GLY A 64 GLN A 66 5 3 HELIX 9 9 ALA A 67 ASP A 79 1 13 HELIX 10 10 ALA B 1 LYS B 8 5 8 HELIX 11 11 ARG B 9 MET B 16 5 8 HELIX 12 12 GLY B 17 THR B 31 1 15 HELIX 13 13 ASN B 35 LYS B 41 1 7 HELIX 14 14 VAL B 42 GLU B 45 5 4 HELIX 15 15 THR B 48 MET B 50 5 3 HELIX 16 16 ASP B 51 SER B 59 1 9 HELIX 17 17 GLY B 64 GLN B 66 5 3 HELIX 18 18 ALA B 67 ASP B 79 1 13 HELIX 19 19 ALA C 1 LYS C 8 5 8 HELIX 20 20 ARG C 9 MET C 16 5 8 HELIX 21 21 GLY C 17 THR C 31 1 15 HELIX 22 22 ASN C 35 LYS C 41 1 7 HELIX 23 23 VAL C 42 GLU C 45 5 4 HELIX 24 24 THR C 48 MET C 50 5 3 HELIX 25 25 ASP C 51 SER C 59 1 9 HELIX 26 26 GLY C 64 GLN C 66 5 3 HELIX 27 27 ALA C 67 ASP C 79 1 13 HELIX 28 28 ALA D 1 LYS D 8 5 8 HELIX 29 29 ARG D 9 MET D 16 5 8 HELIX 30 30 GLY D 17 THR D 31 1 15 HELIX 31 31 ASN D 35 LYS D 41 1 7 HELIX 32 32 VAL D 42 GLU D 45 5 4 HELIX 33 33 THR D 48 MET D 50 5 3 HELIX 34 34 ASP D 51 SER D 59 1 9 HELIX 35 35 GLY D 64 GLN D 66 5 3 HELIX 36 36 ALA D 67 ASP D 79 1 13 HELIX 37 37 ALA E 1 LYS E 8 5 8 HELIX 38 38 ARG E 9 MET E 16 5 8 HELIX 39 39 GLY E 17 THR E 31 1 15 HELIX 40 40 ASN E 35 LYS E 41 1 7 HELIX 41 41 VAL E 42 GLU E 45 5 4 HELIX 42 42 THR E 48 MET E 50 5 3 HELIX 43 43 ASP E 51 SER E 59 1 9 HELIX 44 44 GLY E 64 GLN E 66 5 3 HELIX 45 45 ALA E 67 ASP E 79 1 13 HELIX 46 46 ALA F 1 LYS F 8 5 8 HELIX 47 47 ARG F 9 MET F 16 5 8 HELIX 48 48 GLY F 17 THR F 31 1 15 HELIX 49 49 ASN F 35 LYS F 41 1 7 HELIX 50 50 VAL F 42 GLU F 45 5 4 HELIX 51 51 THR F 48 MET F 50 5 3 HELIX 52 52 ASP F 51 SER F 59 1 9 HELIX 53 53 GLY F 64 GLN F 66 5 3 HELIX 54 54 ALA F 67 ASP F 79 1 13 HELIX 55 55 ALA G 1 LYS G 8 5 8 HELIX 56 56 ARG G 9 MET G 16 5 8 HELIX 57 57 GLY G 17 THR G 31 1 15 HELIX 58 58 ASN G 35 LYS G 41 1 7 HELIX 59 59 VAL G 42 GLU G 45 5 4 HELIX 60 60 THR G 48 MET G 50 5 3 HELIX 61 61 ASP G 51 SER G 59 1 9 HELIX 62 62 GLY G 64 GLN G 66 5 3 HELIX 63 63 ALA G 67 ASP G 79 1 13 HELIX 64 64 ALA H 1 LYS H 8 5 8 HELIX 65 65 ARG H 9 MET H 16 5 8 HELIX 66 66 GLY H 17 THR H 31 1 15 HELIX 67 67 ASN H 35 LYS H 41 1 7 HELIX 68 68 VAL H 42 GLU H 45 5 4 HELIX 69 69 THR H 48 MET H 50 5 3 HELIX 70 70 ASP H 51 SER H 59 1 9 HELIX 71 71 GLY H 64 GLN H 66 5 3 HELIX 72 72 ALA H 67 ASP H 79 1 13 CISPEP 1 LYS A 8 ARG A 9 0 15.49 CISPEP 2 LYS B 8 ARG B 9 0 15.61 CISPEP 3 LYS C 8 ARG C 9 0 15.51 CISPEP 4 LYS D 8 ARG D 9 0 15.63 CISPEP 5 LYS E 8 ARG E 9 0 15.53 CISPEP 6 LYS F 8 ARG F 9 0 15.53 CISPEP 7 LYS G 8 ARG G 9 0 15.53 CISPEP 8 LYS H 8 ARG H 9 0 15.56 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