PDB Short entry for 3GA3 HEADER HYDROLASE 16-FEB-09 3GA3 TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN MDA5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON-INDUCED HELICASE C DOMAIN-CONTAINING PROTEIN 1, COMPND 3 MDA5; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 893-1017; COMPND 6 SYNONYM: INTERFERON-INDUCED WITH HELICASE C DOMAIN PROTEIN 1, COMPND 7 HELICASE WITH 2 CARD DOMAINS, HELICARD, MELANOMA DIFFERENTIATION- COMPND 8 ASSOCIATED PROTEIN 5, MDA-5, RNA HELICASE-DEAD BOX PROTEIN 116, COMPND 9 MURABUTIDE DOWN-REGULATED PROTEIN; COMPND 10 EC: 3.6.1.-; COMPND 11 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: IFIH1, IFIH1 OR MDA5, MDA5, RH116; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS INNATE IMMUNE RECEPTOR, RNA BINIDING, HELICASE, RLR, ALTERNATIVE KEYWDS 2 SPLICING, ANTIVIRAL DEFENSE, ATP-BINDING, CYTOPLASM, DIABETES KEYWDS 3 MELLITUS, HOST-VIRUS INTERACTION, HYDROLASE, IMMUNE RESPONSE, INNATE KEYWDS 4 IMMUNITY, NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 5 RNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR P.LI REVDAT 3 03-APR-24 3GA3 1 REMARK REVDAT 2 21-FEB-24 3GA3 1 REMARK LINK REVDAT 1 24-FEB-09 3GA3 0 JRNL AUTH P.LI,X.LI,C.LU JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN MDA5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 7.5 REMARK 3 NUMBER OF REFLECTIONS : 20278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1590 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 39 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1091 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : -0.91300 REMARK 3 B33 (A**2) : -0.12900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.16200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INDIVIDUAL B REFINEMENT WITH CNS REMARK 4 REMARK 4 3GA3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : OSMIC REMARK 200 OPTICS : OSMIC REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20278 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 64.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.06400 REMARK 200 R SYM FOR SHELL (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 45.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: RIG-I CTD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 14 TO 18% ETHANOL, PH 8.5, REMARK 280 EVAPORATION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.46000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ASN A 898 50.91 -94.55 REMARK 500 LYS A 925 19.81 59.95 REMARK 500 MET A 926 -60.29 -135.26 REMARK 500 ASN A 993 -19.21 51.37 REMARK 500 SER A 995 74.91 32.45 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 907 SG REMARK 620 2 CYS A 910 SG 109.2 REMARK 620 3 CYS A 962 SG 112.8 106.8 REMARK 620 4 CYS A 964 SG 110.7 110.6 106.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 DBREF 3GA3 A 893 1017 UNP Q9BYX4 IFIH1_HUMAN 893 1017 SEQADV 3GA3 LEU A 1018 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 GLU A 1019 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 HIS A 1020 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 HIS A 1021 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 HIS A 1022 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 HIS A 1023 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 HIS A 1024 UNP Q9BYX4 EXPRESSION TAG SEQADV 3GA3 HIS A 1025 UNP Q9BYX4 EXPRESSION TAG SEQRES 1 A 133 ALA LYS HIS TYR LYS ASN ASN PRO SER LEU ILE THR PHE SEQRES 2 A 133 LEU CYS LYS ASN CYS SER VAL LEU ALA CYS SER GLY GLU SEQRES 3 A 133 ASP ILE HIS VAL ILE GLU LYS MET HIS HIS VAL ASN MET SEQRES 4 A 133 THR PRO GLU PHE LYS GLU LEU TYR ILE VAL ARG GLU ASN SEQRES 5 A 133 LYS ALA LEU GLN LYS LYS CYS ALA ASP TYR GLN ILE ASN SEQRES 6 A 133 GLY GLU ILE ILE CYS LYS CYS GLY GLN ALA TRP GLY THR SEQRES 7 A 133 MET MET VAL HIS LYS GLY LEU ASP LEU PRO CYS LEU LYS SEQRES 8 A 133 ILE ARG ASN PHE VAL VAL VAL PHE LYS ASN ASN SER THR SEQRES 9 A 133 LYS LYS GLN TYR LYS LYS TRP VAL GLU LEU PRO ILE THR SEQRES 10 A 133 PHE PRO ASN LEU ASP TYR SER GLU LEU GLU HIS HIS HIS SEQRES 11 A 133 HIS HIS HIS HET ZN A 1 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *204(H2 O) HELIX 1 1 ASN A 899 SER A 901 5 3 HELIX 2 2 GLU A 918 ILE A 920 5 3 HELIX 3 3 PRO A 933 GLU A 937 5 5 HELIX 4 4 LYS A 1002 LEU A 1006 5 5 HELIX 5 5 ASP A 1014 SER A 1016 5 3 HELIX 6 6 GLU A 1017 HIS A 1025 1 9 SHEET 1 A 4 LEU A 913 SER A 916 0 SHEET 2 A 4 ILE A 903 CYS A 907 -1 N PHE A 905 O ALA A 914 SHEET 3 A 4 PHE A 987 PHE A 991 -1 O VAL A 988 N LEU A 906 SHEET 4 A 4 THR A 996 LYS A 998 -1 O LYS A 998 N VAL A 989 SHEET 1 B 3 HIS A 927 VAL A 929 0 SHEET 2 B 3 HIS A 921 ILE A 923 -1 N HIS A 921 O VAL A 929 SHEET 3 B 3 ASN A1012 LEU A1013 1 O LEU A1013 N VAL A 922 SHEET 1 C 3 TYR A 939 ARG A 942 0 SHEET 2 C 3 GLN A 955 CYS A 962 -1 O GLU A 959 N ARG A 942 SHEET 3 C 3 LYS A 949 LYS A 950 -1 N LYS A 949 O ILE A 956 SHEET 1 D 4 TYR A 939 ARG A 942 0 SHEET 2 D 4 GLN A 955 CYS A 962 -1 O GLU A 959 N ARG A 942 SHEET 3 D 4 ALA A 967 HIS A 974 -1 O TRP A 968 N ILE A 960 SHEET 4 D 4 LEU A 977 LEU A 982 -1 O LEU A 979 N MET A 972 LINK ZN ZN A 1 SG CYS A 907 1555 1555 2.35 LINK ZN ZN A 1 SG CYS A 910 1555 1555 2.36 LINK ZN ZN A 1 SG CYS A 962 1555 1555 2.36 LINK ZN ZN A 1 SG CYS A 964 1555 1555 2.32 SITE 1 AC1 4 CYS A 907 CYS A 910 CYS A 962 CYS A 964 CRYST1 28.410 60.920 36.443 90.00 102.58 90.00 P 1 21 1 2 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 0.035199 0.000000 0.007855 0.00000 SCALE2 0.000000 0.016415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028115 0.00000