HEADER SIGNALING PROTEIN 04-FEB-14 3J6C TITLE CRYO-EM STRUCTURE OF MAVS CARD FILAMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL ANTIVIRAL-SIGNALING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CASPASE ACTIVATION RECRUITMENT DOMAIN (UNP RESIDUES 3-93); COMPND 5 SYNONYM: MAVS, CARD ADAPTER INDUCING INTERFERON BETA, CARDIF, COMPND 6 INTERFERON BETA PROMOTER STIMULATOR PROTEIN 1, IPS-1, PUTATIVE NF- COMPND 7 KAPPA-B-ACTIVATING PROTEIN 031N, VIRUS-INDUCED-SIGNALING ADAPTER, COMPND 8 VISA; COMPND 9 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: MAVS, IPS1, KIAA1271, VISA; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCDNA3 KEYWDS INNATE IMMUNITY, HELICAL FILAMENT, SIGNALING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.XU,X.HE,H.ZHENG,L.J.HUANG,F.HOU,Z.YU,M.J.DE LA CRUZ,B.BORKOWSKI, AUTHOR 2 X.ZHANG,Z.J.CHEN,Q.-X.JIANG REVDAT 3 21-FEB-24 3J6C 1 REMARK SEQADV REVDAT 2 18-JUL-18 3J6C 1 REMARK REVDAT 1 05-MAR-14 3J6C 0 JRNL AUTH H.XU,X.HE,H.ZHENG,L.J.HUANG,F.HOU,Z.YU,M.J.DE LA CRUZ, JRNL AUTH 2 B.BORKOWSKI,X.ZHANG,Z.J.CHEN,Q.X.JIANG JRNL TITL STRUCTURAL BASIS FOR THE PRION-LIKE MAVS FILAMENTS IN JRNL TITL 2 ANTIVIRAL INNATE IMMUNITY. JRNL REF ELIFE V. 3 01489 2014 JRNL REFN ESSN 2050-084X JRNL PMID 24569476 JRNL DOI 10.7554/ELIFE.01489 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.POTTER,R.E.RANDALL,G.L.TAYLOR REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN IPS-1/MAVS/VISA/CARDIF CASPASE REMARK 1 TITL 2 ACTIVATION RECRUITMENT DOMAIN. REMARK 1 REF BMC STRUCT.BIOL. V. 8 11 2008 REMARK 1 REFN ESSN 1472-6807 REMARK 1 PMID 18307765 REMARK 1 DOI 10.1186/1472-6807-8-11 REMARK 2 REMARK 2 RESOLUTION. 9.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SITUS, UCSF CHIMERA, EMAN, IMAGIC, MRC, REMARK 3 SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2VGQ REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--RIGID BODY DETAILS--THE REMARK 3 DOCKING OF ONE X-RAY MODEL INTO A SEGMENTED MAP CORRESPONDING TO REMARK 3 ONE SUBUNIT WAS FIRST DONE MANUALLY IN CHIMERA, AND THEN REMARK 3 OPTIMIZED USING SITUS. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.333 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 9.600 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: FINAL DATA WERE CALCULATED FROM THREE SEPARATE REMARK 3 DATASETS FROM THREE SESSIONS OF DATA COLLECTION. THE HANDEDNESS REMARK 3 OF THE MAP WAS DETERMINED BY CRYO-ELECTRON TOMOGRAPHY (HELICAL REMARK 3 DETAILS: IHRSR). REMARK 4 REMARK 4 3J6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000160306. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : MAVS CARD FILAMENT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL GRIDS COATED WITH REMARK 245 THIN CARBON ON TOP REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO LIQUID ETHANE (FEI REMARK 245 VITROBOT MARK III) REMARK 245 SAMPLE BUFFER : 20 MM TRIS-HCL, 50 MM NACL, 1 REMARK 245 MM DTT REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : POLYMER REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 20-OCT-11 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : JEOL 2200FS REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 60000 REMARK 245 CALIBRATED MAGNIFICATION : 61950 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -53.60 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 16.80 ANGSTROMS REMARK 300 IN ADDITION, THERE IS 3-FOLD CIRCULAR REMARK 300 SYMMETRY AROUND THE HELIX AXIS 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 -0.078807 0.996890 0.000000 4.77782 REMARK 350 BIOMT2 1 -0.996890 -0.078807 0.000000 121.06503 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 67.20000 REMARK 350 BIOMT1 2 0.755968 0.654609 0.000000 -23.94688 REMARK 350 BIOMT2 2 -0.654609 0.755968 0.000000 52.41325 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 50.40000 REMARK 350 BIOMT1 3 0.975381 -0.220527 0.000000 14.29816 REMARK 350 BIOMT2 3 0.220527 0.975381 0.000000 -11.42634 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 33.60000 REMARK 350 BIOMT1 4 0.400829 -0.916153 0.000000 88.38128 REMARK 350 BIOMT2 4 0.916153 0.400829 0.000000 -18.48796 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 16.80000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 137.99843 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 36.97657 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.993826 -0.110949 0.000000 122.76099 REMARK 350 BIOMT2 6 0.110949 -0.993826 0.000000 109.81883 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -16.80000 REMARK 350 BIOMT1 7 -0.678673 0.734441 0.000000 55.07231 REMARK 350 BIOMT2 7 -0.734441 -0.678673 0.000000 140.74485 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -33.60000 REMARK 350 BIOMT1 8 0.188924 0.981992 0.000000 -9.96866 REMARK 350 BIOMT2 8 -0.981992 0.188924 0.000000 104.58067 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -50.40000 REMARK 350 BIOMT1 9 0.902736 -0.430196 0.000000 30.76413 REMARK 350 BIOMT2 9 0.430196 0.902736 0.000000 -19.41823 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 67.20000 REMARK 350 BIOMT1 10 0.188924 -0.981992 0.000000 104.58067 REMARK 350 BIOMT2 10 0.981992 0.188924 0.000000 -9.96866 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 50.40000 REMARK 350 BIOMT1 11 -0.678673 -0.734441 0.000000 140.74485 REMARK 350 BIOMT2 11 0.734441 -0.678673 0.000000 55.07231 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 33.60000 REMARK 350 BIOMT1 12 -0.993826 0.110949 0.000000 109.81883 REMARK 350 BIOMT2 12 -0.110949 -0.993826 0.000000 122.76099 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 16.80000 REMARK 350 BIOMT1 13 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 13 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 14 -0.500000 0.866025 0.000000 36.97657 REMARK 350 BIOMT2 14 -0.866025 -0.500000 0.000000 137.99843 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 15 0.400829 0.916153 0.000000 -18.48796 REMARK 350 BIOMT2 15 -0.916153 0.400829 0.000000 88.38128 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 -16.80000 REMARK 350 BIOMT1 16 0.975381 0.220527 0.000000 -11.42634 REMARK 350 BIOMT2 16 -0.220527 0.975381 0.000000 14.29816 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 -33.60000 REMARK 350 BIOMT1 17 0.755968 -0.654609 0.000000 52.41325 REMARK 350 BIOMT2 17 0.654609 0.755968 0.000000 -23.94688 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 -50.40000 REMARK 350 BIOMT1 18 -0.823928 -0.566694 0.000000 139.43305 REMARK 350 BIOMT2 18 0.566694 -0.823928 0.000000 73.32821 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 67.20000 REMARK 350 BIOMT1 19 -0.944892 0.327383 0.000000 94.34121 REMARK 350 BIOMT2 19 -0.327383 -0.944892 0.000000 132.53042 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 50.40000 REMARK 350 BIOMT1 20 -0.296708 0.954968 0.000000 19.93199 REMARK 350 BIOMT2 20 -0.954968 -0.296708 0.000000 131.32903 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 33.60000 REMARK 350 BIOMT1 21 0.592997 0.805204 0.000000 -23.22512 REMARK 350 BIOMT2 21 -0.805204 0.592997 0.000000 70.70198 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 16.80000 REMARK 350 BIOMT1 22 0.592997 -0.805204 0.000000 70.70198 REMARK 350 BIOMT2 22 0.805204 0.592997 0.000000 -23.22512 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 -16.80000 REMARK 350 BIOMT1 23 -0.296708 -0.954968 0.000000 131.32903 REMARK 350 BIOMT2 23 0.954968 -0.296708 0.000000 19.93199 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 -33.60000 REMARK 350 BIOMT1 24 -0.944892 -0.327383 0.000000 132.53042 REMARK 350 BIOMT2 24 0.327383 -0.944892 0.000000 94.34121 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 -50.40000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 PRO A 435 C - N - CD ANGL. DEV. = 12.7 DEGREES 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 LEU A 450 67.74 -105.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5890 RELATED DB: EMDB DBREF 3J6C A 372 462 UNP Q7Z434 MAVS_HUMAN 3 93 SEQADV 3J6C MET A 370 UNP Q7Z434 EXPRESSION TAG SEQADV 3J6C ALA A 371 UNP Q7Z434 EXPRESSION TAG SEQRES 1 A 93 MET ALA PHE ALA GLU ASP LYS THR TYR LYS TYR ILE CYS SEQRES 2 A 93 ARG ASN PHE SER ASN PHE CYS ASN VAL ASP VAL VAL GLU SEQRES 3 A 93 ILE LEU PRO TYR LEU PRO CYS LEU THR ALA ARG ASP GLN SEQRES 4 A 93 ASP ARG LEU ARG ALA THR CYS THR LEU SER GLY ASN ARG SEQRES 5 A 93 ASP THR LEU TRP HIS LEU PHE ASN THR LEU GLN ARG ARG SEQRES 6 A 93 PRO GLY TRP VAL GLU TYR PHE ILE ALA ALA LEU ARG GLY SEQRES 7 A 93 CYS GLU LEU VAL ASP LEU ALA ASP GLU VAL ALA SER VAL SEQRES 8 A 93 TYR GLN HELIX 1 1 MET A 370 ASN A 384 1 15 HELIX 2 2 PHE A 385 CYS A 389 5 5 HELIX 3 3 ASP A 392 LEU A 397 1 6 HELIX 4 4 PRO A 398 LEU A 400 5 3 HELIX 5 5 THR A 404 GLY A 419 1 16 HELIX 6 6 GLY A 419 GLN A 432 1 14 HELIX 7 7 TRP A 437 CYS A 448 1 12 HELIX 8 8 LEU A 450 GLN A 462 1 13 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