HEADER SIGNALING PROTEIN 13-NOV-18 6N2M TITLE NMR SOLUTION STRUCTURE OF THE HOMODIMERIC, AUTOINHIBITED STATE OF THE TITLE 2 CARD9 CARD AND FIRST COILED-COIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE RECRUITMENT DOMAIN-CONTAINING PROTEIN 9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 2-142; COMPND 5 SYNONYM: HCARD9; COMPND 6 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: CARD9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS INNATE IMMUNITY, COILED-COIL, AUTOINHIBITION, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.J.HOLLIDAY,W.J.FAIRBROTHER,E.C.DUEBER REVDAT 4 15-MAY-24 6N2M 1 REMARK REVDAT 3 14-JUN-23 6N2M 1 REMARK REVDAT 2 24-JUL-19 6N2M 1 JRNL REVDAT 1 17-JUL-19 6N2M 0 JRNL AUTH M.J.HOLLIDAY,A.WITT,A.RODRIGUEZ GAMA,B.T.WALTERS,C.P.ARTHUR, JRNL AUTH 2 R.HALFMANN,A.ROHOU,E.C.DUEBER,W.J.FAIRBROTHER JRNL TITL STRUCTURES OF AUTOINHIBITED AND POLYMERIZED FORMS OF CARD9 JRNL TITL 2 REVEAL MECHANISMS OF CARD9 AND CARD11 ACTIVATION. JRNL REF NAT COMMUN V. 10 3070 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31296852 JRNL DOI 10.1038/S41467-019-10953-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, CYANA 3.97 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (CNS), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6N2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000237626. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 300; 900 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] CARD9_2-142, REMARK 210 1 MM ZINC, 95% H2O/5% D2O; 1 MM REMARK 210 [U-13C; U-15N] CARD9_2-142, 1 MM REMARK 210 ZINC, 100% D2O; 1 MM [U-13C; U- REMARK 210 15N; U-2H] CARD9_2-142, 1 MM REMARK 210 ZINC, 95% H2O/5% D2O; 1 MM [U- REMARK 210 13C; U-15N] CARD9_2-142, REMARK 210 UNLABELED 1 MM CARD9_2-142, 2 MM REMARK 210 ZINC, 95% H2O/5% D2O; 1 MM [U- REMARK 210 13C; U-15N] CARD9_2-142, 1 MM REMARK 210 ZINC, 14 MG/ML FILAMENTOUS PF1 REMARK 210 BACTERIOPHAGE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C TROSY REMARK 210 AROMATIC; 3D HNCA; 3D HNCB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D 1H-15N NOESY; 3D (H)CC(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-13C REMARK 210 INTERNOESY ALIPHATIC; 2D IPAP 1H- REMARK 210 15N TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANALYSIS 2.42, CYANA 3.97 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 SER A 2 -170.04 60.25 REMARK 500 1 ARG A 101 41.71 81.94 REMARK 500 1 VAL A 102 47.20 -81.51 REMARK 500 1 LYS A 140 -164.13 -110.21 REMARK 500 1 LEU B 54 44.97 -106.69 REMARK 500 1 ARG B 101 56.10 74.74 REMARK 500 1 VAL B 102 43.27 -77.30 REMARK 500 1 PHE B 103 4.35 -67.74 REMARK 500 2 SER A 2 144.76 -173.89 REMARK 500 2 ASN A 6 -3.92 53.71 REMARK 500 2 ASP A 7 87.11 32.55 REMARK 500 2 VAL A 102 44.64 -82.72 REMARK 500 2 VAL B 24 -62.71 -90.95 REMARK 500 2 PRO B 99 -79.83 -60.18 REMARK 500 2 ALA B 100 -23.52 170.66 REMARK 500 2 ARG B 101 38.69 75.76 REMARK 500 2 PHE B 103 -5.00 -54.16 REMARK 500 3 TYR A 4 -72.43 -75.19 REMARK 500 3 ASP A 7 94.39 -69.60 REMARK 500 3 VAL A 102 46.25 -79.62 REMARK 500 3 TYR B 4 -9.62 -142.93 REMARK 500 3 GLU B 5 -179.41 -65.26 REMARK 500 3 LYS B 38 -1.77 79.25 REMARK 500 3 ASN B 53 -176.92 -176.66 REMARK 500 3 ARG B 57 -35.24 -37.43 REMARK 500 4 LEU A 49 30.85 -86.01 REMARK 500 4 TYR A 87 79.09 -119.76 REMARK 500 4 VAL A 102 45.09 -82.24 REMARK 500 4 VAL B 102 48.19 -81.10 REMARK 500 4 PHE B 103 1.00 -61.19 REMARK 500 5 ASN A 6 -64.85 -156.88 REMARK 500 5 LEU A 85 -61.75 -93.96 REMARK 500 5 ARG A 101 53.25 73.42 REMARK 500 5 VAL A 102 38.36 -77.13 REMARK 500 5 PHE A 103 1.41 -65.29 REMARK 500 5 ASN B 6 -157.77 -126.70 REMARK 500 5 LEU B 49 48.18 -99.62 REMARK 500 5 ASN B 53 -87.87 -61.04 REMARK 500 5 LEU B 54 -7.89 178.52 REMARK 500 5 PRO B 99 112.09 -35.27 REMARK 500 5 VAL B 102 44.63 -81.39 REMARK 500 6 ASN A 53 -155.50 -99.35 REMARK 500 6 PHE A 103 -4.69 -59.87 REMARK 500 6 ASP B 3 -86.80 59.59 REMARK 500 6 ASN B 53 -167.48 -76.93 REMARK 500 6 VAL B 102 45.79 -70.99 REMARK 500 7 PRO A 99 109.04 -46.58 REMARK 500 7 VAL A 102 46.00 -76.07 REMARK 500 7 SER B 2 103.41 -166.62 REMARK 500 7 VAL B 24 -61.89 -94.70 REMARK 500 REMARK 500 THIS ENTRY HAS 163 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 6 ARG B 57 0.07 SIDE CHAIN 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 3 OD1 REMARK 620 2 ASP A 3 OD2 68.9 REMARK 620 3 CYS A 10 SG 97.6 125.2 REMARK 620 4 HIS A 73 ND1 115.3 118.0 115.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 3 OD1 REMARK 620 2 ASP B 3 OD2 61.8 REMARK 620 3 CYS B 10 SG 93.7 102.2 REMARK 620 4 HIS B 73 ND1 154.0 102.5 110.6 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30543 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE HOMODIMERIC, AUTOINHIBITED STATE OF REMARK 900 THE CARD9 CARD AND FIRST COILED-COIL REMARK 900 RELATED ID: 6N2P RELATED DB: PDB DBREF 6N2M A 2 142 UNP Q9H257 CARD9_HUMAN 2 142 DBREF 6N2M B 2 142 UNP Q9H257 CARD9_HUMAN 2 142 SEQADV 6N2M GLY A 1 UNP Q9H257 EXPRESSION TAG SEQADV 6N2M GLY B 1 UNP Q9H257 EXPRESSION TAG SEQRES 1 A 142 GLY SER ASP TYR GLU ASN ASP ASP GLU CYS TRP SER VAL SEQRES 2 A 142 LEU GLU GLY PHE ARG VAL THR LEU THR SER VAL ILE ASP SEQRES 3 A 142 PRO SER ARG ILE THR PRO TYR LEU ARG GLN CYS LYS VAL SEQRES 4 A 142 LEU ASN PRO ASP ASP GLU GLU GLN VAL LEU SER ASP PRO SEQRES 5 A 142 ASN LEU VAL ILE ARG LYS ARG LYS VAL GLY VAL LEU LEU SEQRES 6 A 142 ASP ILE LEU GLN ARG THR GLY HIS LYS GLY TYR VAL ALA SEQRES 7 A 142 PHE LEU GLU SER LEU GLU LEU TYR TYR PRO GLN LEU TYR SEQRES 8 A 142 LYS LYS VAL THR GLY LYS GLU PRO ALA ARG VAL PHE SER SEQRES 9 A 142 MET ILE ILE ASP ALA SER GLY GLU SER GLY LEU THR GLN SEQRES 10 A 142 LEU LEU MET THR GLU VAL MET LYS LEU GLN LYS LYS VAL SEQRES 11 A 142 GLN ASP LEU THR ALA LEU LEU SER SER LYS ASP ASP SEQRES 1 B 142 GLY SER ASP TYR GLU ASN ASP ASP GLU CYS TRP SER VAL SEQRES 2 B 142 LEU GLU GLY PHE ARG VAL THR LEU THR SER VAL ILE ASP SEQRES 3 B 142 PRO SER ARG ILE THR PRO TYR LEU ARG GLN CYS LYS VAL SEQRES 4 B 142 LEU ASN PRO ASP ASP GLU GLU GLN VAL LEU SER ASP PRO SEQRES 5 B 142 ASN LEU VAL ILE ARG LYS ARG LYS VAL GLY VAL LEU LEU SEQRES 6 B 142 ASP ILE LEU GLN ARG THR GLY HIS LYS GLY TYR VAL ALA SEQRES 7 B 142 PHE LEU GLU SER LEU GLU LEU TYR TYR PRO GLN LEU TYR SEQRES 8 B 142 LYS LYS VAL THR GLY LYS GLU PRO ALA ARG VAL PHE SER SEQRES 9 B 142 MET ILE ILE ASP ALA SER GLY GLU SER GLY LEU THR GLN SEQRES 10 B 142 LEU LEU MET THR GLU VAL MET LYS LEU GLN LYS LYS VAL SEQRES 11 B 142 GLN ASP LEU THR ALA LEU LEU SER SER LYS ASP ASP HET ZN A 200 1 HET ZN B 200 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 ASP A 7 CYS A 10 5 4 HELIX 2 AA2 TRP A 11 GLY A 16 1 6 HELIX 3 AA3 PHE A 17 ILE A 25 1 9 HELIX 4 AA4 ASP A 26 CYS A 37 1 12 HELIX 5 AA5 ASN A 41 LEU A 49 1 9 HELIX 6 AA6 ILE A 56 ARG A 70 1 15 HELIX 7 AA7 GLY A 72 TYR A 87 1 16 HELIX 8 AA8 TYR A 87 GLY A 96 1 10 HELIX 9 AA9 PHE A 103 GLY A 111 1 9 HELIX 10 AB1 GLY A 111 SER A 139 1 29 HELIX 11 AB2 ASP B 7 CYS B 10 5 4 HELIX 12 AB3 TRP B 11 GLY B 16 1 6 HELIX 13 AB4 PHE B 17 ILE B 25 1 9 HELIX 14 AB5 ASP B 26 CYS B 37 1 12 HELIX 15 AB6 ASN B 41 LEU B 49 1 9 HELIX 16 AB7 ILE B 56 GLN B 69 1 14 HELIX 17 AB8 GLY B 72 TYR B 87 1 16 HELIX 18 AB9 TYR B 87 GLY B 96 1 10 HELIX 19 AC1 PHE B 103 GLY B 111 1 9 HELIX 20 AC2 GLY B 111 SER B 139 1 29 LINK OD1 ASP A 3 ZN ZN A 200 1555 1555 1.96 LINK OD2 ASP A 3 ZN ZN A 200 1555 1555 1.84 LINK SG CYS A 10 ZN ZN A 200 1555 1555 1.94 LINK ND1 HIS A 73 ZN ZN A 200 1555 1555 1.81 LINK OD1 ASP B 3 ZN ZN B 200 1555 1555 2.23 LINK OD2 ASP B 3 ZN ZN B 200 1555 1555 1.90 LINK SG CYS B 10 ZN ZN B 200 1555 1555 2.04 LINK ND1 HIS B 73 ZN ZN B 200 1555 1555 1.97 SITE 1 AC1 4 ASP A 3 GLU A 5 CYS A 10 HIS A 73 SITE 1 AC2 3 ASP B 3 CYS B 10 HIS B 73 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