HEADER IMMUNE SYSTEM 06-JAN-16 2NAN TITLE NMR STRUCTURE OF HUMAN DCL-1 (CD302) EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD302 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN RESIDUES 23-161; COMPND 5 SYNONYM: C-TYPE LECTIN BIMLEC, C-TYPE LECTIN DOMAIN FAMILY 13 MEMBER COMPND 6 A, DEC205-ASSOCIATED C-TYPE LECTIN 1, TYPE I TRANSMEMBRANE C-TYPE COMPND 7 LECTIN RECEPTOR DCL-1; 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: CD302, CLEC13A, DCL1, KIAA0022; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-30A(+) KEYWDS C-TYPE LECTIN LIKE RECEPTOR, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.POSPISILOVA,Z.KUKACKA,D.KAVAN,P.NOVAK,J.CHMELIK REVDAT 2 14-JUN-23 2NAN 1 REMARK SEQADV REVDAT 1 11-JAN-17 2NAN 0 JRNL AUTH E.POSPISILOVA,Z.KUKACKA,D.KAVAN,P.NOVAK,J.CHMELIK JRNL TITL NMR STRUCTURE OF HUMAN DCL-1 (CD302) EXTRACELLULAR DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, SPARKY, SPARKY, SPARKY, SPARKY, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GODDARD (SPARKY), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (SPARKY), GODDARD (SPARKY), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (SPARKY), BRUNGER, ADAMS, REMARK 3 CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000104630. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.15 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 CD302, 25 MM PIPES, 50 MM SODIUM REMARK 210 CHLORIDE, 1 MM SODIUM AZIDE, 90 % REMARK 210 H2O, 10 % D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-15N REMARK 210 TOCSY; 3D H(CC)(CO)NH; 3D (H) REMARK 210 CC(CO)NH; 2D (HB)CB(CGCD)HD; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-TOCSY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, ARIA, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: MONOMERIC 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: CLOSE CONTACTS 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 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 3 GLU A 71 CG GLU A 71 CD -0.099 REMARK 500 7 GLU A 71 CG GLU A 71 CD -0.101 REMARK 500 8 GLU A 71 CG GLU A 71 CD -0.098 REMARK 500 9 GLU A 71 CG GLU A 71 CD -0.094 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 GLN A 33 -67.89 62.83 REMARK 500 1 ASP A 34 20.91 -156.37 REMARK 500 1 GLN A 41 94.61 -67.57 REMARK 500 1 ILE A 64 151.26 -40.33 REMARK 500 1 TRP A 83 -161.75 -108.25 REMARK 500 1 LYS A 84 -77.05 -70.41 REMARK 500 1 LYS A 114 68.36 -119.15 REMARK 500 1 ASP A 121 -150.77 -95.94 REMARK 500 1 CYS A 128 -169.85 -129.09 REMARK 500 1 SER A 147 22.59 -75.67 REMARK 500 2 GLN A 33 -85.96 60.48 REMARK 500 2 GLN A 41 94.84 -68.23 REMARK 500 2 ILE A 64 146.37 -36.96 REMARK 500 2 TRP A 83 -159.91 -109.66 REMARK 500 2 LYS A 84 -72.26 -68.56 REMARK 500 2 ASN A 107 -11.07 83.65 REMARK 500 2 ASP A 120 178.21 70.66 REMARK 500 2 ASP A 121 -38.36 -150.12 REMARK 500 2 GLU A 122 -74.53 -91.41 REMARK 500 2 CYS A 128 -167.03 -129.30 REMARK 500 2 SER A 147 22.43 -76.20 REMARK 500 3 GLN A 33 -81.74 59.99 REMARK 500 3 ASP A 34 24.32 -145.55 REMARK 500 3 GLN A 41 94.80 -69.47 REMARK 500 3 ILE A 64 144.31 -36.85 REMARK 500 3 TRP A 83 -161.67 -105.88 REMARK 500 3 LYS A 84 -72.03 -74.64 REMARK 500 3 ASP A 120 90.54 -175.41 REMARK 500 3 ASP A 121 -68.32 -121.98 REMARK 500 3 GLU A 122 -99.44 -98.94 REMARK 500 3 CYS A 128 -168.25 -124.48 REMARK 500 3 GLU A 144 35.54 -92.36 REMARK 500 3 SER A 147 21.96 -75.73 REMARK 500 4 GLN A 33 -76.98 62.61 REMARK 500 4 ASP A 34 26.26 -154.37 REMARK 500 4 GLN A 41 94.83 -69.49 REMARK 500 4 ILE A 64 150.54 -40.93 REMARK 500 4 TRP A 83 -166.90 -106.17 REMARK 500 4 LYS A 84 -72.53 -66.20 REMARK 500 4 ALA A 100 61.79 67.01 REMARK 500 4 ASP A 120 175.58 86.17 REMARK 500 4 ASP A 121 -83.44 -126.33 REMARK 500 4 SER A 147 22.78 -74.89 REMARK 500 5 GLN A 33 -86.80 60.51 REMARK 500 5 ASP A 34 26.51 -145.99 REMARK 500 5 GLN A 41 94.94 -67.07 REMARK 500 5 ILE A 64 151.16 -40.99 REMARK 500 5 TRP A 83 -158.58 -105.96 REMARK 500 5 LYS A 84 -74.53 -72.56 REMARK 500 5 ALA A 100 67.85 60.45 REMARK 500 REMARK 500 THIS ENTRY HAS 100 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 2 ARG A 53 0.10 SIDE CHAIN REMARK 500 4 ARG A 53 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25802 RELATED DB: BMRB DBREF 2NAN A 23 161 UNP Q8IX05 CD302_HUMAN 23 161 SEQADV 2NAN MET A 22 UNP Q8IX05 INITIATING METHIONINE SEQRES 1 A 140 MET ASP CYS PRO SER SER THR TRP ILE GLN PHE GLN ASP SEQRES 2 A 140 SER CYS TYR ILE PHE LEU GLN GLU ALA ILE LYS VAL GLU SEQRES 3 A 140 SER ILE GLU ASP VAL ARG ASN GLN CYS THR ASP HIS GLY SEQRES 4 A 140 ALA ASP MET ILE SER ILE HIS ASN GLU GLU GLU ASN ALA SEQRES 5 A 140 PHE ILE LEU ASP THR LEU LYS LYS GLN TRP LYS GLY PRO SEQRES 6 A 140 ASP ASP ILE LEU LEU GLY MET PHE TYR ASP THR ASP ASP SEQRES 7 A 140 ALA SER PHE LYS TRP PHE ASP ASN SER ASN MET THR PHE SEQRES 8 A 140 ASP LYS TRP THR ASP GLN ASP ASP ASP GLU ASP LEU VAL SEQRES 9 A 140 ASP THR CYS ALA PHE LEU HIS ILE LYS THR GLY GLU TRP SEQRES 10 A 140 LYS LYS GLY ASN CYS GLU VAL SER SER VAL GLU GLY THR SEQRES 11 A 140 LEU CYS LYS THR ALA ILE PRO TYR LYS ARG HELIX 1 1 SER A 48 ASP A 58 1 11 HELIX 2 2 ASN A 68 TRP A 83 1 16 SHEET 1 A 4 ILE A 30 PHE A 32 0 SHEET 2 A 4 SER A 35 LEU A 40 -1 O TYR A 37 N ILE A 30 SHEET 3 A 4 THR A 151 ALA A 156 -1 O THR A 155 N CYS A 36 SHEET 4 A 4 ASP A 62 MET A 63 -1 N ASP A 62 O LYS A 154 SHEET 1 B 2 ASP A 88 LEU A 90 0 SHEET 2 B 2 PHE A 130 HIS A 132 -1 O LEU A 131 N ILE A 89 SHEET 1 C 2 MET A 93 ASP A 96 0 SHEET 2 C 2 SER A 101 TRP A 104 -1 O LYS A 103 N PHE A 94 SSBOND 1 CYS A 24 CYS A 36 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 153 1555 1555 2.00 SSBOND 3 CYS A 128 CYS A 143 1555 1555 2.02 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