HEADER IMMUNE SYSTEM 23-APR-12 2LS8 TITLE SOLUTION STRUCTURE OF HUMAN C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER D COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 84-215; COMPND 5 SYNONYM: C-TYPE LECTIN SUPERFAMILY MEMBER 8, C-TYPE LECTIN-LIKE COMPND 6 RECEPTOR 6, CLEC-6; COMPND 7 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: CLEC4D, CLECSF8, MCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: MODIFIED PET23A KEYWDS STRUCTURAL GENOMICS, NEW YORK STRUCTURAL GENOMICS RESEARCH KEYWDS 2 CONSORTIUM, NYSGRC, PSI-BIOLOGY, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.HARRIS,J.GAUDETTE,A.D.BANDARANAYAKE,R.BANU,J.B.BONANNO, AUTHOR 2 D.A.CALARESE,A.CELIKGIL,S.CHAMALA,M.K.CHAN,R.CHAPARRO,B.EVANS, AUTHOR 3 S.GARFORTH,A.GIZZI,B.HILLERICH,A.KAR,J.LAFLEUR,S.LIM,J.LOVE, AUTHOR 4 B.MATIKAINEN,H.PATEL,R.D.SEIDEL,B.SMITH,M.STEAD,M.E.GIRVIN,S.C.ALMO, AUTHOR 5 NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC) REVDAT 3 16-OCT-24 2LS8 1 REMARK REVDAT 2 14-JUN-23 2LS8 1 REMARK SEQADV REVDAT 1 09-MAY-12 2LS8 0 JRNL AUTH R.HARRIS,J.GAUDETTE,A.D.BANDARANAYAKE,R.BANU,J.B.BONANNO, JRNL AUTH 2 D.A.CALARESE,A.CELIKGIL,S.CHAMALA,M.K.CHAN,R.CHAPARRO, JRNL AUTH 3 B.EVANS,S.GARFORTH,A.GIZZI,B.HILLERICH,A.KAR,J.LAFLEUR, JRNL AUTH 4 S.LIM,J.LOVE,B.MATIKAINEN,H.PATEL,R.D.SEIDEL,B.SMITH, JRNL AUTH 5 M.STEAD,M.E.GIRVIN,S.C.ALMO JRNL TITL SOLUTION STRUCTURE OF HUMAN C-TYPE LECTIN DOMAIN FAMILY 4 JRNL TITL 2 MEMBER D JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CCPN 2.1.5, CNS 1.21 REMARK 3 AUTHORS : CCPN (CCPN), BRUNGER, ADAMS, CLORE, GROS, NILGES REMARK 3 AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN A BOX OF WATER REMARK 4 REMARK 4 2LS8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000102768. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] C-TYPE REMARK 210 LECTIN, 10 MM SODIUM ACETATE, REMARK 210 0.1 MM EDTA, 90% H2O, 10% D2O; 1 REMARK 210 MM [U-13C; U-15N] C-TYPE LECTIN, REMARK 210 10 MM SODIUM ACETATE, 0.1 MM REMARK 210 EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N HSQC; 15N NOESY-HSQC; 13C CT REMARK 210 -HSQC; AROMATIC 13C CT-HSQC; 13C REMARK 210 NOESY-HSQC; 13C AROMATIC NOESY- REMARK 210 HSQC; HNCO; HNCACO; HNCOCA; REMARK 210 HNCACB; CBCACONH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPN 2.1.5, CNS 1.21, ARIA 2.3, REMARK 210 NMRPIPE 5.4, VNMRJ 2.2D, TOPSPIN, REMARK 210 MDDNMR 2.0, MDDGUI 1.0 REMARK 210 METHOD USED : SIMULATING ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 STRUCTURES FOR LOWEST 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 HIS A 146 REMARK 465 HIS A 147 REMARK 465 HIS A 148 REMARK 465 TRP A 149 REMARK 465 SER A 150 REMARK 465 HIS A 151 REMARK 465 PRO A 152 REMARK 465 GLN A 153 REMARK 465 PHE A 154 REMARK 465 GLU A 155 REMARK 465 LYS A 156 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 OE2 GLU A 67 HZ3 LYS A 70 1.58 REMARK 500 HG1 THR A 43 OE1 GLU A 46 1.59 REMARK 500 O HIS A 37 H LYS A 127 1.60 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 ILE A 5 -98.11 65.15 REMARK 500 1 GLN A 11 -99.57 60.02 REMARK 500 1 SER A 32 -44.99 75.86 REMARK 500 1 MET A 39 102.33 -53.85 REMARK 500 1 ARG A 57 -31.38 -162.47 REMARK 500 1 ASN A 68 29.92 179.87 REMARK 500 1 GLN A 72 63.59 -100.39 REMARK 500 1 ASP A 77 -59.54 -172.88 REMARK 500 1 GLN A 78 -31.83 163.34 REMARK 500 1 LYS A 90 -159.21 175.79 REMARK 500 1 ASP A 94 -97.40 55.17 REMARK 500 1 ASN A 95 -8.73 175.75 REMARK 500 2 GLN A 11 -68.42 67.64 REMARK 500 2 SER A 12 -28.24 -145.88 REMARK 500 2 SER A 32 -43.91 75.25 REMARK 500 2 MET A 39 99.40 -52.92 REMARK 500 2 ILE A 41 106.08 -55.65 REMARK 500 2 ARG A 56 20.21 -79.05 REMARK 500 2 GLU A 67 -71.04 -74.45 REMARK 500 2 ASN A 68 31.61 -84.67 REMARK 500 2 VAL A 76 -80.72 45.77 REMARK 500 2 ASP A 77 -82.50 -96.33 REMARK 500 2 LYS A 90 -5.59 81.79 REMARK 500 2 GLU A 99 88.58 63.20 REMARK 500 2 ALA A 135 41.60 -91.27 REMARK 500 3 ASP A 6 -51.46 176.68 REMARK 500 3 GLN A 11 -89.11 60.67 REMARK 500 3 SER A 32 -44.92 73.34 REMARK 500 3 MET A 39 103.41 -50.71 REMARK 500 3 ILE A 41 95.80 -66.99 REMARK 500 3 ALA A 69 87.55 62.23 REMARK 500 3 ASP A 77 -168.78 -107.24 REMARK 500 3 PHE A 87 -70.01 66.70 REMARK 500 3 TRP A 88 -158.49 53.49 REMARK 500 3 LYS A 90 -70.90 171.11 REMARK 500 3 ASN A 91 11.75 -140.38 REMARK 500 3 PRO A 93 -151.90 -101.22 REMARK 500 3 ASN A 95 -37.91 -134.67 REMARK 500 3 GLU A 99 74.69 -113.29 REMARK 500 3 ALA A 135 31.22 -85.46 REMARK 500 4 ASP A 6 -33.79 77.81 REMARK 500 4 GLN A 11 -101.53 58.89 REMARK 500 4 SER A 32 -45.11 80.04 REMARK 500 4 MET A 39 98.68 -40.02 REMARK 500 4 ILE A 41 100.72 -59.40 REMARK 500 4 ARG A 56 38.82 -90.23 REMARK 500 4 ARG A 57 -46.83 -142.15 REMARK 500 4 GLU A 67 -78.24 -46.81 REMARK 500 4 ALA A 69 70.87 55.35 REMARK 500 4 ASP A 77 -104.74 -123.89 REMARK 500 REMARK 500 THIS ENTRY HAS 269 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGRC-020344 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 18415 RELATED DB: BMRB DBREF 2LS8 A 3 134 UNP Q8WXI8 CLC4D_HUMAN 84 215 SEQADV 2LS8 MET A 1 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 VAL A 2 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 ALA A 135 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 GLU A 136 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 ASN A 137 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 LEU A 138 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 TYR A 139 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 PHE A 140 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 GLN A 141 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 SER A 142 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 143 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 144 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 145 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 146 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 147 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 148 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 TRP A 149 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 SER A 150 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 HIS A 151 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 PRO A 152 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 GLN A 153 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 PHE A 154 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 GLU A 155 UNP Q8WXI8 EXPRESSION TAG SEQADV 2LS8 LYS A 156 UNP Q8WXI8 EXPRESSION TAG SEQRES 1 A 156 MET VAL CYS PRO ILE ASP TRP ARG ALA PHE GLN SER ASN SEQRES 2 A 156 CYS TYR PHE PRO LEU THR ASP ASN LYS THR TRP ALA GLU SEQRES 3 A 156 SER GLU ARG ASN CYS SER GLY MET GLY ALA HIS LEU MET SEQRES 4 A 156 THR ILE SER THR GLU ALA GLU GLN ASN PHE ILE ILE GLN SEQRES 5 A 156 PHE LEU ASP ARG ARG LEU SER TYR PHE LEU GLY LEU ARG SEQRES 6 A 156 ASP GLU ASN ALA LYS GLY GLN TRP ARG TRP VAL ASP GLN SEQRES 7 A 156 THR PRO PHE ASN PRO ARG ARG VAL PHE TRP HIS LYS ASN SEQRES 8 A 156 GLU PRO ASP ASN SER GLN GLY GLU ASN CYS VAL VAL LEU SEQRES 9 A 156 VAL TYR ASN GLN ASP LYS TRP ALA TRP ASN ASP VAL PRO SEQRES 10 A 156 CYS ASN PHE GLU ALA SER ARG ILE CYS LYS ILE PRO GLY SEQRES 11 A 156 THR THR LEU ASN ALA GLU ASN LEU TYR PHE GLN SER HIS SEQRES 12 A 156 HIS HIS HIS HIS HIS TRP SER HIS PRO GLN PHE GLU LYS HELIX 1 1 THR A 23 CYS A 31 1 9 HELIX 2 2 THR A 43 ILE A 51 1 9 HELIX 3 3 GLY A 130 LEU A 133 5 4 HELIX 4 4 ASN A 134 SER A 142 1 9 SHEET 1 A 5 ARG A 8 PHE A 10 0 SHEET 2 A 5 ASN A 13 LYS A 22 -1 O TYR A 15 N ARG A 8 SHEET 3 A 5 ALA A 122 ILE A 128 -1 O ARG A 124 N LEU A 18 SHEET 4 A 5 SER A 59 ASP A 66 1 N PHE A 61 O SER A 123 SHEET 5 A 5 ARG A 74 TRP A 75 -1 O ARG A 74 N ARG A 65 SHEET 1 B 5 HIS A 37 LEU A 38 0 SHEET 2 B 5 ALA A 122 ILE A 128 -1 O LYS A 127 N HIS A 37 SHEET 3 B 5 SER A 59 ASP A 66 1 N PHE A 61 O SER A 123 SHEET 4 B 5 ASN A 100 ASN A 107 -1 O LEU A 104 N TYR A 60 SHEET 5 B 5 LYS A 110 VAL A 116 -1 O VAL A 116 N CYS A 101 SSBOND 1 CYS A 3 CYS A 14 1555 1555 2.02 SSBOND 2 CYS A 31 CYS A 126 1555 1555 2.02 SSBOND 3 CYS A 101 CYS A 118 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