HEADER CELL ADHESION, SIGNALING PROTEIN 09-NOV-07 2JXA TITLE MOUSE LATROPHILIN-1 GPCR GAL_LECTIN DOMAIN IN COMPLEX WITH RHAMNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LATROPHILIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GAL_LECTIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: LPHN1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X-33; SOURCE 9 OTHER_DETAILS: GENE CONSTRUCT INTEGRATED IN THE ORGANISM'S GENOME KEYWDS LECTIN, BETA-SANDWICH, DISULPHIDE, GLYCOSYLATED, L-RHAMNOSE, COMPLEX, KEYWDS 2 G-PROTEIN COUPLED RECEPTOR, MEMBRANE, RECEPTOR, TRANSDUCER, KEYWDS 3 TRANSMEMBRANE, CELL ADHESION, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR I.VAKONAKIS,I.D.CAMPBELL REVDAT 5 29-JUL-20 2JXA 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 13-JUL-11 2JXA 1 VERSN REVDAT 3 08-DEC-09 2JXA 1 HET HETATM HETNAM FORMUL REVDAT 3 2 1 ATOM REVDAT 2 24-FEB-09 2JXA 1 VERSN REVDAT 1 29-APR-08 2JXA 0 JRNL AUTH I.VAKONAKIS,T.LANGENHAN,S.PROMEL,A.RUSS,I.D.CAMPBELL JRNL TITL SOLUTION STRUCTURE AND SUGAR-BINDING MECHANISM OF MOUSE JRNL TITL 2 LATROPHILIN-1 RBL: A NOVEL 7TM RECEPTOR-ATTACHED LECTIN-LIKE JRNL TITL 3 DOMAIN. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OMEGA BETA 6.0.3B2, X-PLOR NIH 2.17.0 REMARK 3 AUTHORS : GE/BRUKER (OMEGA), SCHWIETERS, KUSZEWSKI, TJANDRA, REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING IN THE PRESENCE OF REMARK 3 RHAMNOSE STARTING FROM AVERAGE APO-PROTEIN COORDINATES REMARK 4 REMARK 4 2JXA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000100406. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 30 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM [U-100% 15N] PROTEIN, 20 REMARK 210 MM SODIUM PHOSPHATE, 0.1 MM DSS, REMARK 210 0.02 % SODIUM AZIDE; 95% H2O/5% REMARK 210 D2O; 1-2 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 0.1 MM DSS, 0.02 % REMARK 210 SODIUM AZIDE; 100% D2O; 1-2 MM REMARK 210 [U-100% 15N] PROTEIN, 20 MM REMARK 210 SODIUM PHOSPHATE, 0.1 MM DSS, REMARK 210 0.02 % SODIUM AZIDE, 4 % PEG REMARK 210 C12E5, 0.96 MOLECULAR RATIO REMARK 210 HEXANOL; 95% H2O/5% D2O; 1-2 MM REMARK 210 [U-100% 13C; U-100% 15N] PROTEIN, REMARK 210 20 MM SODIUM PHOSPHATE, 0.1 MM REMARK 210 DSS, 0.02 % SODIUM AZIDE, 10 MM REMARK 210 L-RHAMNOSE; 100% D2O; 1-2 MM [U- REMARK 210 100% 15N] PROTEIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 0.1 MM DSS, 0.02 % REMARK 210 SODIUM AZIDE, 10 MM L-RHAMNOSE; REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNHA; 3D 1H-15N NOESY; 3D REMARK 210 HNHB; 4D 13C/13C NOESY; 2D 13C REMARK 210 METHYL-CARBONYL; 2D 13C METHYL- REMARK 210 NITROGEN; 15N IPAP-HSQC; 2D 13C- REMARK 210 PURGED/13C-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 500 MHZ; 950 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.4 REV 2006.095.11.35, REMARK 210 PIPP 4.3.7, X-PLOR NIH 2.17.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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 HZ2 LYS A 120 HO3 RAM A 136 1.18 REMARK 500 H THR A 66 HH TYR A 121 1.32 REMARK 500 OD2 ASP A 67 H LYS A 69 1.55 REMARK 500 H THR A 66 OH TYR A 121 1.58 REMARK 500 OE2 GLU A 47 HE ARG A 49 1.58 REMARK 500 OE2 GLU A 42 O3 RAM A 136 2.19 REMARK 500 O THR A 118 O4 RAM A 136 2.19 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 PRO A 31 -157.02 -82.76 REMARK 500 1 MET A 35 117.75 47.96 REMARK 500 1 ASP A 72 109.52 -47.99 REMARK 500 1 ALA A 73 -164.81 -128.35 REMARK 500 1 ALA A 106 37.44 -68.01 REMARK 500 1 SER A 108 -154.84 36.64 REMARK 500 1 PRO A 112 -158.84 -48.61 REMARK 500 1 LYS A 120 -163.01 -76.51 REMARK 500 2 LEU A 34 55.89 -155.36 REMARK 500 2 MET A 35 150.64 57.91 REMARK 500 2 ASP A 68 -0.51 -146.04 REMARK 500 2 ASP A 72 105.09 1.43 REMARK 500 2 ALA A 73 -166.15 -121.70 REMARK 500 2 ALA A 106 38.38 -71.36 REMARK 500 2 SER A 108 -158.90 31.04 REMARK 500 2 PRO A 112 -163.89 -48.76 REMARK 500 2 LYS A 120 -159.27 -81.99 REMARK 500 2 TYR A 131 -96.08 -72.24 REMARK 500 2 LYS A 132 -74.13 -90.29 REMARK 500 3 MET A 35 153.90 58.06 REMARK 500 3 ASP A 68 -0.33 -144.55 REMARK 500 3 CYS A 71 70.56 57.25 REMARK 500 3 ALA A 106 23.56 -66.81 REMARK 500 3 SER A 108 -155.55 94.79 REMARK 500 3 PRO A 112 -156.15 -50.64 REMARK 500 3 LYS A 120 -165.61 -76.05 REMARK 500 4 MET A 35 134.59 50.26 REMARK 500 4 CYS A 71 71.36 53.77 REMARK 500 4 ALA A 106 42.79 -66.57 REMARK 500 4 SER A 108 -150.78 35.82 REMARK 500 4 PRO A 112 -153.07 -52.01 REMARK 500 4 LYS A 120 -156.33 -68.12 REMARK 500 5 LEU A 34 118.50 -163.71 REMARK 500 5 MET A 35 108.46 52.97 REMARK 500 5 ALA A 106 38.71 -68.71 REMARK 500 5 SER A 108 -158.03 31.36 REMARK 500 5 PRO A 112 -159.61 -49.95 REMARK 500 5 CYS A 115 83.84 -155.67 REMARK 500 5 LYS A 120 -166.78 -77.58 REMARK 500 6 MET A 35 150.78 53.95 REMARK 500 6 CYS A 71 70.79 54.63 REMARK 500 6 ALA A 106 41.76 -70.98 REMARK 500 6 SER A 108 -146.56 31.58 REMARK 500 6 PRO A 112 -150.20 -52.18 REMARK 500 6 CYS A 115 80.37 -157.12 REMARK 500 6 LYS A 120 -165.97 -71.47 REMARK 500 6 TYR A 131 -143.09 -72.76 REMARK 500 6 LYS A 132 -81.71 -90.82 REMARK 500 7 MET A 35 136.73 55.02 REMARK 500 7 ALA A 106 41.77 -69.94 REMARK 500 REMARK 500 THIS ENTRY HAS 205 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15553 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS FOR THIS PROTEIN REMARK 900 RELATED ID: 2JX9 RELATED DB: PDB REMARK 900 STRUCTURE OF FREE PROTEIN DBREF 2JXA A 29 134 UNP Q5U4D5 Q5U4D5_MOUSE 29 134 SEQRES 1 A 106 GLY LEU PRO PHE GLY LEU MET ARG ARG GLU LEU ALA CYS SEQRES 2 A 106 GLU GLY TYR PRO ILE GLU LEU ARG CYS PRO GLY SER ASP SEQRES 3 A 106 VAL ILE MET VAL GLU ASN ALA ASN TYR GLY ARG THR ASP SEQRES 4 A 106 ASP LYS ILE CYS ASP ALA ASP PRO PHE GLN MET GLU ASN SEQRES 5 A 106 VAL GLN CYS TYR LEU PRO ASP ALA PHE LYS ILE MET SER SEQRES 6 A 106 GLN ARG CYS ASN ASN ARG THR GLN CYS VAL VAL VAL ALA SEQRES 7 A 106 GLY SER ASP ALA PHE PRO ASP PRO CYS PRO GLY THR TYR SEQRES 8 A 106 LYS TYR LEU GLU VAL GLN TYR ASP CYS VAL PRO TYR LYS SEQRES 9 A 106 VAL GLU MODRES 2JXA ASN A 98 ASN GLYCOSYLATION SITE HET NAG A 135 28 HET RAM A 136 23 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM RAM ALPHA-L-RHAMNOPYRANOSE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 RAM C6 H12 O5 HELIX 1 1 ASP A 74 GLU A 79 1 6 HELIX 2 2 PRO A 86 ASN A 97 1 12 HELIX 3 3 GLY A 107 PHE A 111 5 5 SHEET 1 A 3 ARG A 36 CYS A 41 0 SHEET 2 A 3 TYR A 121 PRO A 130 -1 O TYR A 126 N ARG A 36 SHEET 3 A 3 ASP A 54 GLY A 64 -1 N ASN A 60 O GLN A 125 SHEET 1 B 2 PRO A 45 ARG A 49 0 SHEET 2 B 2 GLN A 101 VAL A 105 -1 O VAL A 104 N ILE A 46 SSBOND 1 CYS A 41 CYS A 71 1555 1555 2.02 SSBOND 2 CYS A 50 CYS A 128 1555 1555 2.02 SSBOND 3 CYS A 83 CYS A 115 1555 1555 2.02 SSBOND 4 CYS A 96 CYS A 102 1555 1555 2.02 LINK ND2 ASN A 98 C1 NAG A 135 1555 1555 1.45 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