PDB Short entry for 2M0P HEADER LIPID BINDING PROTEIN 01-NOV-12 2M0P TITLE SOLUTION STRUCTURE OF THE TENTH COMPLEMENT TYPE REPEAT OF HUMAN TITLE 2 MEGALIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LRP-2, GLYCOPROTEIN 330, GP330, MEGALIN; COMPND 5 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: LRP2; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICAC KEYWDS COMPLEMENT TYPE REPEAT, RECEPTOR, MEGALIN, LDL RECEPTOR FAMILY, LRP2, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.DAGIL,B.KRAGELUND REVDAT 3 14-JUN-23 2M0P 1 REMARK SEQADV LINK REVDAT 2 19-JUN-13 2M0P 1 JRNL REVDAT 1 09-JAN-13 2M0P 0 JRNL AUTH R.DAGIL,C.O'SHEA,A.NYKJAR,A.M.BONVIN,B.B.KRAGELUND JRNL TITL GENTAMICIN BINDS TO THE MEGALIN RECEPTOR AS A COMPETITIVE JRNL TITL 2 INHIBITOR USING THE COMMON LIGAND BINDING MOTIF OF JRNL TITL 3 COMPLEMENT TYPE REPEATS: INSIGHT FROM THE NMR STRUCTURE OF JRNL TITL 4 THE 10TH COMPLEMENT TYPE REPEAT DOMAIN ALONE AND IN COMPLEX JRNL TITL 5 WITH GENTAMICIN. JRNL REF J.BIOL.CHEM. V. 288 4424 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23275343 JRNL DOI 10.1074/JBC.M112.434159 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ANALYSIS 2.2, ARIA REMARK 3 AUTHORS : CCPN (ANALYSIS), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000103061. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 CR10, 100 MM SODIUM CHLORIDE, 50 REMARK 210 MM CALCIUM CHLORIDE, 50 MM TRIS, REMARK 210 0.1 MM DSS, 0.1 % SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 0.6 MM [U-100% REMARK 210 13C; U-100% 15N] CR10, 50 MM REMARK 210 CALCIUM CHLORIDE, 100 MM SODIUM REMARK 210 CHLORIDE, 50 MM TRIS, 0.1 MM DSS, REMARK 210 0.1 % SODIUM AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY AROMATIC; 3D HNCO; REMARK 210 3D HNCA; 3D HNCACB; 3D C(CO)NH; REMARK 210 3D CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HN(CO)CA; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-13C NOESY REMARK 210 AROMATIC; 3D H(CCO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 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 : ANALYSIS 2.2, ARIA, NMRDRAW REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 1149 REMARK 465 HIS A 1150 REMARK 465 HIS A 1151 REMARK 465 HIS A 1152 REMARK 465 HIS A 1153 REMARK 465 HIS A 1154 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: 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 CYS A1109 -163.93 61.73 REMARK 500 1 THR A1146 45.61 -91.52 REMARK 500 2 HIS A1104 76.70 64.15 REMARK 500 2 CYS A1109 -168.48 60.55 REMARK 500 2 ASN A1132 48.54 -84.48 REMARK 500 2 ASN A1142 74.16 -114.26 REMARK 500 2 CYS A1143 -63.79 -141.79 REMARK 500 2 ASN A1144 15.98 -157.35 REMARK 500 3 ASN A1118 25.56 -79.16 REMARK 500 3 CYS A1143 10.12 -140.66 REMARK 500 3 THR A1146 34.60 -88.63 REMARK 500 4 ASN A1142 53.80 -93.39 REMARK 500 4 ASN A1144 -175.87 50.45 REMARK 500 4 SER A1145 -166.60 53.43 REMARK 500 4 THR A1146 42.76 -89.93 REMARK 500 5 ALA A1107 39.63 -80.31 REMARK 500 5 HIS A1119 83.79 66.72 REMARK 500 5 ASN A1132 36.21 -86.31 REMARK 500 5 CYS A1134 154.20 73.26 REMARK 500 5 ASP A1136 -47.15 -158.25 REMARK 500 5 SER A1145 168.50 58.94 REMARK 500 6 SER A1108 37.33 -85.19 REMARK 500 6 ASN A1142 43.31 -81.69 REMARK 500 6 CYS A1143 -54.29 -171.76 REMARK 500 6 THR A1146 47.89 -89.11 REMARK 500 7 HIS A1104 84.54 64.22 REMARK 500 7 LEU A1110 151.26 -48.01 REMARK 500 7 CYS A1143 114.56 -170.23 REMARK 500 7 ASN A1144 58.83 38.08 REMARK 500 7 SER A1145 -81.69 -69.87 REMARK 500 8 CYS A1143 -42.59 -179.81 REMARK 500 9 HIS A1104 93.70 64.20 REMARK 500 9 ASN A1118 30.12 -88.44 REMARK 500 9 ASP A1136 -35.59 -164.91 REMARK 500 9 ASN A1144 36.55 -150.83 REMARK 500 10 THR A1146 45.92 -79.50 REMARK 500 11 HIS A1104 94.94 61.80 REMARK 500 11 CYS A1143 46.09 -162.92 REMARK 500 12 HIS A1104 -58.25 71.29 REMARK 500 12 CYS A1143 59.19 -96.36 REMARK 500 13 ALA A1107 37.35 -93.99 REMARK 500 13 SER A1145 -82.19 -77.50 REMARK 500 14 HIS A1104 -38.28 -168.91 REMARK 500 14 CYS A1109 -166.97 -101.88 REMARK 500 15 ASN A1118 33.37 -92.60 REMARK 500 15 ASP A1133 -39.14 -133.66 REMARK 500 15 CYS A1134 34.76 -77.09 REMARK 500 15 ASN A1144 65.43 39.08 REMARK 500 15 SER A1145 133.97 60.20 REMARK 500 15 THR A1146 98.24 -68.30 REMARK 500 REMARK 500 THIS ENTRY HAS 61 RAMACHANDRAN OUTLIERS. 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 CA A1201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A1126 O REMARK 620 2 ASP A1129 OD1 76.0 REMARK 620 3 ASP A1131 O 156.8 80.9 REMARK 620 4 ASP A1133 OD2 95.8 93.1 82.9 REMARK 620 5 ASP A1139 OD2 86.1 152.5 116.3 109.6 REMARK 620 6 GLU A1140 OE2 97.1 84.2 82.9 165.8 77.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I1P RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE TWELFTH CYSTEINE-RICH LIGAND-BINDING REMARK 900 REPEAT IN RAT MEGALIN REMARK 900 RELATED ID: 2FYJ RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF CALCIUM-LOADED LRP DOUBLE MODULE REMARK 900 RELATED ID: 18816 RELATED DB: BMRB DBREF 2M0P A 1103 1148 UNP P98164 LRP2_HUMAN 1103 1148 SEQADV 2M0P HIS A 1149 UNP P98164 EXPRESSION TAG SEQADV 2M0P HIS A 1150 UNP P98164 EXPRESSION TAG SEQADV 2M0P HIS A 1151 UNP P98164 EXPRESSION TAG SEQADV 2M0P HIS A 1152 UNP P98164 EXPRESSION TAG SEQADV 2M0P HIS A 1153 UNP P98164 EXPRESSION TAG SEQADV 2M0P HIS A 1154 UNP P98164 EXPRESSION TAG SEQRES 1 A 52 THR HIS ALA PRO ALA SER CYS LEU ASP THR GLN TYR THR SEQRES 2 A 52 CYS ASP ASN HIS GLN CYS ILE SER LYS ASN TRP VAL CYS SEQRES 3 A 52 ASP THR ASP ASN ASP CYS GLY ASP GLY SER ASP GLU LYS SEQRES 4 A 52 ASN CYS ASN SER THR GLU THR HIS HIS HIS HIS HIS HIS HET CA A1201 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 GLY A 1137 ASN A 1142 1 6 SHEET 1 A 2 GLN A1113 THR A1115 0 SHEET 2 A 2 CYS A1121 SER A1123 -1 O ILE A1122 N TYR A1114 SSBOND 1 CYS A 1109 CYS A 1121 1555 1555 2.03 SSBOND 2 CYS A 1116 CYS A 1134 1555 1555 2.02 SSBOND 3 CYS A 1128 CYS A 1143 1555 1555 2.03 LINK O TRP A1126 CA CA A1201 1555 1555 2.28 LINK OD1 ASP A1129 CA CA A1201 1555 1555 2.19 LINK O ASP A1131 CA CA A1201 1555 1555 2.25 LINK OD2 ASP A1133 CA CA A1201 1555 1555 2.22 LINK OD2 ASP A1139 CA CA A1201 1555 1555 2.17 LINK OE2 GLU A1140 CA CA A1201 1555 1555 2.25 SITE 1 AC1 6 TRP A1126 ASP A1129 ASP A1131 ASP A1133 SITE 2 AC1 6 ASP A1139 GLU A1140 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