HEADER PROTEIN BINDING 08-FEB-06 2FYJ TITLE NMR SOLUTION STRUCTURE OF CALCIUM-LOADED LRP DOUBLE MODULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LRP, ALPHA-2-MACROGLOBULIN RECEPTOR; 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: LRP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7 KEYWDS DOUBLE MODULE, COMPLEMENT TYPE REPEAT, CALCIUM, BETA-2 HAIRPIN, LOOP- KEYWDS 2 STRUCTURES, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR G.A.JENSEN,O.M.ANDERSEN,A.M.BONVIN,I.BJERRUM-BOHR,M.ETZERODT, AUTHOR 2 C.O'SHEA,F.M.POULSEN,B.B.KRAGELUND REVDAT 3 09-MAR-22 2FYJ 1 REMARK REVDAT 2 24-FEB-09 2FYJ 1 VERSN REVDAT 1 10-OCT-06 2FYJ 0 JRNL AUTH G.A.JENSEN,O.M.ANDERSEN,A.M.BONVIN,I.BJERRUM-BOHR, JRNL AUTH 2 M.ETZERODT,C.O'SHEA,F.M.POULSEN,B.B.KRAGELUND JRNL TITL BINDING SITE STRUCTURE OF ONE LRP-RAP COMPLEX:IMPLICATIONS JRNL TITL 2 FOR A COMMON LIGAND-RECEPTOR BINDING MOTIF. JRNL REF J.MOL.BIOL. V. 362 700 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16938309 JRNL DOI 10.1016/J.JMB.2006.07.013 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.R.NIELSEN,L.ELLGAARD,M.ETZERODT,H.C.THOGERSEN,F.M.POULSEN REMARK 1 TITL THE SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF REMARK 1 TITL 2 ALPHA2-MACROGLOBULIN RECEPTOR-ASSOCIATED PROTEIN. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 94 7521 1997 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 9207124 REMARK 1 DOI 10.1073/PNAS.94.14.7521 REMARK 1 REFERENCE 2 REMARK 1 AUTH O.M.ANDERSEN,L.L.CHRISTENSEN,P.A.CHRSITENSEN,E.S.SORENSEN, REMARK 1 AUTH 2 C.JAKOBSEN,S.K.MOESTRUP,M.ETZERODT,H.C.THOGERSEN REMARK 1 TITL IDENTIFICATION OF THE MINIMAL FUNCTIONAL UNIT IN THE LOW REMARK 1 TITL 2 DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN FOR BINDING THE REMARK 1 TITL 3 RECEPTOR-ASSOCIATED PROTEIN (RAP). A CONSERVED ACIDIC REMARK 1 TITL 4 RESIDUE IN THE COMPLEMENT-TYPE REPEATS IS IMPORTANT FOR REMARK 1 TITL 5 RECOGNITION OF RAP REMARK 1 REF J.BIOL.CHEM. V. 275 21017 2000 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10747921 REMARK 1 DOI 10.1074/JBC.M000507200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FYJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036463. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-99% 15N]-CR56; 0.5MM REMARK 210 CR56 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_15N REMARK 210 -SEPARATED_NOESY; DQF-COSY; 3D- REMARK 210 15N-SEPARATED_TOCSY; 15N,1H-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, CNS, PRONTO3D REMARK 210 20020517 REMARK 210 METHOD USED : SIMMULATED ANNEALING USING XPLOR REMARK 210 -NIH, REFINEMENT IN EXPLICIT REMARK 210 WATER LAYER USING CNS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY, FEWEST VIOLATIONS 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 HD11 ILE A 59 HD21 ASN A 69 1.23 REMARK 500 H PHE A 10 O ILE A 18 1.58 REMARK 500 HH12 ARG A 16 OD2 ASP A 29 1.59 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 ARG A 3 -76.55 70.11 REMARK 500 1 THR A 4 -67.66 -164.73 REMARK 500 1 CYS A 12 -93.28 -58.09 REMARK 500 1 ALA A 13 35.90 -75.82 REMARK 500 1 SER A 14 -47.53 67.74 REMARK 500 1 SER A 21 -26.28 147.24 REMARK 500 1 LEU A 26 82.38 78.39 REMARK 500 1 ASP A 27 -66.73 77.60 REMARK 500 1 ASP A 29 -71.32 -64.91 REMARK 500 1 ASP A 32 -39.25 171.06 REMARK 500 1 SER A 39 -44.50 -168.92 REMARK 500 1 ALA A 41 39.83 -147.62 REMARK 500 1 THR A 44 22.95 -143.48 REMARK 500 1 CYS A 45 -85.22 65.15 REMARK 500 1 LEU A 48 -66.52 -97.22 REMARK 500 1 THR A 49 86.78 -168.62 REMARK 500 1 ASN A 67 -37.07 -179.51 REMARK 500 1 ASP A 68 -166.13 -107.96 REMARK 500 1 ASP A 70 123.89 -39.77 REMARK 500 1 CYS A 71 -56.97 -140.85 REMARK 500 1 ASP A 73 -78.83 -161.05 REMARK 500 1 ASN A 74 19.67 -156.46 REMARK 500 1 SER A 75 -97.04 -90.32 REMARK 500 1 GLU A 77 -20.14 -179.69 REMARK 500 1 ALA A 78 21.17 88.40 REMARK 500 1 CYS A 80 93.42 -66.19 REMARK 500 2 ARG A 3 -27.13 174.75 REMARK 500 2 CYS A 12 -157.82 -73.21 REMARK 500 2 ALA A 13 89.29 -63.02 REMARK 500 2 SER A 14 76.66 40.10 REMARK 500 2 THR A 23 -162.08 -79.22 REMARK 500 2 CYS A 24 99.89 -28.41 REMARK 500 2 ASP A 25 -90.39 -141.55 REMARK 500 2 CYS A 30 34.58 -141.93 REMARK 500 2 ASP A 32 -41.15 174.35 REMARK 500 2 SER A 34 -29.30 73.66 REMARK 500 2 SER A 37 13.15 -143.01 REMARK 500 2 ALA A 38 -31.31 -141.72 REMARK 500 2 CYS A 40 95.83 -61.39 REMARK 500 2 ALA A 41 41.31 -148.16 REMARK 500 2 PHE A 46 95.27 -171.03 REMARK 500 2 LEU A 48 -53.61 -151.90 REMARK 500 2 THR A 49 79.28 -169.51 REMARK 500 2 ASN A 62 36.86 -94.09 REMARK 500 2 ARG A 64 95.71 -68.99 REMARK 500 2 ASP A 66 -74.46 -164.13 REMARK 500 2 ASN A 67 -79.70 -87.82 REMARK 500 2 ASP A 68 -151.40 -122.33 REMARK 500 2 CYS A 71 -56.07 -148.45 REMARK 500 2 GLU A 77 -20.86 161.79 REMARK 500 REMARK 500 THIS ENTRY HAS 378 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5961 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS REMARK 900 RELATED ID: 2FYL RELATED DB: PDB REMARK 900 HADDOCK MODEL OF COMPLEX BETWEEN THIS STRUCTURE (CR56) AND RAP REMARK 900 DOMAIN 1 REMARK 900 RELATED ID: 1LRE RELATED DB: PDB REMARK 900 RAP DOMAIN 1 DBREF 2FYJ A 1 82 UNP Q07954 LRP1_HUMAN 932 1013 SEQRES 1 A 82 SER ALA ARG THR CYS PRO PRO ASN GLN PHE SER CYS ALA SEQRES 2 A 82 SER GLY ARG CYS ILE PRO ILE SER TRP THR CYS ASP LEU SEQRES 3 A 82 ASP ASP ASP CYS GLY ASP ARG SER ASP GLU SER ALA SER SEQRES 4 A 82 CYS ALA TYR PRO THR CYS PHE PRO LEU THR GLN PHE THR SEQRES 5 A 82 CYS ASN ASN GLY ARG CYS ILE ASN ILE ASN TRP ARG CYS SEQRES 6 A 82 ASP ASN ASP ASN ASP CYS GLY ASP ASN SER ASP GLU ALA SEQRES 7 A 82 GLY CYS SER HIS SHEET 1 A 2 GLN A 9 SER A 11 0 SHEET 2 A 2 CYS A 17 PRO A 19 -1 O ILE A 18 N PHE A 10 SHEET 1 B 2 GLN A 50 THR A 52 0 SHEET 2 B 2 CYS A 58 ASN A 60 -1 O ILE A 59 N PHE A 51 SSBOND 1 CYS A 5 CYS A 17 1555 1555 2.03 SSBOND 2 CYS A 12 CYS A 30 1555 1555 2.03 SSBOND 3 CYS A 24 CYS A 40 1555 1555 2.03 SSBOND 4 CYS A 45 CYS A 58 1555 1555 2.02 SSBOND 5 CYS A 53 CYS A 71 1555 1555 2.03 SSBOND 6 CYS A 65 CYS A 80 1555 1555 2.03 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