HEADER LIPID TRANSPORT, ENDOCYTOSIS/EXOCYTOSIS 14-SEP-04 1XFE TITLE SOLUTION STRUCTURE OF THE LA7-EGFA PAIR FROM THE LDL RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 272-353: INCLUDES LDL-RECEPTOR COMPND 5 CLASS A 7 (RESIDUES 274-313), EGF-LIKE 1 (314-353); COMPND 6 SYNONYM: LDL RECEPTOR, LA7-EGFA PAIR; 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: LDLR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PDEST17; SOURCE 11 OTHER_DETAILS: GATEWAY EXPRESSION SYSTEM (INVITROGEN) KEYWDS LIGAND-BINDING REPEAT, EGF-LIKE REPEAT, LIPID TRANSPORT, ENDOCYTOSIS- KEYWDS 2 EXOCYTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR N.BEGLOVA,H.JEON,C.FISHER,S.C.BLACKLOW REVDAT 3 02-MAR-22 1XFE 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1XFE 1 VERSN REVDAT 1 02-NOV-04 1XFE 0 JRNL AUTH N.BEGLOVA,H.JEON,C.FISHER,S.C.BLACKLOW JRNL TITL COOPERATION BETWEEN FIXED AND LOW PH-INDUCIBLE INTERFACES JRNL TITL 2 CONTROLS LIPOPROTEIN RELEASE BY THE LDL RECEPTOR JRNL REF MOL.CELL V. 16 281 2004 JRNL REFN ISSN 1097-2765 JRNL PMID 15494314 JRNL DOI 10.1016/J.MOLCEL.2004.09.038 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS_SOLVE 1.1, CNS_SOLVE 1.1 REMARK 3 AUTHORS : BRUNGER (CNS_SOLVE), BRUNGER (CNS_SOLVE) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 1564 NOE REMARK 3 -DERIVED CONSTRAINTS, 119 DIHEDRAL ANGLE RESTRAINTS, 14 DISTANCE REMARK 3 RESTRAINTS FOR HYDROGEN BONDS, AND 55 RDC CONSTRAINTS. REMARK 4 REMARK 4 1XFE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030299. 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 : 1:6 MOLAR PROTEIN/CACL2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM LA7-EGFA U-15N,13C 2 MM REMARK 210 CACL2; 90% H2O, 10% D2O; 1.5 MM REMARK 210 LA7-EGFA U-15N 10 MM CACL2; 90% REMARK 210 H2O, 10% D2O; 0.6 MMM LA7-EGFA U- REMARK 210 15N, 10% 13C 4 MM CACL2; 99% D2O; REMARK 210 1 MM LA7-EGFA 6 MM CACL2; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED NOESY, TOCSY; REMARK 210 HNHA, HNHB; 2D_NOESY, 2D_TOCSY; REMARK 210 13C_HSQC; HNCA, HNCOCA, HNCO, REMARK 210 HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : GIFA 4.3, XEASY 1.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 43 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 H VAL A 77 O ARG A 81 1.53 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 LYS A 24 8.38 -62.06 REMARK 500 1 GLU A 38 68.15 -106.45 REMARK 500 1 CYS A 48 -76.19 -60.58 REMARK 500 1 ASN A 51 -123.24 -136.31 REMARK 500 1 CYS A 55 -44.98 -139.50 REMARK 500 1 SER A 56 -56.86 -168.84 REMARK 500 1 ARG A 80 -25.50 -161.49 REMARK 500 2 ASN A 10 27.60 40.91 REMARK 500 2 LYS A 24 12.53 -62.27 REMARK 500 2 ASN A 27 -176.93 -66.37 REMARK 500 2 GLU A 38 69.76 -106.60 REMARK 500 2 CYS A 48 -75.10 -60.57 REMARK 500 2 ASP A 50 -9.42 -59.60 REMARK 500 2 ASN A 51 -123.69 -137.67 REMARK 500 2 CYS A 55 -43.43 -140.61 REMARK 500 2 SER A 56 -64.79 -167.75 REMARK 500 2 HIS A 57 -68.99 -106.20 REMARK 500 2 PRO A 71 164.00 -44.23 REMARK 500 2 ARG A 80 -30.95 -158.68 REMARK 500 3 CYS A 6 32.27 -99.23 REMARK 500 3 ASN A 10 20.31 92.70 REMARK 500 3 CYS A 14 -171.34 -63.63 REMARK 500 3 LYS A 24 17.01 -63.42 REMARK 500 3 MET A 28 -53.06 -22.35 REMARK 500 3 ASP A 31 -80.05 -114.31 REMARK 500 3 GLU A 38 66.37 -107.91 REMARK 500 3 CYS A 48 -75.31 -61.24 REMARK 500 3 ASN A 51 -123.33 -133.78 REMARK 500 3 CYS A 55 -47.15 -137.40 REMARK 500 3 SER A 56 -55.95 -166.59 REMARK 500 3 PRO A 71 159.36 -42.33 REMARK 500 3 ARG A 80 -31.51 -160.73 REMARK 500 4 CYS A 6 -68.41 -146.31 REMARK 500 4 LYS A 24 16.08 -63.44 REMARK 500 4 ASN A 27 -176.93 -68.50 REMARK 500 4 TRP A 35 95.38 26.06 REMARK 500 4 GLU A 38 69.38 -105.74 REMARK 500 4 CYS A 48 -74.62 -59.79 REMARK 500 4 ASN A 51 -123.23 -136.94 REMARK 500 4 CYS A 55 -42.69 -140.90 REMARK 500 4 SER A 56 -66.68 -168.33 REMARK 500 4 HIS A 57 -70.90 -104.28 REMARK 500 4 PRO A 71 161.03 -43.91 REMARK 500 4 ARG A 80 -33.14 -157.42 REMARK 500 5 LEU A 5 -75.03 -80.74 REMARK 500 5 ASN A 27 -177.05 -66.72 REMARK 500 5 GLU A 38 69.18 -105.79 REMARK 500 5 CYS A 48 -75.22 -59.75 REMARK 500 5 ASN A 51 -122.49 -137.67 REMARK 500 5 CYS A 55 -50.90 -138.60 REMARK 500 REMARK 500 THIS ENTRY HAS 177 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 A 100 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 24 O REMARK 620 2 VAL A 25 N 43.1 REMARK 620 3 CYS A 26 N 94.1 76.0 REMARK 620 4 ASN A 27 OD1 88.2 130.8 107.9 REMARK 620 5 ASN A 27 N 71.9 96.3 60.3 52.4 REMARK 620 6 ASP A 31 OD2 93.8 111.7 171.7 69.8 120.1 REMARK 620 7 ASP A 37 OD1 132.4 89.8 76.3 139.3 132.8 100.2 REMARK 620 8 GLU A 38 OE2 160.7 146.7 104.6 81.5 113.1 67.4 59.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 42 O REMARK 620 2 THR A 45 O 129.0 REMARK 620 3 THR A 45 OG1 71.0 76.0 REMARK 620 4 GLU A 47 OE1 144.5 64.1 83.8 REMARK 620 5 ASP A 61 OD1 162.0 46.5 117.3 53.2 REMARK 620 6 LEU A 62 O 64.4 117.2 130.5 145.7 100.9 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 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 200 DBREF 1XFE A 2 83 UNP P01130 LDLR_HUMAN 272 353 SEQADV 1XFE GLY A 1 UNP P01130 CLONING ARTIFACT SEQRES 1 A 83 GLY ASN VAL THR LEU CYS GLU GLY PRO ASN LYS PHE LYS SEQRES 2 A 83 CYS HIS SER GLY GLU CYS ILE THR LEU ASP LYS VAL CYS SEQRES 3 A 83 ASN MET ALA ARG ASP CYS ARG ASP TRP SER ASP GLU PRO SEQRES 4 A 83 ILE LYS GLU CYS GLY THR ASN GLU CYS LEU ASP ASN ASN SEQRES 5 A 83 GLY GLY CYS SER HIS VAL CYS ASN ASP LEU LYS ILE GLY SEQRES 6 A 83 TYR GLU CYS LEU CYS PRO ASP GLY PHE GLN LEU VAL ALA SEQRES 7 A 83 GLN ARG ARG CYS GLU HET CA A 100 1 HET CA A 200 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 ALA A 78 ARG A 80 5 3 SHEET 1 A 2 LYS A 11 LYS A 13 0 SHEET 2 A 2 CYS A 19 THR A 21 -1 O ILE A 20 N PHE A 12 SHEET 1 B 2 VAL A 58 LEU A 62 0 SHEET 2 B 2 GLY A 65 LEU A 69 -1 O GLU A 67 N ASN A 60 SHEET 1 C 2 LEU A 76 VAL A 77 0 SHEET 2 C 2 ARG A 81 CYS A 82 -1 O ARG A 81 N VAL A 77 SSBOND 1 CYS A 6 CYS A 19 1555 1555 2.03 SSBOND 2 CYS A 14 CYS A 32 1555 1555 2.03 SSBOND 3 CYS A 26 CYS A 43 1555 1555 2.03 SSBOND 4 CYS A 48 CYS A 59 1555 1555 2.03 SSBOND 5 CYS A 55 CYS A 68 1555 1555 2.03 SSBOND 6 CYS A 70 CYS A 82 1555 1555 2.03 LINK O LYS A 24 CA CA A 100 1555 1555 2.34 LINK N VAL A 25 CA CA A 100 1555 1555 3.29 LINK N CYS A 26 CA CA A 100 1555 1555 2.35 LINK OD1 ASN A 27 CA CA A 100 1555 1555 2.80 LINK N ASN A 27 CA CA A 100 1555 1555 3.03 LINK OD2 ASP A 31 CA CA A 100 1555 1555 2.36 LINK OD1 ASP A 37 CA CA A 100 1555 1555 2.84 LINK OE2 GLU A 38 CA CA A 100 1555 1555 2.15 LINK O GLU A 42 CA CA A 200 1555 1555 2.69 LINK O THR A 45 CA CA A 200 1555 1555 3.35 LINK OG1 THR A 45 CA CA A 200 1555 1555 2.82 LINK OE1 GLU A 47 CA CA A 200 1555 1555 2.85 LINK OD1 ASP A 61 CA CA A 200 1555 1555 2.68 LINK O LEU A 62 CA CA A 200 1555 1555 2.83 SITE 1 AC1 7 LYS A 24 VAL A 25 CYS A 26 ASN A 27 SITE 2 AC1 7 ASP A 31 ASP A 37 GLU A 38 SITE 1 AC2 5 GLU A 42 THR A 45 GLU A 47 ASP A 61 SITE 2 AC2 5 LEU A 62 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