10 20 30 40 50 60 70 80 1XFE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIPID TRANSPORT, ENDOCYTOSIS/EXOCYTOSIS 14-SEP-04 1XFE
TITLE SOLUTION STRUCTURE OF THE LA7-EGFA PAIR FROM THE LDL TITLE 2 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- COMPND 5 RECEPTOR CLASS A 7 (RESIDUES 274-313), EGF-LIKE 1 (314- COMPND 6 353); COMPND 7 SYNONYM: LDL RECEPTOR, LA7-EGFA PAIR; COMPND 8 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, KEYWDS 2 ENDOCYTOSIS/EXOCYTOSIS COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR N.BEGLOVA,H.JEON,C.FISHER,S.C.BLACKLOW
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 JRNL TITL 2 INTERFACES CONTROLS LIPOPROTEIN RELEASE BY THE LDL JRNL TITL 3 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS_SOLVE 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 1564 NOE- REMARK 3 DERIVED CONSTRAINTS, 119 DIHEDRAL ANGLE RESTRAINTS, 14 REMARK 3 DISTANCE 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 04-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB030299.
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 REMARK 210 MM CACL2; 90% H2O, 10% D2O; REMARK 210 1.5 MM LA7-EGFA U-15N 10 MM REMARK 210 CACL2; 90% H2O, 10% D2O; 0.6 REMARK 210 MMM LA7-EGFA U-15N, 10% 13C 4 REMARK 210 MM CACL2; 99% D2O; 1 MM LA7- REMARK 210 EGFA 6 MM CACL2; 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED NOESY, REMARK 210 TOCSY, HNHA, HNHB, 2D_NOESY, REMARK 210 2D_TOCSY, 13C_HSQC, HNCA, REMARK 210 HNCOCA, HNCO, 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 : CNS_SOLVE 1.1, GIFA 4.3, REMARK 210 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 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 5 SER A 56 -62.75 -162.78 REMARK 500 5 HIS A 57 -72.64 -108.44 REMARK 500 5 ALA A 78 177.32 62.92 REMARK 500 5 GLN A 79 40.13 -87.25 REMARK 500 5 ARG A 80 -30.46 -164.94 REMARK 500 6 ASN A 10 -14.37 106.53 REMARK 500 6 LYS A 24 15.54 -62.96 REMARK 500 6 MET A 28 -52.58 -26.96 REMARK 500 6 GLU A 38 66.89 -108.06 REMARK 500 6 CYS A 48 -75.00 -59.92 REMARK 500 6 ASP A 50 -9.36 -59.63 REMARK 500 6 ASN A 51 -122.95 -136.67 REMARK 500 6 CYS A 55 -41.08 -142.48 REMARK 500 6 SER A 56 -65.15 -168.31 REMARK 500 6 HIS A 57 -71.22 -106.14 REMARK 500 6 PRO A 71 170.79 -52.47 REMARK 500 6 ARG A 80 -25.65 -160.25 REMARK 500 7 LEU A 5 -67.85 68.39 REMARK 500 7 ASN A 10 21.95 -147.93 REMARK 500 7 CYS A 14 -174.08 -65.46 REMARK 500 7 LYS A 24 23.63 -66.45 REMARK 500 7 MET A 28 -46.92 -27.00 REMARK 500 7 GLU A 38 65.41 -107.63 REMARK 500 7 CYS A 48 -74.39 -60.13 REMARK 500 7 ASN A 51 -122.98 -137.17 REMARK 500 7 CYS A 55 -44.51 -140.43 REMARK 500 7 SER A 56 -66.92 -165.99 REMARK 500 7 HIS A 57 -72.41 -103.08 REMARK 500 7 PRO A 71 162.64 -43.83 REMARK 500 7 ARG A 80 -30.56 -154.29 REMARK 500 8 LEU A 5 -88.04 163.60 REMARK 500 8 CYS A 6 64.22 173.12 REMARK 500 8 CYS A 14 -174.29 -64.28 REMARK 500 8 TRP A 35 50.89 22.24 REMARK 500 8 GLU A 38 66.08 -107.59 REMARK 500 8 CYS A 48 -77.70 -60.95 REMARK 500 8 ASN A 51 -123.48 -136.66 REMARK 500 8 CYS A 55 -41.31 -140.38 REMARK 500 8 SER A 56 -58.66 -172.82 REMARK 500 8 ARG A 80 -28.41 -160.05 REMARK 500 9 LEU A 5 144.46 -172.73 REMARK 500 9 CYS A 6 39.63 -97.35 REMARK 500 9 CYS A 14 -176.91 -62.95 REMARK 500 9 LYS A 24 15.89 -64.77 REMARK 500 9 GLU A 38 66.11 -106.45 REMARK 500 9 CYS A 48 -77.05 -60.63 REMARK 500 9 ASP A 50 -7.47 -59.30 REMARK 500 9 ASN A 51 -123.27 -145.24 REMARK 500 9 CYS A 55 -37.90 -143.24 REMARK 500 9 SER A 56 -75.12 -170.98 REMARK 500 9 HIS A 57 -71.59 -96.40 REMARK 500 9 CYS A 70 162.90 172.51 REMARK 500 9 PRO A 71 170.09 -54.04 REMARK 500 9 ARG A 80 -35.55 -155.35 REMARK 500 10 LEU A 5 -52.02 -136.97 REMARK 500 10 ASN A 10 50.56 -100.39 REMARK 500 10 GLU A 18 -169.10 -108.57 REMARK 500 10 LYS A 24 16.18 -63.27 REMARK 500 10 MET A 28 -51.47 -25.53 REMARK 500 10 GLU A 38 66.93 -107.51 REMARK 500 10 CYS A 48 -75.34 -60.53 REMARK 500 10 ASN A 51 -122.77 -136.44 REMARK 500 10 CYS A 55 -54.77 -137.78 REMARK 500 10 SER A 56 -59.61 -155.79 REMARK 500 10 HIS A 57 -70.59 -114.01 REMARK 500 10 ALA A 78 -177.24 53.24 REMARK 500 10 GLN A 79 40.28 -90.80 REMARK 500 10 ARG A 80 26.44 -175.29 REMARK 500 11 HIS A 15 -147.35 75.23 REMARK 500 11 LYS A 24 18.99 -66.10 REMARK 500 11 GLU A 38 69.88 -107.38 REMARK 500 11 CYS A 48 -77.48 -61.86 REMARK 500 11 ASP A 50 -9.99 -59.16 REMARK 500 11 ASN A 51 -123.57 -137.12 REMARK 500 11 CYS A 55 -41.92 -140.06 REMARK 500 11 SER A 56 -64.12 -171.49 REMARK 500 11 HIS A 57 -70.09 -105.80 REMARK 500 11 CYS A 70 139.41 -170.87 REMARK 500 11 PRO A 71 163.89 -45.34 REMARK 500 11 ARG A 80 -32.01 -157.05 REMARK 500 12 LEU A 5 -76.27 -67.21 REMARK 500 12 CYS A 14 -167.65 -66.84 REMARK 500 12 LYS A 24 15.41 -64.32 REMARK 500 12 ASN A 27 -176.78 -68.58 REMARK 500 12 GLU A 38 68.85 -106.46 REMARK 500 12 CYS A 48 -75.13 -59.80 REMARK 500 12 ASP A 50 -9.51 -59.62 REMARK 500 12 ASN A 51 -123.66 -137.20 REMARK 500 12 CYS A 55 -45.01 -139.62 REMARK 500 12 SER A 56 -59.98 -168.39 REMARK 500 12 CYS A 70 143.26 -178.33 REMARK 500 12 PRO A 71 171.03 -47.79 REMARK 500 12 ARG A 80 -28.91 -161.80 REMARK 500 13 LEU A 5 -172.51 179.05 REMARK 500 13 LYS A 24 5.35 -69.21 REMARK 500 13 CYS A 26 34.04 71.06 REMARK 500 13 MET A 28 -38.38 -32.58 REMARK 500 13 GLU A 38 66.87 -106.53 REMARK 500 13 CYS A 48 -76.35 -61.13 REMARK 500 13 ASN A 51 -123.54 -135.70 REMARK 500 13 CYS A 55 -45.79 -137.15 REMARK 500 13 SER A 56 -55.78 -169.65 REMARK 500 13 ARG A 80 -28.26 -157.21 REMARK 500 14 CYS A 6 103.26 56.49 REMARK 500 14 PRO A 9 32.88 -87.06 REMARK 500 14 ASN A 10 47.36 -176.26 REMARK 500 14 HIS A 15 -85.83 47.82 REMARK 500 14 LYS A 24 18.06 -66.20 REMARK 500 14 GLU A 38 65.96 -105.58 REMARK 500 14 CYS A 48 -74.75 -59.64 REMARK 500 14 ASN A 51 -122.77 -136.34 REMARK 500 14 CYS A 55 -43.72 -140.75 REMARK 500 14 SER A 56 -68.48 -167.33 REMARK 500 14 HIS A 57 -71.41 -102.33 REMARK 500 14 PRO A 71 162.70 -43.74 REMARK 500 14 ARG A 80 -31.80 -155.25 REMARK 500 15 ASN A 10 51.74 -101.20 REMARK 500 15 CYS A 14 -169.72 -64.74 REMARK 500 15 LYS A 24 11.22 -61.79 REMARK 500 15 ASN A 27 -175.95 -60.47 REMARK 500 15 GLU A 38 69.68 -106.12 REMARK 500 15 CYS A 48 -75.22 -59.76 REMARK 500 15 ASP A 50 -9.00 -59.72 REMARK 500 15 ASN A 51 -123.48 -138.36 REMARK 500 15 CYS A 55 -41.31 -142.74 REMARK 500 15 SER A 56 -63.16 -167.64 REMARK 500 15 ARG A 80 -13.23 -150.10 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 1 CA A 100 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 27 OD1 REMARK 620 2 LYS A 24 O 88.2 REMARK 620 3 ASP A 31 OD2 69.8 93.8 REMARK 620 4 GLU A 38 OE2 81.5 160.7 67.4 REMARK 620 5 ASN A 27 N 52.4 71.9 120.1 113.1 REMARK 620 6 CYS A 26 N 107.9 94.1 171.7 104.6 60.3 REMARK 620 7 ASP A 37 OD1 139.3 132.4 100.2 59.0 132.8 76.3 REMARK 620 8 VAL A 25 N 130.8 43.1 111.7 146.7 96.3 76.0 89.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 CA A 200 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 42 O REMARK 620 2 LEU A 62 O 64.4 REMARK 620 3 THR A 45 O 129.0 117.2 REMARK 620 4 GLU A 47 OE1 144.5 145.7 64.1 REMARK 620 5 ASP A 61 OD1 162.0 100.9 46.5 53.2 REMARK 620 6 THR A 45 OG1 71.0 130.5 76.0 83.8 117.3 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 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 CA CA A 100 OD1 ASN A 27 1555 1555 2.80 LINK CA CA A 100 O LYS A 24 1555 1555 2.34 LINK CA CA A 100 OD2 ASP A 31 1555 1555 2.36 LINK CA CA A 100 OE2 GLU A 38 1555 1555 2.15 LINK CA CA A 100 N ASN A 27 1555 1555 3.03 LINK CA CA A 100 N CYS A 26 1555 1555 2.35 LINK CA CA A 100 OD1 ASP A 37 1555 1555 2.84 LINK CA CA A 100 N VAL A 25 1555 1555 3.29 LINK CA CA A 200 O GLU A 42 1555 1555 2.69 LINK CA CA A 200 O LEU A 62 1555 1555 2.83 LINK CA CA A 200 O THR A 45 1555 1555 3.35 LINK CA CA A 200 OE1 GLU A 47 1555 1555 2.85 LINK CA CA A 200 OD1 ASP A 61 1555 1555 2.68 LINK CA CA A 200 OG1 THR A 45 1555 1555 2.82
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