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(-) Description

Title :  SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR
 
Authors :  N. D. Kurniawan, K. Aliabadizadeh, I. M. Brereton, P. A. Kroon, R. Smith
Date :  23 Jan 01  (Deposition) - 15 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Anti-Parallel Beta Strands, Calcium Binding Sites, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. D. Kurniawan, K. Aliabadizadeh, I. M. Brereton, P. A. Kroon, R. Smith
Nmr Structure And Backbone Dynamics Of A Concatemer Of Epidermal Growth Factor Homology Modules Of The Human Low-Density Lipoprotein Receptor.
J. Mol. Biol. V. 311 341 2001
PubMed-ID: 11478865  |  Reference-DOI: 10.1006/JMBI.2001.4867
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOW DENSITY LIPOPROTEIN RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T;
PET-30A+
    Expression System StrainDH5-ALPHA;
BL21-DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEGF-AB CONCATEMER (RESIDUES 314-395)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLDL RECEPTOR
    TissueLIVER

 Structural Features

(-) Chains, Units

  
NMR Structure (30x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:2 , ASN A:3 , GLU A:4 , CYS A:5 , ASP A:18BINDING SITE FOR RESIDUE CA A 83
2AC2SOFTWAREASP A:41 , ILE A:42 , GLU A:44 , ASN A:57 , LEU A:58BINDING SITE FOR RESIDUE CA A 84

(-) SS Bonds  (6, 6)

NMR Structure
No.Residues
1A:5 -A:16
2A:12 -A:25
3A:27 -A:39
4A:45 -A:55
5A:51 -A:64
6A:66 -A:79

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HZ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (30, 30)

NMR Structure (30, 30)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_072841G314RLDLR_HUMANUnclassified (FH)72658858AG1R
02UniProtVAR_005360C318FLDLR_HUMANDisease (FH)879254739AC5F
03UniProtVAR_062376C318RLDLR_HUMANDisease (FH)879254738AC5R
04UniProtVAR_005359C318YLDLR_HUMANPolymorphism879254739AC5Y
05UniProtVAR_072842S326CLDLR_HUMANUnclassified (FH)879254747AS13C
06UniProtVAR_005361H327YLDLR_HUMANDisease (FH)747507019AH14Y
07UniProtVAR_067196C329FLDLR_HUMANDisease (FH)  ---AC16F
08UniProtVAR_005362C329YLDLR_HUMANDisease (FH)761954844AC16Y
09UniProtVAR_005363G335SLDLR_HUMANPolymorphism544453230AG22S
10UniProtVAR_005364C338SLDLR_HUMANDisease (FH)879254753AC25S
11UniProtVAR_005365D342ELDLR_HUMANUnclassified  ---AD29E
12UniProtVAR_005366D342NLDLR_HUMANUnclassified (FH)139361635AD29N
13UniProtVAR_005367G343SLDLR_HUMANUnclassified (FH)730882096AG30S
14UniProtVAR_005368R350PLDLR_HUMANDisease (FH)875989914AR37P
15UniProtVAR_072843C352RLDLR_HUMANUnclassified (FH)879254769AC39R
16UniProtVAR_005369C352YLDLR_HUMANPolymorphism193922566AC39Y
17UniProtVAR_005370D354GLDLR_HUMANPolymorphism755449669AD41G
18UniProtVAR_005371D354VLDLR_HUMANUnclassified  ---AD41V
19UniProtVAR_007984D356YLDLR_HUMANDisease (FH)  ---AD43Y
20UniProtVAR_005372E357KLDLR_HUMANPolymorphism879254781AE44K
21UniProtVAR_062377C358YLDLR_HUMANDisease (FH)875989915AC45Y
22UniProtVAR_005373C364RLDLR_HUMANPolymorphism879254787AC51R
23UniProtVAR_007985Q366RLDLR_HUMANDisease (FH)746982741AQ53R
24UniProtVAR_005374C368RLDLR_HUMANDisease (FH)  ---AC55R
25UniProtVAR_072844C368YLDLR_HUMANUnclassified (FH)768430352AC55Y
26UniProtVAR_062378N370TLDLR_HUMANDisease (FH)879254792AN57T
27UniProtVAR_072845G373DLDLR_HUMANUnclassified (FH)879254797AG60D
28UniProtVAR_005375C379RLDLR_HUMANPolymorphism879254803AC66R
29UniProtVAR_007986C379YLDLR_HUMANDisease (FH)879254804AC66Y
30UniProtVAR_024519A391TLDLR_HUMANPolymorphism11669576AA78T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 7)

NMR Structure (4, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.LDLR_HUMAN314-353
354-393
  2A:1-40
A:41-80
2ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.LDLR_HUMAN329-340
368-379
  2A:16-27
A:55-66
3EGF_2PS01186 EGF-like domain signature 2.LDLR_HUMAN338-352
377-392
  2A:25-39
A:64-79
4EGF_CAPS01187 Calcium-binding EGF-like domain signature.LDLR_HUMAN354-377  1A:41-64

(-) Exons   (0, 0)

(no "Exon" information available for 1HZ8)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:82
 aligned with LDLR_HUMAN | P01130 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:82
                                   323       333       343       353       363       373       383       393  
           LDLR_HUMAN   314 GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV 395
               SCOP domains d1hz8a1 A:1-41                           d1hz8a2 A:42-82                           SCOP domains
               CATH domains 1hz8A02 A:1-41 Laminin                   1hz8A01 A:42-80 Laminin                -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..eee......eee.....eeee..eee..............ee......ee.....eee......eee. Sec.struct. author
             SAPs(SNPs) (1) R---F-------CY-F-----S--S---ES------P-R-G-YKY-----R-R-R-T--D-----R-----------T---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----R----------Y------------N---------Y-V-------------Y----------Y---------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----Y----------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) EGF_3  PDB: A:1-40 UniProt: 314-353     EGF_3  PDB: A:41-80 UniProt: 354-393    -- PROSITE (1)
                PROSITE (2) ---------------ASX_HYDROXYL---------------------------ASX_HYDROXYL---------------- PROSITE (2)
                PROSITE (3) ------------------------EGF_2          ------------------------EGF_2           --- PROSITE (3)
                PROSITE (4) ----------------------------------------EGF_CA  PDB: A:41-64    ------------------ PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1hz8 A   1 GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAV  82
                                    10        20        30        40        50        60        70        80  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HZ8)

(-) Gene Ontology  (50, 50)

NMR Structure(hide GO term definitions)
Chain A   (LDLR_HUMAN | P01130)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0032050    clathrin heavy chain binding    Interacting selectively and non-covalently with a clathrin heavy chain.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030169    low-density lipoprotein particle binding    Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm.
    GO:0005041    low-density lipoprotein receptor activity    Combining with a low-density lipoprotein particle and delivering the low-density lipoprotein into the cell via endocytosis.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0030229    very-low-density lipoprotein particle receptor activity    Combining with a very-low-density lipoprotein particle and delivering the very-low-density lipoprotein into the cell via endocytosis.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0070508    cholesterol import    The directed movement of cholesterol into a cell or organelle.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0030301    cholesterol transport    The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0030299    intestinal cholesterol absorption    Uptake of cholesterol into the blood by absorption from the small intestine.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0042159    lipoprotein catabolic process    The chemical reactions and pathways resulting in the breakdown of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0034383    low-density lipoprotein particle clearance    The process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0015914    phospholipid transport    The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester.
    GO:0010867    positive regulation of triglyceride biosynthetic process    Any process that increases the rate, frequency, or extent of triglyceride biosynthesis. Triglyceride biosynthesis is the collection of chemical reactions and pathways resulting in the formation of triglyceride, any triester of glycerol.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:2000188    regulation of cholesterol homeostasis    Any process that modulates the frequency, rate or extent of cholesterol homeostasis.
    GO:0010899    regulation of phosphatidylcholine catabolic process    Any process that modulates the rate, frequency or extent of phosphatidylcholine catabolism. Phosphatidylcholine catabolic processes are the chemical reactions and pathways resulting in the breakdown of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:1990666    PCSK9-LDLR complex    A protein complex consisting of the serine protease PCSK9 (Proprotein convertase subtilisin/kexin-9) and a low-density lipoprotein receptor (LDLR). Interaction typically occurs through the epidermal growth factor-like repeat A (EGF-A) domain of the LDLR, and complex formation promotes degradation of the LDLR through the endosome/lysosome pathway.
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0034362    low-density lipoprotein particle    A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LDLR_HUMAN | P011301ajj 1d2j 1f5y 1f8z 1hj7 1i0u 1ijq 1ldl 1ldr 1lrx 1n7d 1xfe 2fcw 2kri 2lgp 2m7p 2mg9 2w2m 2w2n 2w2o 2w2p 2w2q 3bps 3gcw 3gcx 3m0c 3p5b 3p5c 3so6 4ne9

(-) Related Entries Specified in the PDB File

1f5y 1F5Y CONTAINS LIGAND BINDING MODULES (LB1-2) OF THE HUMAN LDL RECEPTOR
1i0u 1I0U IS THE MINIMIZED AVERAGE STRUCTURE
1lrx 1LRX CONTAINS YWTD MODULES OF THE HUMAN LDL RECEPTOR