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(-) Description

Title :  SOLUTION STRUCTURE OF THE TENTH COMPLEMENT TYPE REPEAT OF HUMAN MEGALIN
 
Authors :  R. Dagil, B. Kragelund
Date :  01 Nov 12  (Deposition) - 09 Jan 13  (Release) - 19 Jun 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Complement Type Repeat, Receptor, Megalin, Ldl Receptor Family, Lrp2, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Dagil, C. O'Shea, A. Nykjar, A. M. Bonvin, B. B. Kragelund
Gentamicin Binds To The Megalin Receptor As A Competitive Inhibitor Using The Common Ligand Binding Motif Of Complement Type Repeats: Insight From The Nmr Structure Of The 10Th Complement Type Repeat Domain Alone And In Complex With Gentamicin.
J. Biol. Chem. V. 288 4424 2013
PubMed-ID: 23275343  |  Reference-DOI: 10.1074/JBC.M112.434159

(-) Compounds

Molecule 1 - LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICAC
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneLRP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLRP-2, GLYCOPROTEIN 330, GP330, MEGALIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:1126 , ASP A:1129 , ASP A:1131 , ASP A:1133 , ASP A:1139 , GLU A:1140BINDING SITE FOR RESIDUE CA A 1201

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:1109 -A:1121
2A:1116 -A:1134
3A:1128 -A:1143

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M0P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M0P)

(-) PROSITE Motifs  (2, 3)

NMR Structure (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRA_2PS50068 LDL-receptor class A (LDLRA) domain profile.LRP2_HUMAN27-63
66-104
107-143
146-180
182-218
221-257
265-308
1025-1061
1066-1102
1108-1144
1148-1184
1186-1223
1229-1267
1270-1306
1304-1349
2699-2737
2740-2776
2779-2818
2821-2860
2863-2900
2905-2944
2947-2989
2992-3028
3031-3069
3074-3110
3511-3549
3552-3590
3593-3631
3634-3672
3677-3715
3718-3755
3758-3794
3797-3833
3841-3879
3882-3921
3927-3963
  2-
-
-
-
-
-
-
-
-
A:1108-1144
A:1148-1148
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2LDLRA_1PS01209 LDL-receptor class A (LDLRA) domain signature.LRP2_HUMAN40-62
80-103
120-142
195-217
234-256
1038-1060
1079-1101
1121-1143
1161-1183
1200-1222
1243-1266
1283-1305
1325-1348
2712-2736
2753-2775
2835-2859
2876-2899
2918-2943
3005-3027
3044-3068
3087-3109
3525-3548
3606-3630
3647-3671
3692-3714
3732-3754
3771-3793
3810-3832
3854-3878
3896-3920
3940-3962
  1-
-
-
-
-
-
-
A:1121-1143
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
NMR Structure * (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRA_2PS50068 LDL-receptor class A (LDLRA) domain profile.LRP2_HUMAN27-63
66-104
107-143
146-180
182-218
221-257
265-308
1025-1061
1066-1102
1108-1144
1148-1184
1186-1223
1229-1267
1270-1306
1304-1349
2699-2737
2740-2776
2779-2818
2821-2860
2863-2900
2905-2944
2947-2989
2992-3028
3031-3069
3074-3110
3511-3549
3552-3590
3593-3631
3634-3672
3677-3715
3718-3755
3758-3794
3797-3833
3841-3879
3882-3921
3927-3963
  2-
-
-
-
-
-
-
-
-
A:1108-1144
A:1148-1148
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2LDLRA_1PS01209 LDL-receptor class A (LDLRA) domain signature.LRP2_HUMAN40-62
80-103
120-142
195-217
234-256
1038-1060
1079-1101
1121-1143
1161-1183
1200-1222
1243-1266
1283-1305
1325-1348
2712-2736
2753-2775
2835-2859
2876-2899
2918-2943
3005-3027
3044-3068
3087-3109
3525-3548
3606-3630
3647-3671
3692-3714
3732-3754
3771-3793
3810-3832
3854-3878
3896-3920
3940-3962
  1-
-
-
-
-
-
-
A:1121-1143
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2M0P)

(-) 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:46
 aligned with LRP2_HUMAN | P98164 from UniProtKB/Swiss-Prot  Length:4655

    Alignment length:46
                                  1112      1122      1132      1142      
          LRP2_HUMAN   1103 THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTET 1148
               SCOP domains d2m0pa_ A: automated matches                   SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....eee.............hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----LDLRA_2  PDB: A:1108-1144            ---L PROSITE (1)
                PROSITE (2) ------------------LDLRA_1                ----- PROSITE (2)
                 Transcript ---------------------------------------------- Transcript
                2m0p A 1103 THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTET 1148
                                  1112      1122      1132      1142      

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M0P)

(-) Gene Ontology  (36, 36)

NMR Structure(hide GO term definitions)
Chain A   (LRP2_HUMAN | P98164)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0042954    lipoprotein transporter activity    Enables the directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0035904    aorta development    The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0060976    coronary vasculature development    The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
    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:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    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:0042953    lipoprotein transport    The directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
    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:0001523    retinoid metabolic process    The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    GO:0003281    ventricular septum development    The progression of the ventricular septum over time from its formation to the mature structure.
    GO:0042359    vitamin D metabolic process    The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
    GO:0006766    vitamin metabolic process    The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
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: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:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    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:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    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

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(-) Related Entries Specified in the PDB File

2fyj NMR SOLUTION STRUCTURE OF CALCIUM-LOADED LRP DOUBLE MODULE RELATED ID: 18816 RELATED DB: BMRB
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