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(-) Description

Title :  SOLUTION STRUCTURE OF THE TWELFTH CYSTEINE-RICH LIGAND-BINDING REPEAT IN RAT MEGALIN
 
Authors :  C. A. Wolf, F. Dancea, M. Shi, V. Bade-Noskova, H. Rueterjans, D. Kerjaschki, C. Luecke
Date :  14 Aug 06  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Low Density Lipoprotein Receptor, Cysteine-Rich Repeat, Ligand Binding Domain, Calcium Cage, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Wolf, F. Dancea, M. Shi, V. Bade-Noskova, H. Rueterjans, D. Kerjaschki, C. Luecke
Solution Structure Of The Twelfth Cysteine-Rich Ligand-Binding Repeat In Rat Megalin.
J. Biomol. Nmr V. 37 321 2007
PubMed-ID: 17245526  |  Reference-DOI: 10.1007/S10858-006-9129-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKM263
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMEG-A12
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymMEGALIN, GLYCOPROTEIN 330, GP330

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:1206 , ASP A:1209 , VAL A:1211 , ASP A:1213 , ASP A:1219 , GLU A:1220BINDING SITE FOR RESIDUE CA A 1230

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:1188 -A:1201
2A:1195 -A:1214
3A:1208 -A:1223

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I1P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I1P)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRA_2PS50068 LDL-receptor class A (LDLRA) domain profile.LRP2_RAT27-63
66-104
107-143
141-180
182-218
221-257
264-307
1024-1060
1065-1102
1109-1145
1149-1185
1187-1224
1230-1268
1271-1307
1312-1350
2700-2738
2741-2777
2780-2819
2864-2902
2822-2861
2907-2946
2949-2991
2994-3030
3033-3071
3076-3112
3513-3551
3554-3592
3595-3633
3636-3674
3679-3717
3720-3757
3760-3796
3799-3835
3843-3881
3884-3923
3929-3965
  1-
-
-
-
-
-
-
-
-
-
-
A:1187-1224
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2LDLRA_1PS01209 LDL-receptor class A (LDLRA) domain signature.LRP2_RAT40-62
80-103
120-142
195-217
234-256
1037-1059
1079-1101
1122-1144
1162-1184
1201-1223
1244-1267
1284-1306
1326-1349
2713-2737
2754-2776
2836-2860
2878-2901
2920-2945
3007-3029
3046-3070
3089-3111
3527-3550
3608-3632
3649-3673
3694-3716
3734-3756
3773-3795
3812-3834
3856-3880
3898-3922
3942-3964
  1-
-
-
-
-
-
-
-
-
A:1201-1223
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2I1P)

(-) 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:48
 aligned with LRP2_RAT | P98158 from UniProtKB/Swiss-Prot  Length:4660

    Alignment length:52
                                  1187      1197      1207      1217      1227  
            LRP2_RAT   1178 GSDEAGCVLNCTSAQFKCADGSSCINSRYRCDGVYDCRDNSDEAGCPTRPPG 1229
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains 2    i1pA00 A:1182-1229                              CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .----..........ee......eehhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LDLRA_2 -LDLRA_2  PDB: A:1187-1224             ----- PROSITE (1)
                PROSITE (2) LDLRA_1----------------LDLRA_1                ------ PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                2i1p A 1182 G----AMVLNCTSAQFKCADGSSCINSRYRCDGVYDCRDNSDEAGCPTRPPG 1229
                            |    |1187      1197      1207      1217      1227  
                            | 1183                                              
                         1182                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 2I1P)

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I1P)

(-) Gene Ontology  (38, 38)

NMR Structure(hide GO term definitions)
Chain A   (LRP2_RAT | P98158)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    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:0030492    hemoglobin binding    Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
    GO:0042562    hormone binding    Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone.
    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:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    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).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any 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.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    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:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0020028    hemoglobin import    The directed movement into a tissue, cell or organelle of externally available hemoglobin.
    GO:0046879    hormone secretion    The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
    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:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within 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:0010165    response to X-ray    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0033280    response to vitamin D    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
    GO:0045056    transcytosis    The directed movement of endocytosed material through the cell and its exocytosis from the plasma membrane at the opposite side.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LRP2_RAT | P981583v2o 3v2x

(-) Related Entries Specified in the PDB File

7263 CHEMICAL SHIFT ASSIGNMENTS OF MEG-A12