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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A HEMOJUVELIN-BINDING FRAGMENT OF NEOGENIN
 
Authors :  F. Yang, A. P. West Jr. , P. J. Bjorkman
Date :  06 Oct 10  (Deposition) - 17 Nov 10  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron Homeostasis, Hemojuvelin Receptor, Fniii Domain, Fibronectin Type Iii, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Yang, A. P. West, P. J. Bjorkman
Crystal Structure Of A Hemojuvelin-Binding Fragment Of Neogenin At 1. 8A.
J. Struct. Biol. V. 174 239 2011
PubMed-ID: 20971194  |  Reference-DOI: 10.1016/J.JSB.2010.10.005

(-) Compounds

Molecule 1 - NEOGENIN
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineBTI-TN-5B1-4
    Expression System PlasmidPACGP67
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentBINDING-DOMAIN, RESIDUES 853-1051
    GeneNEO1, IGDCC2, NGN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIMMUNOGLOBULIN SUPERFAMILY DCC SUBCLASS MEMBER 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3P4L)

(-) Sites  (0, 0)

(no "Site" information available for 3P4L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P4L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P4L)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.NEO1_HUMAN441-535
541-631
636-731
741-831
856-952
957-1054
  2-
-
-
-
A:856-952
A:957-1052

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003393621ENSE00002172289chr15:73344875-73345146272NEO1_HUMAN1-44440--
1.2ENST000003393622ENSE00001675359chr15:73408881-73409198318NEO1_HUMAN44-1501070--
1.3ENST000003393623ENSE00001769067chr15:73414866-73415141276NEO1_HUMAN150-242930--
1.4ENST000003393624ENSE00001670832chr15:73418758-73418911154NEO1_HUMAN242-293520--
1.5ENST000003393625ENSE00000697549chr15:73428232-73428368137NEO1_HUMAN293-339470--
1.6ENST000003393626ENSE00001210876chr15:73468744-73468898155NEO1_HUMAN339-390520--
1.7ENST000003393627ENSE00001210873chr15:73470648-73470768121NEO1_HUMAN391-431410--
1.8bENST000003393628bENSE00001210869chr15:73528688-73528847160NEO1_HUMAN431-484540--
1.9ENST000003393629ENSE00001110167chr15:73536685-73536839155NEO1_HUMAN484-536530--
1.10ENST0000033936210ENSE00000943178chr15:73541401-73541549149NEO1_HUMAN536-585500--
1.11ENST0000033936211ENSE00000943179chr15:73541924-73542062139NEO1_HUMAN586-632470--
1.12ENST0000033936212ENSE00000943180chr15:73545741-7354579050NEO1_HUMAN632-648170--
1.13ENST0000033936213ENSE00000943181chr15:73547023-73547170148NEO1_HUMAN649-698500--
1.14ENST0000033936214ENSE00000943182chr15:73551107-73551217111NEO1_HUMAN698-735380--
1.15ENST0000033936215ENSE00000943183chr15:73552612-73552806195NEO1_HUMAN735-800660--
1.16ENST0000033936216ENSE00000943184chr15:73558657-7355875296NEO1_HUMAN800-832330--
1.17aENST0000033936217aENSE00001164418chr15:73562351-73562574224NEO1_HUMAN832-906751A:852-906 (gaps)55
1.18ENST0000033936218ENSE00001164373chr15:73562657-73562795139NEO1_HUMAN907-953471A:907-95347
1.19ENST0000033936219ENSE00001110147chr15:73564796-73564903108NEO1_HUMAN953-989371A:953-98937
1.20ENST0000033936220ENSE00001322047chr15:73566152-73566346195NEO1_HUMAN989-1054661A:989-105264
1.21ENST0000033936221ENSE00001210834chr15:73567033-7356706533NEO1_HUMAN1054-1065120--
1.22ENST0000033936222ENSE00001210830chr15:73570472-7357054069NEO1_HUMAN1065-1088240--
1.23ENST0000033936223ENSE00000885623chr15:73575305-73575452148NEO1_HUMAN1088-1137500--
1.24ENST0000033936224ENSE00001319812chr15:73580654-73580892239NEO1_HUMAN1137-1217810--
1.25ENST0000033936225ENSE00000373859chr15:73581487-7358157993NEO1_HUMAN1217-1248320--
1.27ENST0000033936227ENSE00000697751chr15:73590689-73590952264NEO1_HUMAN1248-1336890--
1.28ENST0000033936228ENSE00000697755chr15:73593662-73593798137NEO1_HUMAN1336-1381460--
1.29aENST0000033936229aENSE00001389723chr15:73594954-735975432590NEO1_HUMAN1382-1408270--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:198
 aligned with NEO1_HUMAN | Q92859 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:201
                                   861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051 
          NEO1_HUMAN    852 TPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGTTFELVPTSPPKDVTVVSKEGKPKTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTP 1052
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.....eeeeee..............eeeeeeee..---...eeeee...eeee.......eeeeeeeeee..ee......eeee..........eeeeeeee..eeeeeeeeee..........eeeeeee.....hhhhheeeeee....eeee.......eeeeeeeeee..ee......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----FN3  PDB: A:856-952 UniProt: 856-952                                                             ----FN3  PDB: A:957-1052 UniProt: 957-1054                                                           PROSITE
           Transcript 1 (1) Exon 1.17a  PDB: A:852-906 (gaps) UniProt: 832-906     Exon 1.18  PDB: A:907-953 UniProt: 907-953     -----------------------------------Exon 1.20  PDB: A:989-1052 UniProt: 989-1054 [INCOMPLETE]        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------Exon 1.19  PDB: A:953-989            --------------------------------------------------------------- Transcript 1 (2)
                3p4l A  852 LPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNI---TKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGTTFELVPTSPPKDVTVVSKEGKPKTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTP 1052
                                   861       871       881       891       | - |     911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051 
                                                                         899 903                                                                                                                                                     

   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 3P4L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P4L)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEO1_HUMAN | Q92859)
molecular function
    GO:0039706    co-receptor binding    Interacting selectively and non-covalently with a coreceptor. A coreceptor acts in cooperation with a primary receptor to transmit a signal within the cell.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0030513    positive regulation of BMP signaling pathway    Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0098797    plasma membrane protein complex    Any protein complex that is part of the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEO1_HUMAN | Q928591x5f 1x5g 1x5h 1x5i 1x5j 1x5k

(-) Related Entries Specified in the PDB File

1x5j THE SOLUTION STRUCTURE OF THE FIFTH FIBRONECTIN TYPE III DOMAIN OF HUMAN NEOGENIN
1x5k THE SOLUTION STRUCTURE OF THE SIXTH FIBRONECTIN TYPE III DOMAIN OF HUMAN NEOGENIN