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(-) Description

Title :  CRYSTAL STRUCTURE OF K206E MUTANT OF N-LOBE HUMAN TRANSFERRIN
 
Authors :  H. M. Baker, D. Nurizzo, A. B. Mason, E. N. Baker
Date :  12 Dec 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  X
Keywords :  Human Transferrin, Iron Binding And Release, Dilysine Pair, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. M. Baker, D. Nurizzo, A. B. Mason, E. N. Baker
Structures Of Two Mutants That Probe The Role In Iron Release Of The Dilysine Pair In The N-Lobe Of Human Transferrin.
Acta Crystallogr. , Sect. D V. 63 408 2007
PubMed-ID: 17327678  |  Reference-DOI: 10.1107/S0907444907000182
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEROTRANSFERRIN
    ChainsX
    EngineeredYES
    Expression SystemMESOCRICETUS AURATUS
    Expression System Cell LineBHK
    Expression System CommonGOLDEN HAMSTER
    Expression System OrganKIDNEY
    Expression System PlasmidPNUT
    Expression System Taxid10036
    Expression System Vector TypePLASMID
    FragmentN-LOBE
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRANSFERRIN, SIDEROPHILIN, BETA-1-METAL-BINDING GLOBULIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2FE1Ligand/IonFE (III) ION
3K1Ligand/IonPOTASSIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP X:63 , TYR X:95 , TYR X:188 , HIS X:249 , CO3 X:600BINDING SITE FOR RESIDUE FE X 500
2AC2SOFTWAREASP X:63 , TYR X:95 , THR X:120 , ARG X:124 , SER X:125 , ALA X:126 , GLY X:127 , TYR X:188 , FE X:500BINDING SITE FOR RESIDUE CO3 X 600
3AC3SOFTWAREALA X:151 , ASN X:152 , PHE X:154 , GLN X:169BINDING SITE FOR RESIDUE K X 601

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1X:9 -X:48
2X:19 -X:39
3X:118 -X:194
4X:137 -X:331
5X:158 -X:174
6X:161 -X:179
7X:171 -X:177
8X:227 -X:241

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala X:73 -Pro X:74
2Glu X:141 -Pro X:142
3Lys X:144 -Pro X:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034569R42LTRFE_HUMANPolymorphism41298293XR23L
2UniProtVAR_029280S55RTRFE_HUMANPolymorphism8177318XS36R
3UniProtVAR_034570A76VTRFE_HUMANPolymorphism41298977XA57V
4UniProtVAR_038810D77NTRFE_HUMANDisease (ATRAF)121918681XD58N
5UniProtVAR_011997G142STRFE_HUMANPolymorphism1799830XG123S
6UniProtVAR_011998G277STRFE_HUMANPolymorphism1799899XG258S
7UniProtVAR_007544D296GTRFE_HUMANPolymorphism8177238XD277G
8UniProtVAR_007545H319RTRFE_HUMANPolymorphism41295774XH300R

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSFERRIN_LIKE_4PS51408 Transferrin-like domain profile.TRFE_HUMAN25-347
361-683
  1X:6-328
-
2TRANSFERRIN_LIKE_1PS00205 Transferrin-like domain signature 1.TRFE_HUMAN114-123  1X:95-104
3TRANSFERRIN_LIKE_2PS00206 Transferrin-like domain signature 2.TRFE_HUMAN207-223
536-551
  1X:188-204
-
4TRANSFERRIN_LIKE_3PS00207 Transferrin-like domain signature 3.TRFE_HUMAN241-271
577-607
  1X:222-252
-

(-) Exons   (0, 0)

(no "Exon" information available for 2O84)

(-) 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 X from PDB  Type:PROTEIN  Length:329
 aligned with TRFE_HUMAN | P02787 from UniProtKB/Swiss-Prot  Length:698

    Alignment length:329
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341         
           TRFE_HUMAN    22 DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTC 350
               SCOP domains d2o84x_ X: Transferrin                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2o84X01 X:3-84,X:250-331 Periplasmic binding protein-like II                      2o84X02 X:85-249 Periplasmic binding protein-like II                                                                                                                 2o84X01 X:3-84,X:250-331 Periplasmic binding protein-like II                       CATH domains
               Pfam domains ---Transferrin-2o84X01 X:6-328                                                                                                                                                                                                                                                                                                        --- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhh.....eeehhhhhhhhhh.....eeeeeeee........eeeeeeeee.....hhhhh....eee........hhhhhhhh.........hhhhhhhhhh..ee........hhhhhh.............hhhhhhhhhhhh....eeeee..hhhhh..hhhhhh.eeee.....eee.hhhhhh..eeee..eeee.....hhhhhhhhhhhhhhhhh.......................eeeeee.....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------L------------R--------------------VN----------------------------------------------------------------S--------------------------------------------------------------------------------------------------------------------------------------S------------------G----------------------R------------------------------- SAPs(SNPs)
                PROSITE (1) ---TRANSFERRIN_LIKE_4  PDB: X:6-328 UniProt: 25-347                                                                                                                                                                                                                                                                                   --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------TRANSFERRIN_LIKE_-----------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o84 X   3 DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVEHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTC 331
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322         

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (TRFE_HUMAN | P02787)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0015091    ferric iron transmembrane transporter activity    Enables the transfer of ferric iron (Fe(III) or Fe3+) ions from one side of a membrane to the other.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:1990459    transferrin receptor binding    Interacting selectively and non-covalently with the transferrin receptor.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0071281    cellular response to iron ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006826    iron ion transport    The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0033572    transferrin transport    The directed movement of transferrin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
cellular component
    GO:1990712    HFE-transferrin receptor complex    A protein complex containing at least HFE and a transferrin receptor (either TFR1/TFRC or TFR2), proposed to play a role in the sensing of transferrin-bound Fe (Fe2-Tf) on the plasma membrane to regulate hepcidin transcription.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0045178    basal part of cell    The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
    GO:0009925    basal plasma membrane    The region of the plasma membrane located at the basal end 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:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0031232    extrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its external surface, but not integrated into the hydrophobic region.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0034774    secretory granule lumen    The volume enclosed by the membrane of a secretory granule.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRFE_HUMAN | P027871a8e 1a8f 1b3e 1bp5 1btj 1d3k 1d4n 1dtg 1fqe 1fqf 1jqf 1n7w 1n7x 1n84 1oqg 1oqh 1ryo 1suv 2hau 2hav 2o7u 3fgs 3qyt 3s9l 3s9m 3s9n 3skp 3v83 3v89 3v8x 3ve1 4h0w 4x1b 4x1d 5dyh

(-) Related Entries Specified in the PDB File

1eh3 1h43 2o7u