Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HUMAN SERUM TRANSFERRIN, N-TERMINAL LOBE, EXPRESSED IN PICHIA PASTORIS
 
Authors :  M. C. Bewley, B. M. Tam, J. Grewal, S. He, S. Shewry, M. E. P. Murphy, A. B. Mason, R. C. Woodworth, E. N. Baker, R. T. A. Macgillivray
Date :  09 Dec 98  (Deposition) - 26 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron Transport, Glycoprotein, Transferrin, Pichia Pastoris, Glycosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Bewley, B. M. Tam, J. Grewal, S. He, S. Shewry, M. E. Murphy, A. B. Mason, R. C. Woodworth, E. N. Baker, R. T. Macgillivray
X-Ray Crystallography And Mass Spectroscopy Reveal That The N-Lobe Of Human Transferrin Expressed In Pichia Pastoris Is Folded Correctly But Is Glycosylated On Serine-32.
Biochemistry V. 38 2535 1999
PubMed-ID: 10029548  |  Reference-DOI: 10.1021/BI9824543
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (SERUM TRANSFERRIN)
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    FragmentN-TERMINAL LOBE
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:63 , TYR A:95 , TYR A:188 , HIS A:249 , CO3 A:401BINDING SITE FOR RESIDUE FE A 400
2AC2SOFTWAREASP A:63 , TYR A:95 , THR A:120 , ARG A:124 , SER A:125 , ALA A:126 , GLY A:127 , TYR A:188 , HIS A:249 , FE A:400BINDING SITE FOR RESIDUE CO3 A 401
3FEAUTHORASP A:63 , TYR A:95 , TYR A:188 , HIS A:249FERRIC ION BINDING SITE.

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:73 -Pro A:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034569R42LTRFE_HUMANPolymorphism41298293AR23L
2UniProtVAR_029280S55RTRFE_HUMANPolymorphism8177318AS36R
3UniProtVAR_034570A76VTRFE_HUMANPolymorphism41298977AA57V
4UniProtVAR_038810D77NTRFE_HUMANDisease (ATRAF)121918681AD58N
5UniProtVAR_011997G142STRFE_HUMANPolymorphism1799830AG123S
6UniProtVAR_011998G277STRFE_HUMANPolymorphism1799899AG258S
7UniProtVAR_007544D296GTRFE_HUMANPolymorphism8177238AD277G
8UniProtVAR_007545H319RTRFE_HUMANPolymorphism41295774AH300R

  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
  1A:6-328
-
2TRANSFERRIN_LIKE_1PS00205 Transferrin-like domain signature 1.TRFE_HUMAN114-123  1A:95-104
3TRANSFERRIN_LIKE_2PS00206 Transferrin-like domain signature 2.TRFE_HUMAN207-223
536-551
  1A:188-204
-
4TRANSFERRIN_LIKE_3PS00207 Transferrin-like domain signature 3.TRFE_HUMAN241-271
577-607
  1A:223-252
-

(-) Exons   (0, 0)

(no "Exon" information available for 1B3E)

(-) 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:330
 aligned with TRFE_HUMAN | P02787 from UniProtKB/Swiss-Prot  Length:698

    Alignment length:330
                                    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       332       342       352
           TRFE_HUMAN    23 KTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPE 352
               SCOP domains d1b3ea_ A: Transferrin                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1b3eA01 A:4-84,A:250-311 Periplasmic binding protein-like II                     1b3eA02 A:85-249 Periplasmic binding protein-like II                                                                                                                 1b3eA01 A:4-84,A:250-311 Periplasmic binding protein-like II  ---------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhh......eee.hhhhhhhh.....eeeeeeeee........eeeeeeeee......hhh.....eee.........hhhhhhhh.........hhhhhhhh...eee........hhhh...............hhhhhhhhhh.....eeeee..hhhhh...hhhhhheeee.....eee.........eeee..eeeee.....hhhhhhhhhhhhhhh........................eeeeee......hhhhh.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------L------------R--------------------VN----------------------------------------------------------------S--------------------------------------------------------------------------------------------------------------------------------------S------------------G----------------------R--------------------------------- SAPs(SNPs)
                PROSITE (1) --TRANSFERRIN_LIKE_4  PDB: A:6-328 UniProt: 25-347                                                                                                                                                                                                                                                                                   ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------TRANSFERRIN_LIKE_-----------------TRANSFERRIN_LIKE_3             --------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b3e A   4 KTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDNYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPE 333
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

   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  (0, 0)

(no "Pfam Domain" information available for 1B3E)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    FE  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:73 - Pro A:74   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1b3e
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TRFE_HUMAN | P02787
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  209300
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TRFE_HUMAN | P02787
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TRFE_HUMAN | P027871a8e 1a8f 1bp5 1btj 1d3k 1d4n 1dtg 1fqe 1fqf 1jqf 1n7w 1n7x 1n84 1oqg 1oqh 1ryo 1suv 2hau 2hav 2o7u 2o84 3fgs 3qyt 3s9l 3s9m 3s9n 3skp 3v83 3v89 3v8x 3ve1 4h0w 4x1b 4x1d 5dyh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B3E)