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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CU-ADDUCT OF HUMAN H-FERRITIN VARIANT 4HIS-DELTA C-STAR
 
Authors :  F. A. Tezcan, D. J. E. Huard
Date :  29 Feb 12  (Deposition) - 23 Jan 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (24x)
Keywords :  Four-Helix Bundle, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Huard, K. M. Kane, F. A. Tezcan
Re-Engineering Protein Interfaces Yields Copper-Inducible Ferritin Cage Assembly.
Nat. Chem. Biol. V. 9 169 2013
PubMed-ID: 23340339  |  Reference-DOI: 10.1038/NCHEMBIO.1163

(-) Compounds

Molecule 1 - FERRITIN HEAVY CHAIN
    ChainsA
    EC Number1.16.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneFTH1, FTH, FTHL6, OK/SW-CL.84, PIG15
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFERRITIN H SUBUNIT, CELL PROLIFERATION-INDUCING GENE 15 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (24x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CU4Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:56 , HIS A:60 , HIS A:63 , HIS A:67 , HOH A:391BINDING SITE FOR RESIDUE CU A 201
2AC2SOFTWAREHIS A:173 , HOH A:456 , HOH A:502BINDING SITE FOR RESIDUE CU A 202
3AC3SOFTWAREGLU A:27 , GLU A:62 , HIS A:65 , CU A:204 , HOH A:341 , HOH A:399BINDING SITE FOR RESIDUE CU A 203
4AC4SOFTWAREGLU A:62 , GLU A:107 , CU A:203 , HOH A:355 , HOH A:399BINDING SITE FOR RESIDUE CU A 204
5AC5SOFTWAREASP A:84 , GLN A:86BINDING SITE FOR RESIDUE CA A 205
6AC6SOFTWAREASP A:131 , GLU A:134 , CA A:207BINDING SITE FOR RESIDUE CA A 206
7AC7SOFTWAREASP A:131 , GLU A:134 , CA A:206 , HOH A:449BINDING SITE FOR RESIDUE CA A 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DYX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DYX)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERRITIN_LIKEPS50905 Ferritin-like diiron domain profile.FRIH_HUMAN11-160  1A:10-159
2FERRITIN_1PS00540 Ferritin iron-binding regions signature 1.FRIH_HUMAN62-80  1A:61-79
3FERRITIN_2PS00204 Ferritin iron-binding regions signature 2.FRIH_HUMAN127-147  1A:126-146
Biological Unit 1 (3, 72)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERRITIN_LIKEPS50905 Ferritin-like diiron domain profile.FRIH_HUMAN11-160  24A:10-159
2FERRITIN_1PS00540 Ferritin iron-binding regions signature 1.FRIH_HUMAN62-80  24A:61-79
3FERRITIN_2PS00204 Ferritin iron-binding regions signature 2.FRIH_HUMAN127-147  24A:126-146

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002735501aENSE00001408170chr11:61735132-61734784349FRIH_HUMAN1-38381A:5-3733
1.3bENST000002735503bENSE00001119153chr11:61732987-61732841147FRIH_HUMAN39-87491A:38-8649
1.3eENST000002735503eENSE00001119152chr11:61732584-61732459126FRIH_HUMAN88-129421A:87-12842
1.3lENST000002735503lENSE00001430448chr11:61732363-61731757607FRIH_HUMAN130-183541A:129-17648

(-) Sequences/Alignments

Asymmetric 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:172
 aligned with FRIH_HUMAN | P02794 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:172
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  
           FRIH_HUMAN     6 TSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 177
               SCOP domains d4dyxa_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----FERRITIN_LIKE  PDB: A:10-159 UniProt: 11-160                                                                                                          ----------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------FERRITIN_1         ----------------------------------------------FERRITIN_2           ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1a  PDB: A:5-37           Exon 1.3b  PDB: A:38-86 UniProt: 39-87           Exon 1.3e  PDB: A:87-128 UniProt: 88-129  Exon 1.3l  PDB: A:129-176 UniProt: 130-183       Transcript 1
                 4dyx A   5 TSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFHHQSHEEHEHAHKLMKLQNQRGGRIFLQDIQKPDEDDWESGLNAMEAALHLEKNVNQSLLELHKLATDKNDPHLADFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DYX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DYX)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (FRIH_HUMAN | P02794)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0004322    ferroxidase activity    Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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: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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006880    intracellular sequestering of iron ion    The process of binding or confining iron ions in an intracellular area such that they are separated from other components of a biological system.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0048147    negative regulation of fibroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0008043    intracellular ferritin complex    A ferritin complex located in the cell. Intracellular ferritin complexes contain 24 subunits, in a mixture of L (light) chains and H (heavy) chains.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FRIH_HUMAN | P027941fha 2cei 2chi 2cih 2clu 2cn6 2cn7 2fha 2iu2 2z6m 3ajo 3ajp 3ajq 3erz 3es3 4dyy 4dyz 4dz0 4oyn 4y08 4ykh 4zjk 5cmq 5cmr 5gn8 5gou 5jkk 5jkl 5jkm 5up7 5up8 5vtd

(-) Related Entries Specified in the PDB File

2cei 4dyy 4dyz 4dz0