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(-) Description

Title :  APOCYTOCHROME B5, PH 6.2, 298 K, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  C. J. Falzone, J. T. J. Lecomte
Date :  20 Apr 96  (Deposition) - 21 Apr 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. J. Falzone, M. R. Mayer, E. L. Whiteman, C. D. Moore, J. T. Lecomte
Design Challenges For Hemoproteins: The Solution Structure Of Apocytochrome B5.
Biochemistry V. 35 6519 1996
PubMed-ID: 8639599  |  Reference-DOI: 10.1021/BI960501Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOCYTOCHROME B5
    Cell LineBL21
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System GeneCYTB5
    Expression System PlasmidPET-3D
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    GeneCYTB5
    OrganLIVER
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IET)

(-) Sites  (0, 0)

(no "Site" information available for 1IET)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IET)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IET)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IET)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5_RAT9-85  1A:4-80
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5_RAT40-47  1A:35-42

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000204461ENSRNOE00000145553chr18:81415962-81416156195CYB5_RAT1-43431A:1-3838
1.2ENSRNOT000000204462ENSRNOE00000218963chr18:81434867-81434995129CYB5_RAT44-86431A:39-8143
1.3ENSRNOT000000204463ENSRNOE00000145848chr18:81436683-8143671230CYB5_RAT87-96101A:82-9110
1.5ENSRNOT000000204465ENSRNOE00000145949chr18:81449591-8144962535CYB5_RAT97-108121A:92-943
1.6ENSRNOT000000204466ENSRNOE00000145993chr18:81452246-81452606361CYB5_RAT108-134270--

(-) 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:94
 aligned with CYB5_RAT | P00173 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:94
                                    15        25        35        45        55        65        75        85        95    
              CYB5_RAT    6 DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELHPDDRSKIAKPSETL 99
               SCOP domains d1ieta_ A: Cytochrome b5                                                                       SCOP domains
               CATH domains 1ietA00 A:1-94 Flavocytochrome B2, subunit A, domain 1                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.......eee....eee...hhh......................................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYTOCHROME_B5_2  PDB: A:4-80 UniProt: 9-85                                   -------------- PROSITE (1)
                PROSITE (2) ----------------------------------CYTOCHRO---------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-38 UniProt: 1-43   Exon 1.2  PDB: A:39-81 UniProt: 44-86      Exon 1.3  1.5 Transcript 1
                  1iet A  1 DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELHPDDRSKIAKPSETL 94
                                    10        20        30        40        50        60        70        80        90    

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (CYB5_RAT | P00173)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    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.
    GO:0046686    response to cadmium ion    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 cadmium (Cd) ion stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYB5_RAT | P001731aqa 1aw3 1axx 1b5a 1b5b 1bfx 1blv 1i87 1i8c 1ib7 1ieu 1jex 1mny 2axx

(-) Related Entries Specified in the PDB File

1ieu