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(-) Description

Title :  STRUCTURE OF A CYTOCHROME B5 CORE-SWAP MUTANT
 
Authors :  S. Terzyan, S. Parthasarathy, X. C. Zhang, D. Benson
Date :  27 Sep 10  (Deposition) - 14 Sep 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  B
Keywords :  Hibrid Cytochrome B5, Heme, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Parthasarathy, S. Terzyan, X. C. Zhang, D. Benson
Structure Of A Cytochrome B5 Core-Swap Mutant
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOCHROME B5
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PLASMID
    Fragment: N-TERMINAL HEME-BINDING DOMAIN (UNP RESIDUES 8-89)
    Gene: CYB5, CYB5A, CYB5B, CYB5M, OMB5
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:19 , MET B:23 , ILE B:32 , PHE B:35 , HIS B:39 , PRO B:40 , GLY B:41 , VAL B:45 , LEU B:46 , GLN B:49 , SER B:57 , PHE B:58 , VAL B:61 , HIS B:63 , SER B:64 , ALA B:67 , LEU B:71 , HOH B:87 , HOH B:200 , HOH B:208BINDING SITE FOR RESIDUE HEM B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5_BOVIN9-85  1B:4-80
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5_BOVIN40-47  1B:35-42

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000159441ENSBTAE00000393096chr24:4050846-4051086241CYB5_BOVIN1-43431B:3-3836
1.2ENSBTAT000000159442ENSBTAE00000129704chr24:4080076-4080204129CYB5_BOVIN44-86431B:39-8143
1.3ENSBTAT000000159443ENSBTAE00000129730chr24:4082277-408230630CYB5_BOVIN87-96101B:82-843
1.4ENSBTAT000000159444ENSBTAE00000129757chr24:4086121-408615535CYB5_BOVIN97-108120--
1.5ENSBTAT000000159445ENSBTAE00000365447chr24:4088024-4088393370CYB5_BOVIN108-134270--

(-) 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 B from PDB  Type:PROTEIN  Length:82
 aligned with CYB5_BOVIN | P00171 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:82
                                    17        27        37        47        57        67        77        87  
            CYB5_BOVIN    8 AVKYYTLEEIQKHNNSKSTWLILHYKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTFIIGELHPDDR 89
               SCOP domains d3ozzb_ B: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhh..ee..eeeeee..eeee.hhhh......hhhhhhh....hhhhhhhhh.hhhhhhhhhh.eeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYTOCHROME_B5_2  PDB: B:4-80 UniProt: 9-85                                   ---- PROSITE (1)
                PROSITE (2) --------------------------------CYTOCHRO------------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:3-38 UniProt: 1-43 Exon 1.2  PDB: B:39-81 UniProt: 44-86      1.3 Transcript 1
                  3ozz B  3 AVKYYTLEEIQKHNNAKSTWMIIHYKVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKTFIIGELHPDDR 84
                                    12        22        32        42        52        62        72        82
   Legend:   → Mismatch (orange background)
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    → 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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (CYB5_BOVIN | P00171)
molecular function
    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.
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.
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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  3ozz
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  CYB5_BOVIN | P00171
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYB5_BOVIN | P00171: 1cyo 1ehb 1es1 1f03 1f04 1hko 1i5u 1j0q 1lqx 1lr6 1m20 1m2i 1m2m 1m59 1nx7 1sh4 1u9m 1u9u 4hin

(-) Related Entries Specified in the PDB File

1icc RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 TRIPLE MUTANT
1ljo STRUCTURE OF QUINTUPLE MUTANT OF THE RAT OUTER CYTOCHROME B5.
2i89 STRUCTURE OF SEPTUPLE MUTANT OF RAT OUTER MITOCHONDRIAL
3mus 2A RESOLUTION STRUCTURE OF RAT TYPE B CYTOCHROME B5