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(-) Description

Title :  STRUCTURE OF HUMAN TYPE B CYTOCHROME B5
 
Authors :  S. Terzyan, C. Zhang, M. Rivera, D. B. Benson
Date :  09 Jun 10  (Deposition) - 25 May 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytochrome B5, Heme, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Parthasarathy, A. Altuve, S. Terzyan, X. Zhang, K. Kuczera, M. Rivera, D. R. Benson
Accommodating A Non-Conservative Internal Mutation By Water-Mediated Hydrogen-Bonding Between Beta-Sheet Strands: A Comparison Of Human And Rat Type B (Mitochondrial) Cytochrome B5
Biochemistry V. 50 5544 2011
PubMed-ID: 21574570  |  Reference-DOI: 10.1021/BI2004729

(-) Compounds

Molecule 1 - CYTOCHROME B5 TYPE B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL HEME-BINDING DOMAIN (UNP RESIDUES 12-103)
    Gene: CYB5B, CYB5M, OMB5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:28 , VAL 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 , MET B:70 , LEU B:71 , TYR B:74 , HOH B:100 , HOH B:126 , HOH B:142 , HOH B:150 , HOH B:216 , HOH B:218 , HOH B:262 , HOH B:288BINDING SITE FOR RESIDUE HEM B 201
2AC2SOFTWAREHOH B:88 , HOH B:90 , HOH B:91 , HOH B:93 , HOH B:95BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWARELYS A:19 , ASP A:60 , ARG B:28 , LYS B:72 , TYR B:75 , HOH B:141 , HOH B:157 , HOH B:204BINDING SITE FOR RESIDUE SO4 B 302
4AC4SOFTWAREILE A:25 , VAL A:32 , PHE A:35 , HIS A:39 , PRO A:40 , GLY A:41 , VAL A:45 , LEU A:46 , SER A:57 , PHE A:58 , VAL A:61 , HIS A:63 , SER A:64 , ALA A:67 , LEU A:71 , TYR A:74 , HOH A:129 , HOH A:175 , HOH A:205 , HOH A:294 , HIS B:26BINDING SITE FOR RESIDUE HEM A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_B5_2PS50255 Cytochrome b5 family, heme-binding domain profile.CYB5B_HUMAN20-96
 		  2A:4-80
B:4-80
2CYTOCHROME_B5_1PS00191 Cytochrome b5 family, heme-binding domain signature.CYB5B_HUMAN51-58
 		  2A:35-42
B:35-42

(-) Exons   (0, 0)

(no "Exon" information available for 3NER)

(-) 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:90
 aligned with CYB5B_HUMAN | O43169 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:90
                                    22        32        42        52        62        72        82        92       102
          CYB5B_HUMAN    13 GQEVETSVTYYRLEEVAKRNSLKELWLVIHGRVYDVTRFLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAREMLKQYYIGDIHPSDLKP 102
               SCOP domains d3nera_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eehhhhhh..ee..eeeeee..eeee.hhhh......hhhhhh.....hhhhhhhh..hhhhhhhhh..eeeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------CYTOCHROME_B5_2  PDB: A:4-80 UniProt: 20-96                                  ------ PROSITE (1)
                PROSITE (2) --------------------------------------CYTOCHRO-------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3ner A  -3 GQEVETSVTYYRLEEVAKRNSLKELWLVIHGRVYDVTRFLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAREMLKQYYIGDIHPSDLKP  86
                                     6        16        26        36        46        56        66        76        86


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with CYB5B_HUMAN | O43169 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:91
                                    21        31        41        51        61        71        81        91       101 
          CYB5B_HUMAN    12 KGQEVETSVTYYRLEEVAKRNSLKELWLVIHGRVYDVTRFLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAREMLKQYYIGDIHPSDLKP 102
               SCOP domains d3nerb_ B: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Cyt-b5-3nerB01 B:6-80                                                      ------ Pfam domains (1)
           Pfam domains (2) ----------Cyt-b5-3nerB02 B:6-80                                                      ------ Pfam domains (2)
         Sec.struct. author ..........eehhhhhhh.ee..eeeeee..eeee.hhhh......hhhhhh.....hhhhhhhhh.hhhhhhhhh..eeeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------CYTOCHROME_B5_2  PDB: B:4-80 UniProt: 20-96                                  ------ PROSITE (1)
                PROSITE (2) ---------------------------------------CYTOCHRO-------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3ner B  -4 KGQEVETSVTYYRLEEVAKRNSLKELWLVIHGRVYDVTRFLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAREMLKQYYIGDIHPSDLKP  86
                                     5        15        25        35        45        55        65        75        85
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Cyt-b5] (29)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CYB5B_HUMAN | O43169)
molecular function
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1icc RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 TRIPLE MUTANT
2i89 STRUCTURE OF SEPTUPLE MUTANT OF RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
3mus STRUCTURE OF RAT TYPE B CYTOCHROME B5