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(-) Description

Title :  DIMERIC HORSE MYOGLOBIN
 
Authors :  S. Nagao, H. Osuka, T. Yamada, T. Uni, Y. Shomura, K. Imai, Y. Higuchi, S.
Date :  09 Dec 11  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Myoglobin, Oxygen Storage, Oxygen Binding, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nagao, H. Osuka, T. Yamada, T. Uni, Y. Shomura, K. Imai, Y. Higuchi, S. Hirota
Structural And Oxygen Binding Properties Of Dimeric Horse Myoglobin
Dalton Trans V. 41 11378 2012
PubMed-ID: 22885714  |  Reference-DOI: 10.1039/C2DT30893B

(-) Compounds

Molecule 1 - MYOGLOBIN
    Chains: A, B
    Organism Common: HORSE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2O2Ligand/IonOXYGEN ATOM

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:43 , HIS A:64 , VAL A:68 , HEM B:154BINDING SITE FOR RESIDUE O B 155
2AC2SOFTWARELEU A:89 , SER A:92 , HIS A:93 , HIS A:97 , ILE A:99 , TYR A:103 , O A:155 , HOH A:1089 , HOH A:3180 , HOH A:3190 , HOH A:3194 , HOH A:3295 , HOH A:3390 , HOH A:3534 , THR B:39 , LYS B:42 , PHE B:43 , HIS B:64 , VAL B:67 , VAL B:68 , ALA B:71BINDING SITE FOR RESIDUE HEM A 154
3AC3SOFTWARETHR A:39 , LYS A:42 , PHE A:43 , LYS A:45 , HIS A:64 , VAL A:67 , VAL A:68 , LEU B:89 , SER B:92 , HIS B:93 , HIS B:97 , ILE B:99 , TYR B:103 , O B:155 , HOH B:1036 , HOH B:1041 , HOH B:1155 , HOH B:3224 , HOH B:3415 , HOH B:3613BINDING SITE FOR RESIDUE HEM B 154
4AC4SOFTWAREHEM A:154 , HIS B:64 , VAL B:68BINDING SITE FOR RESIDUE O A 155

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VM9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.MYG_HORSE3-148
 		  2A:2-147
B:2-147

(-) Exons   (0, 0)

(no "Exon" information available for 3VM9)

(-) 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:153
 aligned with MYG_HORSE | P68082 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
            MYG_HORSE     2 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 154
               SCOP domains d3vm9a_ A: Myoglobin                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-147 UniProt: 3-148                                                                                                               ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vm9 A   1 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with MYG_HORSE | P68082 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
            MYG_HORSE     2 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 154
               SCOP domains d3vm9b_ B: Myoglobin                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:2-147 UniProt: 3-148                                                                                                               ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vm9 B   1 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VM9)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MYG_HORSE | P68082)
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.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    GO:0050873    brown fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0043353    enucleate erythrocyte differentiation    The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYG_HORSE | P68082: 1azi 1bje 1dwr 1dws 1dwt 1gjn 1hrm 1hsy 1npf 1npg 1nz2 1nz3 1nz4 1nz5 1rse 1wla 1xch 1yma 1ymb 1ymc 2frf 2fri 2frj 2frk 2in4 2nsr 2nss 2o58 2o5b 2o5l 2o5m 2o5o 2o5q 2o5s 2o5t 2v1e 2v1f 2v1g 2v1h 2v1i 2v1j 2v1k 2vlx 2vly 2vlz 2vm0 3ba2 3hc9 3hen 3heo 3hep 3lr7 3lr9 3rj6 3rjn 3v2v 3v2z 3vau 3wft 3wfu 3wi8 3wyo 4dc7 4dc8 4ns2 4twu 4twv 5azq 5azr 5cmv 5cn4 5cn5 5cn6 5cn7 5cn8 5cn9 5cnb 5cnc 5cnd 5cne 5cnf 5cng 5d5r

(-) Related Entries Specified in the PDB File

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