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(-) Description

Title :  CRYSTAL STRUCTURE OF BLUEFIN TUNA HEMOGLOBIN DEOXY FORM AT PH5.0
 
Authors :  T. Yokoyama, K. T. Chong, Y. Miyazaki, T. Nakatsukasa, S. Unzai, G. Miyazaki, H. Morimoto, R. H. T. Jeremy, S. Y. Park
Date :  19 Nov 03  (Deposition) - 06 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxygen Transport, Heme, Respiratory Protein, Erythrocyte, Root Effect, Swim Bladder, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Yokoyama, K. T. Chong, G. Miyazaki, H. Morimoto, D. T. Shih, S. Unzai, J. R. Tame, S. Y. Park
Novel Mechanisms Of Ph Sensitivity In Tuna Hemoglobin: A Structural Explanation Of The Root Effect
J. Biol. Chem. V. 279 28632 2004
PubMed-ID: 15117955  |  Reference-DOI: 10.1074/JBC.M401740200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOGLOBIN ALPHA CHAIN
    ChainsA, C
    Organism CommonBLUEFIN TUNA
    Organism ScientificTHUNNUS THYNNUS
    Organism Taxid8237
    TissueRED CELL
 
Molecule 2 - HEMOGLOBIN BETA CHAIN
    ChainsB, D
    Organism CommonBLUEFIN TUNA
    Organism ScientificTHUNNUS THYNNUS
    Organism Taxid8237
    TissueRED CELL

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:43 , PHE A:44 , HIS A:46 , HIS A:60 , LYS A:63 , VAL A:64 , LEU A:85 , HIS A:89 , MET A:93 , VAL A:95 , ASN A:99 , PHE A:100 , LEU A:103 , LEU A:138BINDING SITE FOR RESIDUE HEM A 144
2AC2SOFTWAREGLU A:87 , THR B:238 , TYR B:241 , TYR B:245 , HIS B:263 , LYS B:266 , VAL B:267 , LEU B:291 , HIS B:292 , LEU B:296 , ASN B:302 , PHE B:303 , LEU B:341BINDING SITE FOR RESIDUE HEM B 347
3AC3SOFTWAREMET C:433 , TYR C:443 , PHE C:444 , TRP C:447 , HIS C:460 , LYS C:463 , VAL C:464 , LEU C:485 , HIS C:489 , MET C:493 , VAL C:495 , ASN C:499 , PHE C:500 , LEU C:503 , LEU C:538BINDING SITE FOR RESIDUE HEM C 544
4AC4SOFTWARETHR D:638 , TYR D:641 , TYR D:645 , HIS D:663 , VAL D:667 , ARG D:673 , LEU D:688 , LEU D:691 , HIS D:692 , LEU D:696 , VAL D:698 , ASN D:702 , PHE D:703BINDING SITE FOR RESIDUE HEM D 747

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V4X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V4X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V4X)

(-) Exons   (0, 0)

(no "Exon" information available for 1V4X)

(-) 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:144
 aligned with Q8AYM0_THUTH | Q8AYM0 from UniProtKB/TrEMBL  Length:144

    Alignment length:144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    
         Q8AYM0_THUTH     1 MTTLSDKDKSTVKALWGKISKSADAIGADALGRMLAVYPQTKTYFSHWPDMSPGSGPVKAHGKKVMGGVALAVSKIDDLTTGLGDLSELHAFKMRVDPSNFKILSHCILVVVAKMFPKEFTPDAHVSLDKFLASVALALAERYR 144
               SCOP domains d1v4xa_ A: Hemoglobin, alpha-chain                                                                                                               SCOP domains
               CATH domains -1v4xA00 A:1-143 Globins                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v4x A   0 xTTLSDKDKSTVKALWGKISKSADAIGADALGRMLAVYPQTKTYFSHWPDMSPGSGPVKAHGKKVMGGVALAVSKIDDLTTGLGDLSELHAFKMRVDPSNFKILSHCILVVVAKMFPKEFTPDAHVSLDKFLASVALALAERYR 143
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139    
                            |                                                                                                                                               
                            0-ACE                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with Q8AYM1_THUTH | Q8AYM1 from UniProtKB/TrEMBL  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
         Q8AYM1_THUTH     2 VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLSTPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVDPDNFRILGDCLTVVIAANLGDAFTVETQCAFQKFLAVVVFALGRKYH 147
               SCOP domains d1v4xb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1v4xB00 B:201-346 Globins                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4x B 201 VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLSTPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVDPDNFRILGDCLTVVIAANLGDAFTVETQCAFQKFLAVVVFALGRKYH 346
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340      

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with Q8AYM0_THUTH | Q8AYM0 from UniProtKB/TrEMBL  Length:144

    Alignment length:144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    
         Q8AYM0_THUTH     1 MTTLSDKDKSTVKALWGKISKSADAIGADALGRMLAVYPQTKTYFSHWPDMSPGSGPVKAHGKKVMGGVALAVSKIDDLTTGLGDLSELHAFKMRVDPSNFKILSHCILVVVAKMFPKEFTPDAHVSLDKFLASVALALAERYR 144
               SCOP domains d1v4xc_ C: Hemoglobin, alpha-chain                                                                                                               SCOP domains
               CATH domains -1v4xC00 C:401-543 Globins                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v4x C 400 xTTLSDKDKSTVKALWGKISKSADAIGADALGRMLAVYPQTKTYFSHWPDMSPGSGPVKAHGKKVMGGVALAVSKIDDLTTGLGDLSELHAFKMRVDPSNFKILSHCILVVVAKMFPKEFTPDAHVSLDKFLASVALALAERYR 543
                            |      409       419       429       439       449       459       469       479       489       499       509       519       529       539    
                          400-ACE                                                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with Q8AYM1_THUTH | Q8AYM1 from UniProtKB/TrEMBL  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
         Q8AYM1_THUTH     2 VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLSTPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVDPDNFRILGDCLTVVIAANLGDAFTVETQCAFQKFLAVVVFALGRKYH 147
               SCOP domains d1v4xd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1v4xD00 D:601-746 Globins                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4x D 601 VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLSTPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVDPDNFRILGDCLTVVIAANLGDAFTVETQCAFQKFLAVVVFALGRKYH 746
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740      

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V4X)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (Q8AYM0_THUTH | Q8AYM0)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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: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: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: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:0005833    hemoglobin complex    An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B,D   (Q8AYM1_THUTH | Q8AYM1)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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: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: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: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:0005833    hemoglobin complex    An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8AYM0_THUTH | Q8AYM01v4u 1v4w
        Q8AYM1_THUTH | Q8AYM11v4u 1v4w

(-) Related Entries Specified in the PDB File

1v4u BLUEFIN TUNA CARBONMONOXY-HEMOGLOBIN AT PH7.5, AT 2.00 A
1v4w BLUEFIN TUNA HEMOGLOBIN DEOXY FORM AT PH7.5, AT 1.70 A