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(-) Description

Title :  CRYSTAL STRUCTURE OF BLUEFIN TUNA HEMOGLOBIN DEOXY FORM AT PH7.5
 
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 :  1.70
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
    Chains: A, C
    Organism Common: BLUEFIN TUNA
    Organism Scientific: THUNNUS THYNNUS
    Organism Taxid: 8237
    Tissue: RED CELL
 
Molecule 2 - HEMOGLOBIN BETA CHAIN
    Chains: B, D
    Organism Common: BLUEFIN TUNA
    Organism Scientific: THUNNUS THYNNUS
    Organism Taxid: 8237
    Tissue: RED 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 , TRP A:47 , HIS A:60 , LYS A:63 , LEU A:85 , LEU A:88 , HIS A:89 , MET A:93 , VAL A:95 , ASN A:99 , LEU A:103 , LEU A:138 , GLN D:5 , GLN D:6BINDING SITE FOR RESIDUE HEM A 144
2AC2SOFTWARETYR B:41 , TYR B:45 , HIS B:63 , LYS B:66 , VAL B:67 , LEU B:91 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:141 , HOH B:175BINDING SITE FOR RESIDUE HEM B 147
3AC3SOFTWARETYR C:43 , PHE C:44 , HIS C:46 , TRP C:47 , HIS C:60 , LYS C:63 , VAL C:64 , LEU C:85 , HIS C:89 , MET C:93 , VAL C:95 , ASN C:99 , PHE C:100 , LEU C:103 , LEU C:138BINDING SITE FOR RESIDUE HEM C 144
4AC4SOFTWARETHR D:38 , TYR D:41 , TYR D:45 , HIS D:63 , LYS D:66 , VAL D:67 , LEU D:71 , LEU D:91 , HIS D:92 , LEU D:96 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141BINDING SITE FOR RESIDUE HEM D 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V4W)

(-) Exons   (0, 0)

(no "Exon" information available for 1V4W)

(-) 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 d1v4wa_ A: Hemoglobin, alpha-chain                                                                                                               SCOP domains
               CATH domains -1v4wA00 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
                 1v4w 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 d1v4wb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1v4wB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4w B   1 VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLSTPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVDPDNFRILGDCLTVVIAANLGDAFTVETQCAFQKFLAVVVFALGRKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


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 d1v4wc_ C: Hemoglobin, alpha-chain                                                                                                               SCOP domains
               CATH domains -1v4wC00 C:1-143 Globins                                                                                                                         CATH domains
           Pfam domains (1) -------Globin-1v4wC01 C:7-108                                                                                ----------------------------------- Pfam domains (1)
           Pfam domains (2) -------Globin-1v4wC02 C:7-108                                                                                ----------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v4w C   0 xTTLSDKDKSTVKALWGKISKSADAIGADALGRMLAVYPQTKTYFSHWPDMSPGSGPVKAHGKKVMGGVALAVSKIDDLTTGLGDLSELHAFKMRVDPSNFKILSHCILVVVAKMFPKEFTPDAHVSLDKFLASVALALAERYR 143
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139    
                            0-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 d1v4wd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1v4wD00 D:1-146 Globins                                                                                                                            CATH domains
           Pfam domains (1) ------Globin-1v4wD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-1v4wD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4w D   1 VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLSTPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVDPDNFRILGDCLTVVIAANLGDAFTVETQCAFQKFLAVVVFALGRKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) 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 | Q8AYM0: 1v4u 1v4x
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(-) Related Entries Specified in the PDB File

1v4u BLUEFIN TUNA CARBONMONOXY-HEMOGLOBIN AT PH7.5, AT 2.00 A
1v4x BLUEFIN TUNA HEMOGLOBIN DEOXY FORM AT PH5.0, AT 1.60 A