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(-) Description

Title :  STRUCTURE OF THE PARTIALLY UNLIGANDED MET STATE OF 400 KDA HEMOGLOBIN: INSIGHTS INTO LIGAND-INDUCED STRUCTURAL CHANGES OF GIANT HEMOGLOBINS
 
Authors :  N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, K. Miki
Date :  08 Jan 08  (Deposition) - 22 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (6x)
Keywords :  Hemoglobin, Polychaete, Annelida, Unliganded, Heme, Iron, Metal- Binding, Oxygen Transport, Secreted, Transport, Oxygen Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, K. Miki
Structure Of The Partially Unliganded Met State Of 400 Kda Hemoglobin: Insights Into Ligand-Induced Structural Changes Of Giant Hemoglobins
Proteins V. 73 113 2008
PubMed-ID: 18398907  |  Reference-DOI: 10.1002/PROT.22040

(-) Compounds

Molecule 1 - EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT A1
    ChainsA
    Organism CommonBEARD WORM
    Organism ScientificOLIGOBRACHIA MASHIKOI
    Organism Taxid55676
    SynonymMAJOR GLOBIN CHAIN B
 
Molecule 2 - EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT A2
    ChainsB
    Organism CommonBEARD WORM
    Organism ScientificOLIGOBRACHIA MASHIKOI
    Organism Taxid55676
    SynonymMAJOR GLOBIN CHAIN A5
 
Molecule 3 - EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT B2
    ChainsC
    Organism CommonBEARD WORM
    Organism ScientificOLIGOBRACHIA MASHIKOI
    Organism Taxid55676
    SynonymMAJOR GLOBIN CHAIN C
 
Molecule 4 - EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT B1
    ChainsD
    Organism CommonBEARD WORM
    Organism ScientificOLIGOBRACHIA MASHIKOI
    Organism Taxid55676
    SynonymMAJOR GLOBIN CHAIN D

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (6x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY1Ligand/IonOXYGEN MOLECULE
Biological Unit 1 (3, 42)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2HEM24Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY6Ligand/IonOXYGEN MOLECULE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:45 , PHE A:46 , VAL A:49 , ARG A:65 , HIS A:94 , ARG A:97 , LEU A:99 , ASN A:103 , TYR A:131 , ILE A:138 , OXY A:201 , HOH A:1102 , HOH A:1188 , HOH A:1193 , HIS D:91 , GLN D:95 , HOH D:1197BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREPHE A:32 , PHE A:46 , HIS A:62 , VAL A:66 , HEM A:200BINDING SITE FOR RESIDUE OXY A 201
3AC3SOFTWARELEU B:45 , PHE B:46 , ARG B:48 , VAL B:49 , ARG B:65 , GLY B:69 , LEU B:70 , GLN B:93 , HIS B:94 , ILE B:99 , GLY B:103 , TYR B:104 , PHE B:107 , ILE B:140 , HOH B:1027 , HOH B:1339 , HIS C:93 , GLN C:97BINDING SITE FOR RESIDUE HEM B 200
4AC4SOFTWAREGLU B:20 , GLY B:21 , THR B:22 , ASN B:23 , HOH B:1227 , ASN C:82BINDING SITE FOR RESIDUE GOL B 501
5AC5SOFTWAREARG B:89 , GLN B:93 , LEU C:49 , PHE C:50 , VAL C:53 , HIS C:66 , ARG C:69 , VAL C:70 , GLY C:73 , LEU C:74 , GLN C:97 , HIS C:98 , ARG C:101 , HIS C:108 , PHE C:109 , MET C:112 , ILE C:143 , HOH C:1125 , HOH C:1463BINDING SITE FOR RESIDUE HEM C 200
6AC6SOFTWAREARG B:122 , ASN C:82 , ASP C:83 , PRO C:84 , HOH C:1057 , HOH C:1439 , SER D:124 , ALA D:125 , HIS D:126 , HOH D:1281BINDING SITE FOR RESIDUE GOL C 502
7AC7SOFTWAREHIS A:89 , GLN A:93 , HOH A:1049 , HOH A:1193 , MET D:49 , PHE D:50 , GLN D:64 , ARG D:67 , VAL D:68 , ALA D:72 , HIS D:96 , ILE D:99 , ALA D:106 , VAL D:107 , LEU D:110 , ILE D:141 , HOH D:1009 , HOH D:1237BINDING SITE FOR RESIDUE HEM D 200

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:2 -A:130
2A:121 -C:126
3B:2 -B:132
4C:3 -D:2
5C:4 -C:135
6D:3 -D:133

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZFO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZFO)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLBA1_OLIMA22-151  1A:6-135
GLBB1_OLIMA27-154  1D:11-138
GLBB2_OLIMA34-157  1C:18-141
Biological Unit 1 (1, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.GLBA1_OLIMA22-151  6A:6-135
GLBB1_OLIMA27-154  6D:11-138
GLBB2_OLIMA34-157  6C:18-141

(-) Exons   (0, 0)

(no "Exon" information available for 2ZFO)

(-) Sequences/Alignments

Asymmetric 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:140
 aligned with GLBA1_OLIMA | Q7M419 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:140
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156
          GLBA1_OLIMA    17 VCNRLEQILVKTQWAQSYGEAENRAAFSRDLFSELFNIQGSSRALFSGVGVDDMNSAAFTAHCLRVTGALNRLISQLDQQATINADLAHLAGQHASRNLDASNFAAMGQAVMSVVPTHLDCFNQHAWGECYERIASGISG 156
               SCOP domains d2zfoa_ A: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----GLOBIN  PDB: A:6-135 UniProt: 22-151                                                                                              ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfo A   1 VCNRLEQILVKTQWAQSYGEAENRAAFSRDLFSELFNIQGSSRALFSGVGVDDMNSAAFTAHCLRVTGALNRLISQLDQQATINADLAHLAGQHASRNLDASNFAAMGQAVMSVVPTHLDCFNQHAWGECYERIASGISG 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with GLBA2_OLIMA | Q7M413 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:142
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156  
          GLBA2_OLIMA    17 DCTSLNRLLVKRQWAEAYGEGTNRELLGNRIWEDLFANMPDARGLFSRVNGNDIDSSEFQAHSLRVLGGLDMCVASLDDVPVLNALLARLNSQHDSRGIPAAGYPAFVASAISAVRATVGARSFDNDAWNSCMNQIVSGISG 158
               SCOP domains d2zfob_ B: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfo B   1 DCTSLNRLLVKRQWAEAYGEGTNRELLGNRIWEDLFANMPDARGLFSRVNGNDIDSSEFQAHSLRVLGGLDMCVASLDDVPVLNALLARLNSQHDSRGIPAAGYPAFVASAISAVRATVGARSFDNDAWNSCMNQIVSGISG 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with GLBB2_OLIMA | Q7M418 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:147
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       
          GLBB2_OLIMA    17 SSCCSSEDRANVMHNWDAAWSAAYSDRRVALAQAVFASLFSRDAAAQGLFSGVSADNPDSADFRAHCVRVVNGLDVAINMLNDPAVLNEQLAHLSAQHQARAGVAAAHFDVMAEAFAEVMPQVSSCFSSDSWNRCFARIANGISAGL 163
               SCOP domains d2zfoc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------GLOBIN  PDB: C:18-141 UniProt: 34-157                                                                                       ------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfo C   1 SSCCSSEDRANVMHNWDAAWSAAYSDRRVALAQAVFASLFSRDAAAQGLFSGVSADNPDSADFRAHCVRVVNGLDVAINMLNDPAVLNEQLAHLSAQHQARAGVAAAHFDVMAEAFAEVMPQVSSCFSSDSWNRCFARIANGISAGL 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with GLBB1_OLIMA | Q5KSB7 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:155
                                                                      57                                                                                                               
                                                                    56 |                                                                                                               
                                                          47      54 | |                             84                           113             128                 147              
                                                        46 |    53 | | |               74  75      83 |                         112 |           127 |               146 |              
                                    26        36        46 |     |54 | |    63        73|   |   80  | |   89        99       109  | |  118        |-|      137        |-|      156     
          GLBB1_OLIMA    17 ECCSRGDAEVVISEWDQVFNAAMAGSSESA-VGVAIFD-AFF-ASSGVSPSMFPGGGDSNN---PEFLAQVSR-VVSGADIAINSLTNRATCDSLLSHLNAQH-RAISGVTGAAVTHLS-QAISSVVAQVLPSAHIDAW-EYCMAYIAAGIGAGL 161
               SCOP domains d2zfod_ D: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------GLOBIN  PDB: D:11-138 UniProt: 27-154                                                                                                     ------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfo D   1 ECCSRGDAEVVISEWDQVFNAAMAGSSESAIVGVAIFDVAFFTASSGVSPSMFPGGGDSSNSNAPEFLAQVSRVIVSGADIAINSLTNRATCDSLLSHLNAQHKRAISGVTGAAVTHLSEQAISSVVAQVLPSAHIDAWGEYCMAYIAAGIGAGL 145
                                    10        20        30        38        47        57        64        73        83        93       102       112       121       131       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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZFO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZFO)

(-) Gene Ontology  (9, 36)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLBA1_OLIMA | Q7M419)
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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   (GLBA2_OLIMA | Q7M413)
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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 C   (GLBB2_OLIMA | Q7M418)
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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 D   (GLBB1_OLIMA | Q5KSB7)
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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/Swiss-Prot
        GLBA1_OLIMA | Q7M4192d2m 2d2n 2zs0 2zs1
        GLBA2_OLIMA | Q7M4132d2m 2d2n 2zs0 2zs1
        GLBB1_OLIMA | Q5KSB72d2m 2d2n 2zs0 2zs1
        GLBB2_OLIMA | Q7M4182d2m 2d2n 2zs0 2zs1

(-) Related Entries Specified in the PDB File

2d2m THE SAME PROTEIN IN THE OXY FORM
2d2n THE SAME PROTEIN, HG DERIVATIVE