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Title :   THE CRYSTAL STRUCTURE OF HEMOGLOBIN I FROM TREMATOMUS NEWNESI IN DEOXYGENATED STATE

Authors :   A. Vergara, L. Vitagliano, A. Merlino, F. Sica, K. Marino, L. Mazzarell

Date :   10 Jun 10 (Deposition) - 07 Jul 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Root Effect, Fish Hemoglobin, Antarctic Fish, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Vergara, L. Vitagliano, A. Merlino, F. Sica, K. Marino, C. Verde, G. Di Prisco, L. Mazzarella
An Order-Disorder Transition Plays A Role In Switching Off The Root Effect In Fish Hemoglobins.
J. Biol. Chem. V. 285 32568 2010
PubMed-ID: 20610398 | Reference-DOI: 10.1074/JBC.M110.143537

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA-1
	Chains	:	A, C
	Organism Common	:	DUSKY NOTOTHEN
	Organism Scientific	:	TREMATOMUS NEWNESI
	Organism Taxid	:	35730
	Synonym	:	HEMOGLOBIN ALPHA-1 CHAIN, ALPHA-1-GLOBIN

Molecule 2 - HEMOGLOBIN SUBUNIT BETA-1/2
	Chains	:	B, D
	Organism Common	:	DUSKY NOTOTHEN
	Organism Scientific	:	TREMATOMUS NEWNESI
	Organism Taxid	:	35730
	Synonym	:	HEMOGLOBIN BETA-1/2 CHAIN, BETA-1/2-GLOBIN

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , PHE A:43 , HIS A:59 , LYS A:62 , VAL A:63 , GLN A:87 , HIS A:88 , LEU A:92 , ASN A:98 , LEU A:102	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	TYR B:41 , PHE B:42 , HIS B:63 , LYS B:66 , LEU B:88 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:141	BINDING SITE FOR RESIDUE HEM B 400
3	AC3	SOFTWARE	MET C:32 , TYR C:42 , PHE C:43 , HIS C:45 , TRP C:46 , HIS C:59 , VAL C:63 , GLN C:87 , HIS C:88 , LEU C:92 , ASN C:98 , LEU C:102	BINDING SITE FOR RESIDUE HEM C 600
4	AC4	SOFTWARE	TYR D:41 , PHE D:42 , HIS D:63 , LYS D:66 , VAL D:67 , LEU D:91 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , PHE D:103 , LEU D:141 , HOH D:1094	BINDING SITE FOR RESIDUE HEM D 800

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

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

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBA1_TRENE	2-142	2	A:2-142 C:2-142
1	GLOBIN	PS01033	Globin family profile.	HBB_TRENE	4-146	2	B:4-146 D:4-146

(no "Exon" information available for 3NFE)

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:143
 aligned with HBA1_TRENE | P45718 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
           HBA1_TRENE     - -SLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d3nfea_ A: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfe A   0 xSLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        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 HBB_TRENE | P45720 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_TRENE     1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLYNAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAAVVSALGKQYH 146
               SCOP domains d3nfeb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: B:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfe B   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLYNAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAAVVSALGKQYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with HBA1_TRENE | P45718 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:143
                             1                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139   
           HBA1_TRENE     - -SLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
               SCOP domains d3nfec_ C: Hemoglobin, alpha-chain                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Globin-3nfeC01 C:6-107                                                                                ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-3nfeC02 C:6-107                                                                                ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: C:2-142 UniProt: 2-142                                                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfe C   0 xSLSDKDKAAVRALWSKIGKSSDAIGNDALSRMIVVYPQTKIYFSHWPDVTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSNFKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR 142
                            |        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 HBB_TRENE | P45720 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_TRENE     1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLYNAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAAVVSALGKQYH 146
               SCOP domains d3nfed_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Globin-3nfeD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-3nfeD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: D:4-146 UniProt: 4-146                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfe D   1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLYNAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVDPDNFKLLSDCITIVLAAKMGHAFTAETQGAFQKFLAAVVSALGKQYH 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: Hemoglobin, alpha-chain (292)

Antarctic fish (Trematomus newnesi) [TaxId: 35730] (6)

1a	d3nfea_	A:
1b	d3nfec_	C:

Protein domain: Hemoglobin, beta-chain (292)

Antarctic fish (Trematomus newnesi) [TaxId: 35730] (6)

2a	d3nfeb_	B:
2b	d3nfed_	D:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Trematomus newnesi (Dusky notothen) (4)

1a	Globin-3nfeC01	C:6-107
1b	Globin-3nfeC02	C:6-107
1c	Globin-3nfeD01	D:7-111
1d	Globin-3nfeD02	D:7-111

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA1_TRENE | P45718)

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 (HBB_TRENE | P45720)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nfe)

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	3nfe
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	HBB_TRENE \| P45720
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UniProtKB/Swiss-Prot
	HBA1_TRENE \| P45718	:	1la6 1t1n 2aa1 3d1k 3ng6
	HBB_TRENE \| P45720	:	1la6 1t1n 3d1k 3ng6

1la6	THE CRYSTAL STRUCTURE OF TREMATOMUS NEWNESI HEMOGLOBIN IN A PARTIAL HEMICHROME STATE
1t1n	CRYSTAL STRUCTURE OF CARBONMONOXY FORM OF THE HEMOGLOBIN I FROM TREMATOMUS NEWNESI
2aa1	CRYSTAL STRUCTURE OF THE CATHODIC HEMOGLOBIN ISOLATED FROM THE ANTARCTIC FISH TREMATOMUS NEWNESI
3d1k	R/T INTERMEDIATE QUATERNARY STRUCTURE OF AN ANTARCTIC FISH HEMOGLOBIN IN AN ALPHA(CO)-BETA(PENTACOORDINATE) STATE
3ng6

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (8, 16)

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