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Title :   CRYSTAL STRUCTURE OF HEMOGLOBIN FROM MOUSE (MUS MUSCULUS)AT 2.8

Authors :   S. S. Sundaresan, P. Ramesh, M. N. Ponnuswamy

Date :   10 Jun 09 (Deposition) - 23 Jun 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Heme, Iron, Metal-Binding, Oxygen Transport, Polymorphism, Transport, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Sundaresan, P. Ramesh, M. N. Ponnuswamy
Crystal Structure Of Hemoglobin From Mouse (Mus Musculus)At 2. 8
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
	Chains	:	A, C
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	HEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN
	Tissue	:	RED BLOOD CELLS

Molecule 2 - HEMOGLOBIN SUBUNIT BETA-1
	Chains	:	B, D
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	HEMOGLOBIN BETA-1 CHAIN, BETA-1-GLOBIN, HEMOGLOBIN BETA-MAJOR CHAIN
	Tissue	:	RED BLOOD CELLS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	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:45 , HIS A:58 , LYS A:61 , VAL A:62 , LEU A:83 , LEU A:86 , HIS A:87 , LEU A:91 , ASN A:97 , LEU A:101 , VAL A:132 , LEU A:136 , HOH A:144	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	THR B:38 , TYR B:41 , PHE B:42 , PHE B:45 , HIS B:63 , LYS B:66 , VAL B:67 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:141	BINDING SITE FOR RESIDUE HEM B 200
3	AC3	SOFTWARE	TYR C:42 , PHE C:43 , HIS C:45 , PHE C:46 , HIS C:58 , LYS C:61 , VAL C:62 , LEU C:66 , LEU C:83 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , PHE C:98 , HOH C:144 , HOH C:152	BINDING SITE FOR RESIDUE HEM C 200
4	AC4	SOFTWARE	TYR D:41 , PHE D:42 , HIS D:63 , LYS D:66 , VAL D:67 , ALA D:70 , LEU D:88 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141 , HOH D:147 , HOH D:150	BINDING SITE FOR RESIDUE HEM D 200

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

Asymmetric/Biological Unit

No.	Residues
1	Ser C:3	-	Gly C:4

Asymmetric/Biological Unit (10, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_HBB1_MOUSE_001 *	C	14	G	HBB1_MOUSE	---	---	B/D	C	13	G
02	UniProt	VAR_HBB1_MOUSE_002 *	S	21	A	HBB1_MOUSE	---	---	B/D	S	20	A
03	UniProt	VAR_HBA_MOUSE_001 *	G	26	V	HBA_MOUSE	---	---	A/C	G	25	V
04	UniProt	VAR_HBA_MOUSE_002 *	V	63	I	HBA_MOUSE	---	---	A/C	V	62	I
05	UniProt	VAR_HBA_MOUSE_003 *	S	69	N	HBA_MOUSE	---	---	A/C	S	68	N
06	UniProt	VAR_HBA_MOUSE_004 *	S	69	T	HBA_MOUSE	---	---	A/C	S	68	T
07	UniProt	VAR_HBB1_MOUSE_003 *	D	74	E	HBB1_MOUSE	---	---	B/D	D	73	E
08	UniProt	VAR_HBA_MOUSE_005 *	G	79	A	HBA_MOUSE	---	---	A/C	G	78	A
09	UniProt	VAR_HBB1_MOUSE_004 *	V	135	M	HBB1_MOUSE	---	---	B/D	V	134	M
10	UniProt	VAR_HBB1_MOUSE_005 *	T	140	A	HBB1_MOUSE	---	---	B/D	T	139	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBB1_MOUSE	2-147	2	B:1-146 D:1-146
1	GLOBIN	PS01033	Globin family profile.	HBA_MOUSE	3-142	2	A:2-141 C:2-141

(no "Exon" information available for 3HRW)

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:141
 aligned with HBA_MOUSE | P01942 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_MOUSE     2 VLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHGKKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTPAVHASLDKFLASVSTVLTSKYR 142
               SCOP domains d3hrwa_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 3hrwA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ------------------------V------------------------------------I-----N---------A--------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------T------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrw A   1 VLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHGKKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTPAVHASLDKFLASVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB1_MOUSE | P02088 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
           HBB1_MOUSE     2 VHLTDAEKAAVSCLWGKVNSDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNAKVKAHGKKVITAFNDGLNHLDSLKGTFASLSELHCDKLHVDPENFRLLGNMIVIVLGHHLGKDFTPAAQAAFQKVVAGVATALAHKYH 147
               SCOP domains d3hrwb_ B: automated matches                                                                                                                       SCOP domains
               CATH domains 3hrwB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------G------A----------------------------------------------------E------------------------------------------------------------M----A------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: B:1-146 UniProt: 2-147                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrw B   1 VHLTDAEKAAVSCLWGKVNSDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNAKVKAHGKKVITAFNDGLNHLDSLKGTFASLSELHCDKLHVDPENFRLLGNMIVIVLGHHLGKDFTPAAQAAFQKVVAGVATALAHKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA_MOUSE | P01942 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_MOUSE     2 VLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHGKKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTPAVHASLDKFLASVSTVLTSKYR 142
               SCOP domains d3hrwc_ C: automated matches                                                                                                                  SCOP domains
               CATH domains 3hrwC00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ------------------------V------------------------------------I-----N---------A--------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------T------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrw C   1 VLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHGKKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTPAVHASLDKFLASVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with HBB1_MOUSE | P02088 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
           HBB1_MOUSE     2 VHLTDAEKAAVSCLWGKVNSDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNAKVKAHGKKVITAFNDGLNHLDSLKGTFASLSELHCDKLHVDPENFRLLGNMIVIVLGHHLGKDFTPAAQAAFQKVVAGVATALAHKYH 147
               SCOP domains d3hrwd_ D: automated matches                                                                                                                       SCOP domains
               CATH domains 3hrwD00 D:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------G------A----------------------------------------------------E------------------------------------------------------------M----A------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: D:1-146 UniProt: 2-147                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrw D   1 VHLTDAEKAAVSCLWGKVNSDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNAKVKAHGKKVITAFNDGLNHLDSLKGTFASLSELHCDKLHVDPENFRLLGNMIVIVLGHHLGKDFTPAAQAAFQKVVAGVATALAHKYH 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: automated matches (99)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d3hrwa_	A:
1b	d3hrwb_	B:
1c	d3hrwc_	C:
1d	d3hrwd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Mouse (Mus musculus) (6)

1a	3hrwB00	B:1-146
1b	3hrwD00	D:1-146
1c	3hrwA00	A:1-141
1d	3hrwC00	C:1-141

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA_MOUSE | P01942)

molecular function
	GO:0031720	haptoglobin binding	Interacting selectively and non-covalently with a haptoglobin, any alpha2 globulin of blood plasma that can combine with free oxyhemoglobin to form a stable complex.
	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.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0048821	erythrocyte development	The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	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:0035634	response to stilbenoid	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 exposure to a stilbenoid. Stilbenoids are secondary products of heartwood formation in trees that can act as phytoalexins. Stilbenoids are hydroxylated derivatives of stilbene. They belong to the family of phenylpropanoids and share most of their biosynthesis pathway with chalcones.
	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:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0022627	cytosolic small ribosomal subunit	The small subunit of a ribosome located in the cytosol.
	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.
	GO:0031838	haptoglobin-hemoglobin complex	A protein complex formed by the stable binding of a haptoglobin to hemoglobin.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

Chain B,D (HBB1_MOUSE | P02088)

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:0048821	erythrocyte development	The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	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:0010999	regulation of eIF2 alpha phosphorylation by heme	Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a result of heme levels.
	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.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

Asymmetric/Biological Unit
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		Ser C:3 - Gly C:4	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3HRW)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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