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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HUMAN MYOGLOBIN MUTANT K45R

Authors :   S. R. Hubbard

Date :   08 Apr 11 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

Keywords :   Heme, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. R. Hubbard, S. G. Lambright, S. G. Boxer, W. A. Hendrickson
X-Ray Crystal Structure Of A Recombinant Human Myoglobin Mutant At 2. 8 A Resolution
J. Mol. Biol. V. 20 215 1990
PubMed-ID: 2342104

Molecule 1 - MYOGLOBIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	MB
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:42 , PHE A:43 , ARG A:45 , HIS A:48 , GLU A:54 , ALA A:57 , HIS A:64 , VAL A:68 , LEU A:89 , SER A:92 , HIS A:93 , HIS A:97 , ILE A:99 , TYR A:103 , PHE A:138 , HOH A:200 , HOH A:207 , HOH A:211 , HOH A:219 , HOH A:290	BINDING SITE FOR RESIDUE HEM A 154
2	AC2	SOFTWARE	LYS A:79 , HIS A:81 , LYS A:102 , TYR A:103 , LYS A:147 , HOH A:212	BINDING SITE FOR RESIDUE SO4 A 300
3	AC3	SOFTWARE	ARG A:45 , LYS A:63 , HIS A:64 , THR A:67 , HOH A:267	BINDING SITE FOR RESIDUE SO4 A 301
4	AC4	SOFTWARE	LYS A:34 , SER A:51 , GLU A:52 , ASP A:53 , LYS A:96	BINDING SITE FOR RESIDUE SO4 A 302

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

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

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_003180	E	55	K	MYG_HUMAN	Polymorphism	145465287	A	E	54	K
2	UniProt	VAR_003181	K	134	N	MYG_HUMAN	Polymorphism	766095327	A	K	133	N
3	UniProt	VAR_003182	R	140	Q	MYG_HUMAN	Polymorphism	142225854	A	R	139	Q
4	UniProt	VAR_003183	R	140	W	MYG_HUMAN	Polymorphism	767663245	A	R	139	W

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	MYG_HUMAN	3-148	1	A:2-147

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.8b	ENST00000397328	8b	ENSE00001528218	chr22:36013555-36013409	147	MYG_HUMAN	-	0	0	-	-
1.8e	ENST00000397328	8e	ENSE00000880019	chr22:36013312-36013210	103	MYG_HUMAN	1-32	32	1	A:1-31	31
1.10b	ENST00000397328	10b	ENSE00002190375	chr22:36007153-36006931	223	MYG_HUMAN	32-106	75	1	A:31-105	75
1.11d	ENST00000397328	11d	ENSE00001106915	chr22:36003490-36002811	680	MYG_HUMAN	107-154	48	1	A:106-149	44

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:149
 aligned with MYG_HUMAN | P02144 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
            MYG_HUMAN     2 GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKEL 150
               SCOP domains d3rgka_ A: Myoglobin                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Globin-3rgkA01 A:6-112                                                                                     ------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------K------------------------------------------------------------------------------N-----Q---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------W---------- SAPs(SNPs) (2)
                    PROSITE -GLOBIN  PDB: A:2-147 UniProt: 3-148                                                                                                               -- PROSITE
           Transcript 1 (1) ------------------------------Exon 1.10b  PDB: A:31-105 UniProt: 32-106                                  Exon 1.11d  PDB: A:106-149 UniProt: 107-154  Transcript 1 (1)
           Transcript 1 (2) Exon 1.8e  PDB: A:1-31         ---------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3rgk A   1 GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDRFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKEL 149
                                    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: Myoglobin (324)

Human (Homo sapiens) [TaxId: 9606] (1)

d3rgka_

(no "CATH Domain" information available for 3RGK, only for superseded entry 2MM1 replaced by 3RGK)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Homo sapiens (Human) (107)

Globin-3rgkA01

A:6-112

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MYG_HUMAN | P02144)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0050873	brown fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
	GO:0043353	enucleate erythrocyte differentiation	The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	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:0009725	response to hormone	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 a hormone stimulus.
	GO:0042542	response to hydrogen peroxide	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 a hydrogen peroxide (H2O2) stimulus.
	GO:0001666	response to hypoxia	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 a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0031444	slow-twitch skeletal muscle fiber contraction	A process in which force is generated within slow-twitch skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The slow-twitch skeletal muscle is characterized by slow time parameters, low force development and resistance to fatigue.
	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: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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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