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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF BONE MORPHOGENETIC PROTEIN-6 VARIANT B2 (B2-BMP-6)

Authors :   T. D. Mueller, W. Sebald

Date :   03 Sep 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Bmp6, Vgr, Tgf-Beta Ligand, Chondrogenesis, Cleavage On Pair Of Basic Residues, Cytokine, Developmental Protein, Differentiation, Glycoprotein, Growth Factor, Osteogenesis, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Saremba, J. Nickel, A. Seher, A. Kotzsch, W. Sebald, T. D. Mueller
Type I Receptor Binding Of Bone Morphogenetic Protein 6 Is Dependent On N-Glycosylation Of The Ligand.
Febs J. V. 275 172 2007
PubMed-ID: 18070108 | Reference-DOI: 10.1111/J.1742-4658.2007.06187.X
(for further references see the PDB file header)

Molecule 1 - BONE MORPHOGENETIC PROTEIN 6
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PN25
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	BMP-6 VARIANT B2, MATURE PART
	Gene	:	BMP6, VGR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BMP-6

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:42 , LEU A:43 , PRO B:52 , HOH B:166	BINDING SITE FOR RESIDUE MPD B 1
2	AC2	SOFTWARE	TRP A:45 , ASN B:76	BINDING SITE FOR RESIDUE MPD B 2
3	AC3	SOFTWARE	ASN A:76 , ILE A:79 , MET B:124	BINDING SITE FOR RESIDUE MPD A 3

Asymmetric/Biological Unit

No.	Residues
1	A:31	-	A:97
2	A:60	-	A:129
3	A:64	-	A:131
4	A:96	-	B:96
5	B:31	-	B:97
6	B:60	-	B:129
7	B:64	-	B:131

Asymmetric/Biological Unit

No.	Residues
1	Ala A:51	-	Pro A:52
2	Phe A:66	-	Pro A:67
3	Ala B:51	-	Pro B:52
4	Phe B:66	-	Pro B:67

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036201	P	476	L	BMP6_HUMAN	Unclassified	---	A/B	P	95	L

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TGF_BETA_2	PS51362	TGF-beta family profile.	BMP6_HUMAN	394-513	2	A:28-132 B:28-132
2	TGF_BETA_1	PS00250	TGF-beta family signature.	BMP6_HUMAN	430-445	2	A:49-64 B:49-64

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000283147	1	ENSE00001009161	chr6:7727030-7727852	823	BMP6_HUMAN	1-222	222	0	-	-
1.2	ENST00000283147	2	ENSE00001083364	chr6:7845373-7845565	193	BMP6_HUMAN	222-286	65	0	-	-
1.3	ENST00000283147	3	ENSE00001154874	chr6:7861684-7861832	149	BMP6_HUMAN	286-336	51	0	-	-
1.4	ENST00000283147	4	ENSE00001083374	chr6:7862534-7862731	198	BMP6_HUMAN	336-402	67	2	A:26-27 B:26-27	2 2
1.5	ENST00000283147	5	ENSE00001154858	chr6:7879307-7879383	77	BMP6_HUMAN	402-427	26	2	A:28-46 (gaps) B:28-46 (gaps)	20 20
1.6	ENST00000283147	6	ENSE00001154849	chr6:7880224-7880334	111	BMP6_HUMAN	428-464	37	2	A:47-83 B:47-83	37 37
1.7	ENST00000283147	7	ENSE00001258022	chr6:7880427-7881655	1229	BMP6_HUMAN	465-513	49	2	A:84-132 B:84-132	49 49

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:107
 aligned with BMP6_HUMAN | P22004 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:134
                                   389       399       409       419       429       439       449       459       469       479       489       499       509    
           BMP6_HUMAN   380 RRQQSRNRSTQSQDVARVSSASDYNSSELKTACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 513
               SCOP domains d2                          r5 3a_ A: automated matches                                                                                SCOP domains
               CATH domains 2r                          53 A00 A:26-132 Cystine-knot cytokines                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------------------------..-..eee..eee.........eee..eee..eee.............hhhhhhhhhhhhhh.......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------TGF_BETA_2  PDB: A:28-132 UniProt: 394-513                                                                               PROSITE (1)
                PROSITE (2) --------------------------------------------------TGF_BETA_1      -------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4  PDB: A:26-27 -------------------------Exon 1.6  PDB: A:47-83               Exon 1.7  PDB: A:84-132 UniProt: 465-513          Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.5 UniProt: 402-427 -------------------------------------------------------------------------------------- Transcript 1 (2)
                 2r53 A  26 KR--------------------------LK-ACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 132
                             |       -         -        29 |      38        48        58        68        78        88        98       108       118       128    
                             |                         28| |                                                                                                      
                            27                          29 |                                                                                                      
                                                          30

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with BMP6_HUMAN | P22004 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:134
                                   389       399       409       419       429       439       449       459       469       479       489       499       509    
           BMP6_HUMAN   380 RRQQSRNRSTQSQDVARVSSASDYNSSELKTACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 513
               SCOP domains d2                          r5 3b_ B: automated matches                                                                                SCOP domains
               CATH domains 2r                          53 B00 B:26-132 Cystine-knot cytokines                                                                     CATH domains
           Pfam domains (1) -------------------------------TGF_beta-2r53B01 B:30-132                                                                               Pfam domains (1)
           Pfam domains (2) -------------------------------TGF_beta-2r53B02 B:30-132                                                                               Pfam domains (2)
         Sec.struct. author ..--------------------------..-..eee..eeehhhhh....eee..eee..eee.......hhhhh.hhhhhhhhhhhhhh.......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------TGF_BETA_2  PDB: B:28-132 UniProt: 394-513                                                                               PROSITE (1)
                PROSITE (2) --------------------------------------------------TGF_BETA_1      -------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4  PDB: B:26-27 -------------------------Exon 1.6  PDB: B:47-83               Exon 1.7  PDB: B:84-132 UniProt: 465-513          Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.5 UniProt: 402-427 -------------------------------------------------------------------------------------- Transcript 1 (2)
                 2r53 B  26 KR--------------------------LK-ACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH 132
                             |       -         -        29 |      38        48        58        68        78        88        98       108       118       128    
                            27                         28| |                                                                                                      
                                                        29 |                                                                                                      
                                                          30

Legend:		→ Mismatch	(orange background)
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	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: Small proteins (3458)

Fold: Cystine-knot cytokines (124)

Superfamily: Cystine-knot cytokines (124)

Family: Transforming growth factor (TGF)-beta (41)

Protein domain: automated matches (7)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d2r53a_	A:
1b	d2r53b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Cystine Knot Cytokines, subunit B (102)

Homologous Superfamily: Cystine-knot cytokines (102)

Human (Homo sapiens) (84)

1a	2r53A00	A:26-132
1b	2r53B00	B:26-132

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cystine-knot (56)

Family: TGF_beta (29)

Homo sapiens (Human) (28)

1a	TGF_beta-2r53B01	B:30-132
1b	TGF_beta-2r53B02	B:30-132

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BMP6_HUMAN | P22004)

molecular function
	GO:0070700	BMP receptor binding	Interacting selectively and non-covalently with a BMP receptor.
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0005160	transforming growth factor beta receptor binding	Interacting selectively and non-covalently with the transforming growth factor beta receptor.
biological process
	GO:0030509	BMP signaling pathway	A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0060395	SMAD protein signal transduction	The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0071773	cellular response to BMP stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
	GO:0071281	cellular response to iron ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0001958	endochondral ossification	Replacement ossification wherein bone tissue replaces cartilage.
	GO:0001654	eye development	The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	GO:0030539	male genitalia development	The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0060586	multicellular organismal iron ion homeostasis	Any process involved in the maintenance of the distribution of iron stores within tissues and organs of a multicellular organism.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
	GO:2000105	positive regulation of DNA-dependent DNA replication	Any process that activates or increases the frequency, rate or extent of DNA-dependent DNA replication.
	GO:0060391	positive regulation of SMAD protein import into nucleus	Any process that increases the rate, frequency or extent of SMAD protein import into the nucleus, i.e. the directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:0032349	positive regulation of aldosterone biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone.
	GO:2000860	positive regulation of aldosterone secretion	Any process that activates or increases the frequency, rate or extent of aldosterone secretion.
	GO:0030501	positive regulation of bone mineralization	Any process that activates or increases the frequency, rate or extent of bone mineralization.
	GO:0032332	positive regulation of chondrocyte differentiation	Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
	GO:0045603	positive regulation of endothelial cell differentiation	Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0050679	positive regulation of epithelial cell proliferation	Any process that activates or increases the rate or extent of epithelial cell proliferation.
	GO:0031666	positive regulation of lipopolysaccharide-mediated signaling pathway	Any process that activates or increases the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
	GO:0045666	positive regulation of neuron differentiation	Any process that activates or increases the frequency, rate or extent of neuron differentiation.
	GO:0045669	positive regulation of osteoblast differentiation	Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
	GO:0010862	positive regulation of pathway-restricted SMAD protein phosphorylation	Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:0050714	positive regulation of protein secretion	Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0043408	regulation of MAPK cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0014823	response to activity	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 an activity stimulus.
	GO:0051384	response to glucocorticoid	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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
	GO:0010039	response to iron ion	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 an iron ion stimulus.
	GO:0032026	response to magnesium ion	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 magnesium ion stimulus.
	GO:0032526	response to retinoic acid	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 retinoic acid stimulus.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	GO:0003323	type B pancreatic cell development	The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric/Biological Unit
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		Ala A:51 - Pro A:52	[ RasMol ]
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		Phe A:66 - Pro A:67	[ RasMol ]
		Phe B:66 - Pro B:67	[ RasMol ]

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	2r53
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	BMP6_HUMAN \| P22004
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UniProtKB/Swiss-Prot
	BMP6_HUMAN \| P22004	:	2qcw 2r52

1rew	BINARY LIGAND-RECEPTOR COMPLEX BMP-2 AND ITS TYPE I RECEPTOR BMPR-IA
2h62	TERNARY LIGAND-RECEPTOR COMPLEX OF BMP-2 BOUND TO ITS TYPE I RECEPTOR BMPR-IA AND ITS TYPE II RECEPTOR ACTR-IIB
2h64	TERNARY LIGAND-RECEPTOR COMPLEX OF A BMP-2 VARIANT BOUND TO ITS TYPE I RECEPTOR BMPR-IA AND ITS TYPE II RECEPTOR ACTR- IIB
2r52
3bmp	BMP-2 LIGAND STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (3, 3)

SS Bonds (7, 7)

Cis Peptide Bonds (4, 4)

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Exons (4, 8)

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