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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF HUMAN ACTIVIN A

Authors :   A. E. Harrington, S. A. Morris-Triggs, B. T. Ruotolo, C. V. Robinson, S. M. Hyvonen

Date :   22 Aug 05 (Deposition) - 07 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Homodimer, Cystine Knot, Disulfide Linked, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. E. Harrington, S. A. Morris-Triggs, B. T. Ruotolo, C. V. Robinson, S. Ohnuma, M. Hyvonen
Structural Basis For The Inhibition Of Activin Signalling B Follistatin
Embo J. V. 25 1035 2006
PubMed-ID: 16482217 | Reference-DOI: 10.1038/SJ.EMBOJ.7601000

Molecule 1 - INHIBIN BETA A CHAIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PBAT4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	INHBA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACTIVIN BETA-A CHAIN, ERYTHROID DIFFERENTIATION PROTEIN, EDF

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	1PG	1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:14 , GLN A:15 , HIS A:65 , ARG A:69 , TRP B:25 , HOH B:124	BINDING SITE FOR RESIDUE SO4 A 117
2	AC2	SOFTWARE	GLY A:1 , LYS A:21 , SER A:33 , GLY A:53 , SER A:54 , HOH A:159	BINDING SITE FOR RESIDUE SO4 A 118
3	AC3	SOFTWARE	LYS A:7 , ALA A:31 , PRO A:32 , SER A:90 , MET A:91 , SO4 A:120 , HOH A:136	BINDING SITE FOR RESIDUE SO4 A 119
4	AC4	SOFTWARE	ASN A:9 , SER A:90 , LYS A:102 , SO4 A:119 , HOH A:127	BINDING SITE FOR RESIDUE SO4 A 120
5	AC5	SOFTWARE	PHE A:16 , PHE A:17 , THR A:61 , HOH B:133	BINDING SITE FOR RESIDUE 1PG B 117
6	AC6	SOFTWARE	GLY A:1 , LEU A:2 , ILE A:10 , CYS A:11 , ILE A:48 , THR A:51 , GLY A:53 , CYS A:113 , HOH A:125	BINDING SITE FOR RESIDUE GOL A 121
7	AC7	SOFTWARE	PRO A:45 , SER A:46	BINDING SITE FOR RESIDUE GOL A 122
8	AC8	SOFTWARE	GLY A:50 , THR A:51 , SER A:57 , SER A:60 , THR A:84 , CYS A:115	BINDING SITE FOR RESIDUE GOL A 123

Asymmetric/Biological Unit

No.	Residues
1	A:4	-	A:12
2	A:11	-	A:81
3	A:40	-	A:113
4	A:44	-	A:115
5	A:80	-	B:80
6	B:4	-	B:12
7	B:11	-	B:81
8	B:40	-	B:113
9	B:44	-	B:115

Asymmetric/Biological Unit

No.	Residues
1	Ala A:31	-	Pro A:32
2	Ser A:72	-	Pro A:73
3	Ala B:31	-	Pro B:32

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_072641	N	386	S	INHBA_HUMAN	Unclassified	---	A/B	N	76	S

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TGF_BETA_1	PS00250	TGF-beta family signature.	INHBA_HUMAN	339-354	2	A:29-44 B:29-44

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000242208	1	ENSE00001410976	chr7:41742706-41742603	104	INHBA_HUMAN	-	0	0	-	-
1.2b	ENST00000242208	2b	ENSE00001410336	chr7:41740115-41739585	531	INHBA_HUMAN	1-130	130	0	-	-
1.4c	ENST00000242208	4c	ENSE00001887422	chr7:41730140-41724712	5429	INHBA_HUMAN	130-426	297	2	A:1-116 B:1-116 (gaps)	116 116

Asymmetric/Biological Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:116
 aligned with INHBA_HUMAN | P08476 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:116
                                   320       330       340       350       360       370       380       390       400       410       420      
          INHBA_HUMAN   311 GLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPSHIAGTSGSSLSFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS 426
               SCOP domains d2arva_ A: Activin A (Inhibin beta A)                                                                                SCOP domains
               CATH domains 2arvA00 A:1-116 Cystine-knot cytokines                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eee.........eee..eee..eee...hhhhh.ee..eehhhhhhhhhhhhh...........eeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------S---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------TGF_BETA_1      ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4c  PDB: A:1-116 UniProt: 130-426 [INCOMPLETE]                                                                Transcript 1
                 2arv A   1 GLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPSHIAGTSGSSLSFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS 116
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with INHBA_HUMAN | P08476 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:116
                                   320       330       340       350       360       370       380       390       400       410       420      
          INHBA_HUMAN   311 GLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPSHIAGTSGSSLSFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS 426
               SCOP domains d2arvb_ B: Activin A (Inhibin beta A)                                                                                SCOP domains
               CATH domains 2arvB00 B:1-116 Cystine-knot cytokines                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........eee..eee.........eee..eee..eee.....----------hhhhhhhhhhhhh...........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------S---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------TGF_BETA_1      ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4c  PDB: B:1-116 (gaps) UniProt: 130-426 [INCOMPLETE]                                                         Transcript 1
                 2arv B   1 GLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPS----------SFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS 116
                                    10        20        30        40     |   -      | 60        70        80        90       100       110      
                                                                        46         57

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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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Small proteins (3458)

Fold: Cystine-knot cytokines (124)

Superfamily: Cystine-knot cytokines (124)

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

Protein domain: Activin A (Inhibin beta A) (8)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d2arva_	A:
1b	d2arvb_	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	2arvB00	B:1-116
1b	2arvA00	A:1-116

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (INHBA_HUMAN | P08476)

molecular function
	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:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0034711	inhibin binding	Interacting selectively and non-covalently with an inhibin monomer, any of the polypeptides that combine to form activin and inhibin dimers.
	GO:0017046	peptide hormone binding	Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0005160	transforming growth factor beta receptor binding	Interacting selectively and non-covalently with the transforming growth factor beta receptor.
	GO:0070699	type II activin receptor binding	Interacting selectively and non-covalently with a type II activin receptor.
biological process
	GO:0000082	G1/S transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
	GO:0097154	GABAergic neuron differentiation	The process in which a neuroblast acquires the specialized structural and functional features of a GABAergic neuron.
	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:0032924	activin receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0048468	cell development	The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
	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:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0071397	cellular response to cholesterol	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 cholesterol stimulus.
	GO:0071372	cellular response to follicle-stimulating hormone 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 follicle-stimulating hormone stimulus.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0030218	erythrocyte differentiation	The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
	GO:0097191	extrinsic apoptotic signaling pathway	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
	GO:0061029	eyelid development in camera-type eye	The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0001942	hair follicle development	The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
	GO:0002244	hematopoietic progenitor cell differentiation	The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
	GO:0042541	hemoglobin biosynthetic process	The chemical reactions and pathways resulting in the formation of hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
	GO:0008584	male gonad development	The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
	GO:0001707	mesoderm formation	The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
	GO:0048333	mesodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.
	GO:0045578	negative regulation of B cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation.
	GO:0045786	negative regulation of cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0046882	negative regulation of follicle-stimulating hormone secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of follicle-stimulating hormone.
	GO:0045077	negative regulation of interferon-gamma biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
	GO:0045650	negative regulation of macrophage differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation.
	GO:0042326	negative regulation of phosphorylation	Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0042476	odontogenesis	The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
	GO:0001541	ovarian follicle development	The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
	GO:0060021	palate development	The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
	GO:0032270	positive regulation of cellular protein metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
	GO:0045648	positive regulation of erythrocyte differentiation	Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
	GO:2001241	positive regulation of extrinsic apoptotic signaling pathway in absence of ligand	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
	GO:0046881	positive regulation of follicle-stimulating hormone secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of follicle-stimulating hormone.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0060279	positive regulation of ovulation	Any process that activates or increases the frequency, rate or extent of ovulation, the release of a mature ovum/oocyte from an ovary.
	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: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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042701	progesterone secretion	The regulated release of progesterone, a steroid hormone, by the corpus luteum of the ovary and by the placenta.
	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:0046880	regulation of follicle-stimulating hormone secretion	Any process that modulates the frequency, rate or extent of the regulated release of follicle-stimulating hormone.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0021773	striatal medium spiny neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a medium spiny neuron residing in the striatum.
cellular component
	GO:0043509	activin A complex	A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A).
	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.
	GO:0043512	inhibin A complex	Heterodimeric hormone composed of an inhibin alpha subunit complexed with an inhibin beta-A subunit.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:31 - Pro A:32	[ RasMol ]
		Ala B:31 - Pro B:32	[ RasMol ]
		Ser A:72 - Pro A:73	[ RasMol ]

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	2arv
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	INHBA_HUMAN \| P08476
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	INHBA_HUMAN \| P08476	:	1nys 1nyu 1s4y 2arp 2b0u 2p6a 3b4v 4mid 5hly 5hlz

2arp	COMPLEX OF ACTIVIN A WITH FOLLISTATIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (9, 9)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (1, 2)

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SCOP Domains (1, 2)

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Gene Ontology (66, 66)

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