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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTIVIN RECEPTOR
 
Authors :  J. Greenwald, W. Fischer, W. Vale, S. Choe
Date :  01 Sep 98  (Deposition) - 09 Feb 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Receptor, Serine Kinase, Ligand Binding Domain, Three-Finger Toxin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Greenwald, W. H. Fischer, W. W. Vale, S. Choe
Three-Finger Toxin Fold For The Extracellular Ligand-Bindin Domain Of The Type Ii Activin Receptor Serine Kinase.
Nat. Struct. Biol. V. 6 18 1999
PubMed-ID: 9886286  |  Reference-DOI: 10.1038/4887

(-) Compounds

Molecule 1 - PROTEIN (ACTIVIN RECEPTOR TYPE II)
    Chains: A, B
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Strain: SMD1168
    Expression System Taxid: 4922
    Fragment: LIGAND-BINDING DOMAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:13 , ASN A:24 , GLN A:25 , THR A:26 , GLY A:27 , VAL A:28 , HOH A:189 , HOH A:192 , HOH A:202 , HOH A:218BINDING SITE FOR RESIDUE NAG A 124
2AC2SOFTWAREPHE B:13 , ASN B:24 , GLN B:25 , THR B:26 , GLY B:27 , VAL B:28 , HOH B:158 , HOH B:183 , HOH B:219BINDING SITE FOR RESIDUE NAG B 124
3AC3SOFTWARETRP A:45 , ASN A:47 , GLY A:50 , ILE A:52 , TYR A:97 , HOH A:150 , HOH A:176 , HOH A:221 , HOH A:230 , TRP B:60 , LEU B:61 , ASP B:62BINDING SITE FOR RESIDUE NAG A 147
4AC4SOFTWARETRP B:45 , ASN B:47 , GLY B:50 , TYR B:82 , TYR B:97 , HOH B:181 , HOH B:192BINDING SITE FOR RESIDUE NAG B 147
5NAGAUTHORASN A:24 , ASN A:47 , ASN B:24 , ASN B:47GLYCOSYLATION SITE

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:41
2A:31 -A:59
3A:66 -A:85
4A:72 -A:84
5A:86 -A:91
6B:11 -B:41
7B:31 -B:59
8B:66 -B:85
9B:72 -B:84
10B:86 -B:91

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BTE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BTE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BTE)

(-) Exons   (0, 0)

(no "Exon" information available for 1BTE)

(-) Sequences/Alignments

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:92
 aligned with AVR2A_MOUSE | P27038 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:96
                                    35        45        55        65        75        85        95       105       115      
          AVR2A_MOUSE    26 ETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPEME 121
               SCOP domains d1btea_ A: Type II activin     receptor                                                          SCOP domains
               CATH domains 1bteA00 A:7-102 CD59                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhh....eeeee...----..eeeeeeeee..eeeeeeeeee...........eee.......eeeee....hhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1bte A   7 ETQECLFFNANWERDRTNQTGVEPCYG----RRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPEME 102
                                    16        26      |  - |      46        56        66        76        86        96      
                                                     33   38                                                                


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with AVR2A_MOUSE | P27038 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:94
                                    35        45        55        65        75        85        95       105       115    
          AVR2A_MOUSE    26 ETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPE 119
               SCOP domains d1bteb_ B: Type II activin receptor                                                            SCOP domains
               CATH domains 1bteB00 B:7-100 CD59                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhh....eeeee.........eeeeeeeee..eeeeeeeeee...........eee.......eeeee....hhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1bte B   7 ETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPE 100
                                    16        26        36        46        56        66        76        86        96
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BTE)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AVR2A_MOUSE | P27038)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0098821    BMP receptor activity    Combining with a member of the bone morphogenetic protein (BMP) family, and transmitting a signal across the plasma membrane to initiate a change in cell activity.
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0048185    activin binding    Interacting selectively and non-covalently with activin, a dimer of inhibin-beta subunits.
    GO:0017002    activin-activated receptor activity    Combining with activin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Activin is one of two gonadal glycoproteins related to transforming growth factor beta.
    GO:0015026    coreceptor activity    Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004702    signal transducer, downstream of receptor, with serine/threonine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004675    transmembrane receptor protein serine/threonine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
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:0060011    Sertoli cell proliferation    The multiplication or reproduction of Sertoli cells, resulting in the expansion of the Sertoli cell population. A Sertoli cell is a supporting cell projecting inward from the basement membrane of seminiferous tubules.
    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:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    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:0007368    determination of left/right symmetry    The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.
    GO:0048706    embryonic skeletal system development    The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
    GO:0001702    gastrulation with mouth forming second    A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
    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:0007498    mesoderm development    The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
    GO:0043084    penile erection    The hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0032927    positive regulation of activin receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of the activity of any activin receptor signaling pathway.
    GO:0030501    positive regulation of bone mineralization    Any process that activates or increases the frequency, rate or extent of bone mineralization.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte 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:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0030510    regulation of BMP signaling pathway    Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway.
    GO:0050999    regulation of nitric-oxide synthase activity    Any process that modulates the activity of the enzyme nitric-oxide synthase.
    GO:0009966    regulation of signal transduction    Any process that modulates the frequency, rate or extent of signal transduction.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
    GO:0042713    sperm ejaculation    The expulsion of seminal fluid, thick white fluid containing spermatozoa, from the male genital tract.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0007178    transmembrane receptor protein serine/threonine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0034673    inhibin-betaglycan-ActRII complex    A protein complex that consists of inhibin, type III transforming growth factor beta receptor (also known as betaglycan), and the type II activin receptor ActRII. The complex is thought to negatively regulate the activity of activin B.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AVR2A_MOUSE | P27038: 1lx5 2goo

(-) Related Entries Specified in the PDB File

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