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(-) Description

Title :  STRUCTURE OF THE W148R MUTANT OF HUMAN FILAMIN B ACTIN BINDING DOMAIN AT 1.95 ANGSTROM RESOLUTION
 
Authors :  G. M. Sawyer, A. R. Clark, S. P. Robertson, A. J. Sutherland-Smith
Date :  03 Feb 09  (Deposition) - 23 Jun 09  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Disease Mutation, Skeletal Dysplasia, Structural Protein, Actin- Crosslinking, Myogenesis, Cytoskeleton, Actin-Binding, Calponin Homology Domain, Phosphoprotein, Differentiation, Atelosteogenesis, Mutant, Filamin, Dwarfism, Ch Domain, Developmental Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. M. Sawyer, A. R. Clark, S. P. Robertson, A. J. Sutherland-Smith
Disease-Associated Substitutions In The Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity In Th Absence Of Major Structural Disturbance: Insights From The Crystal Structures Of Filamin B Actin Binding Domains.
J. Mol. Biol. V. 390 1030 2009
PubMed-ID: 19505475  |  Reference-DOI: 10.1016/J.JMB.2009.06.009

(-) Compounds

Molecule 1 - FILAMIN-B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEXHTB-FLNB-ABDW148R
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPPROEX HTB
    FragmentACTIN-BINDING DOMAIN, RESIDUES 2-242
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-FILAMIN, ACTIN-BINDING-LIKE PROTEIN, THYROID AUTOANTIGEN, TRUNCATED ACTIN-BINDING PROTEIN, ABP-280 HOMOLOG, ABP- 278, FILAMIN 3, FILAMIN HOMOLOG 1, FLN-B, TRUNCATED ABP, FH1, W148R MUTANT FILAMIN B ACTIN-BINDING DOMAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CO32Ligand/IonCARBONATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:206 , HOH A:2017BINDING SITE FOR RESIDUE CO3 A 1240
2AC2SOFTWAREASN A:34 , LEU A:156 , ASP A:167 , LYS A:169 , HOH A:2113BINDING SITE FOR RESIDUE CO3 A 1241

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WA6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WA6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033069F161CFLNB_HUMANDisease (LRS)80356506AF161C
2UniProtVAR_033070G168SFLNB_HUMANDisease (LRS)80356504AG168S
3UniProtVAR_033071L171RFLNB_HUMANDisease (BOOMD)80356494AL171R
4UniProtVAR_033072A173VFLNB_HUMANDisease (AO1)28937586AA173V
5UniProtVAR_033073S188PFLNB_HUMANDisease (AO1)  ---AS188P
6UniProtVAR_033074M202VFLNB_HUMANDisease (AO3)28939707AM202V
7UniProtVAR_033075E227KFLNB_HUMANDisease (LRS)80356508AE227K
8UniProtVAR_033076L234VFLNB_HUMANDisease (LRS)80356507AL234V
9UniProtVAR_033077S235PFLNB_HUMANDisease (BOOMD)121908896AS235P

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

(-) PROSITE Motifs  (3, 4)

Asymmetric/Biological Unit (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.FLNB_HUMAN16-122
139-239
  2A:16-122
A:139-239
2ACTININ_1PS00019 Actinin-type actin-binding domain signature 1.FLNB_HUMAN18-27  1A:18-27
3ACTININ_2PS00020 Actinin-type actin-binding domain signature 2.FLNB_HUMAN94-118  1A:94-118

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002959561ENSE00001415463chr3:57994127-57994583457FLNB_HUMAN1-98981A:8-9891
1.2ENST000002959562ENSE00001298400chr3:58062773-58063021249FLNB_HUMAN98-181841A:98-181 (gaps)84
1.4ENST000002959564ENSE00001315475chr3:58064444-5806454198FLNB_HUMAN181-213331A:181-21333
1.5ENST000002959565ENSE00001299267chr3:58067356-58067503148FLNB_HUMAN214-263501A:214-23926
1.6ENST000002959566ENSE00001661279chr3:58080563-58080681119FLNB_HUMAN263-302400--
1.7ENST000002959567ENSE00001295579chr3:58081868-5808194578FLNB_HUMAN303-328260--
1.8ENST000002959568ENSE00001312484chr3:58083542-58083704163FLNB_HUMAN329-383550--
1.9ENST000002959569ENSE00001316025chr3:58084438-58084635198FLNB_HUMAN383-449670--
1.10ENST0000029595610ENSE00001295364chr3:58087930-58088067138FLNB_HUMAN449-495470--
1.11ENST0000029595611ENSE00001180356chr3:58089686-58089812127FLNB_HUMAN495-537430--
1.12ENST0000029595612ENSE00001296552chr3:58090807-58090943137FLNB_HUMAN537-583470--
1.13ENST0000029595613ENSE00001313345chr3:58092407-58092600194FLNB_HUMAN583-647650--
1.14ENST0000029595614ENSE00001180347chr3:58094185-58094298114FLNB_HUMAN648-685380--
1.15ENST0000029595615ENSE00001180346chr3:58094906-58095049144FLNB_HUMAN686-733480--
1.16ENST0000029595616ENSE00001180344chr3:58095303-58095426124FLNB_HUMAN734-775420--
1.17ENST0000029595617ENSE00001180363chr3:58095737-58095897161FLNB_HUMAN775-828540--
1.18ENST0000029595618ENSE00001212915chr3:58097518-5809760891FLNB_HUMAN829-859310--
1.19ENST0000029595619ENSE00001212911chr3:58097876-58098045170FLNB_HUMAN859-915570--
1.20ENST0000029595620ENSE00001180403chr3:58104599-58104716118FLNB_HUMAN916-955400--
1.21ENST0000029595621ENSE00001077282chr3:58106968-58107230263FLNB_HUMAN955-1042880--
1.22ENST0000029595622ENSE00001077198chr3:58108820-58109417598FLNB_HUMAN1043-12422000--
1.23ENST0000029595623ENSE00001180390chr3:58110059-58110232174FLNB_HUMAN1242-1300590--
1.24ENST0000029595624ENSE00001077200chr3:58111308-58111470163FLNB_HUMAN1300-1354550--
1.25ENST0000029595625ENSE00000861937chr3:58112329-58112489161FLNB_HUMAN1354-1408550--
1.26ENST0000029595626ENSE00001328202chr3:58116468-58116635168FLNB_HUMAN1408-1464570--
1.28bENST0000029595628bENSE00001306228chr3:58118535-58118658124FLNB_HUMAN1464-1505420--
1.29ENST0000029595629ENSE00000861956chr3:58120343-58120499157FLNB_HUMAN1505-1557530--
1.30ENST0000029595630ENSE00001306477chr3:58121706-58121895190FLNB_HUMAN1558-1621640--
1.31ENST0000029595631ENSE00001077270chr3:58124009-58124256248FLNB_HUMAN1621-1703830--
1.32bENST0000029595632bENSE00001302065chr3:58127585-5812765672FLNB_HUMAN1704-1727240--
1.33ENST0000029595633ENSE00001077215chr3:58128377-58128479103FLNB_HUMAN1728-1762350--
1.34ENST0000029595634ENSE00000861939chr3:58129200-58129340141FLNB_HUMAN1762-1809480--
1.35ENST0000029595635ENSE00001321882chr3:58131648-58131776129FLNB_HUMAN1809-1852440--
1.36bENST0000029595636bENSE00001794478chr3:58132547-58132720174FLNB_HUMAN1852-1910590--
1.37ENST0000029595637ENSE00001077251chr3:58133933-58134091159FLNB_HUMAN1910-1963540--
1.38ENST0000029595638ENSE00001077284chr3:58134376-58134579204FLNB_HUMAN1963-2031690--
1.39bENST0000029595639bENSE00001299342chr3:58135577-58135729153FLNB_HUMAN2031-2082520--
1.40aENST0000029595640aENSE00001077210chr3:58135832-58135954123FLNB_HUMAN2082-2123420--
1.42bENST0000029595642bENSE00002184457chr3:58139102-58139368267FLNB_HUMAN2123-2212900--
1.43bENST0000029595643bENSE00001690887chr3:58140518-58140655138FLNB_HUMAN2212-2258470--
1.44aENST0000029595644aENSE00001770288chr3:58141687-58141802116FLNB_HUMAN2258-2296390--
1.45aENST0000029595645aENSE00001794279chr3:58145281-58145413133FLNB_HUMAN2297-2341450--
1.46aENST0000029595646aENSE00001646117chr3:58148881-58149057177FLNB_HUMAN2341-2400600--
1.48aENST0000029595648aENSE00001767941chr3:58154167-58154385219FLNB_HUMAN2400-2473740--
1.48cENST0000029595648cENSE00001616994chr3:58155317-58155520204FLNB_HUMAN2473-2541690--
1.49dENST0000029595649dENSE00001627815chr3:58156302-581579781677FLNB_HUMAN2541-2602620--

(-) 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:227
 aligned with FLNB_HUMAN | O75369 from UniProtKB/Swiss-Prot  Length:2602

    Alignment length:232
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  
           FLNB_HUMAN     8 LAEDAPWKKIQQNTFTRWCNEHLKCVNKRIGNLQTDLSDGLRLIALLEVLSQKRMYRKYHQRPTFRQMQLENVSVALEFLDRESIKLVSIDSKAIVDGNLKLILGLVWTLILHYSISMPVWEDEGDDDAKKQTPKQRLLGWIQNKIPYLPITNFNQNWQDGKALGALVDSCAPGLCPDWESWDPQKPVDNAREAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK 239
               SCOP domains d2wa6a1 A:8-124 automated matches                                                                                    ------------d2wa6a2 A:137-239 automated matches                                                                     SCOP domains
               CATH domains 2wa6A01 A:8-126 Actin-binding Protein, T-fimbrin; domain 1                                                             ----------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------CH-2wa6A01 A:142-239                                                                               Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------CH-2wa6A02 A:142-239                                                                               Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh.........-----...hhhhhhhhhhhhhh........hhhhh.hhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------C------S--R-V--------------P-------------V------------------------K------VP---- SAPs(SNPs)
                PROSITE (1) --------CH  PDB: A:16-122 UniProt: 16-122                                                                          ----------------CH  PDB: A:139-239 UniProt: 139-239                                                                   PROSITE (1)
                PROSITE (2) ----------ACTININ_1 ------------------------------------------------------------------ACTININ_2  PDB: A:94-118 ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:8-98 UniProt: 1-98 [INCOMPLETE]                                           ----------------------------------------------------------------------------------Exon 1.4  PDB: A:181-213         Exon 1.5  PDB: A:214-239   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.2  PDB: A:98-181 (gaps) UniProt: 98-181                                      ---------------------------------------------------------- Transcript 1 (2)
                 2wa6 A   8 LAEDAPWKKIQQNTFTRWCNEHLKCVNKRIGNLQTDLSDGLRLIALLEVLSQKRMYRKYHQRPTFRQMQLENVSVALEFLDRESIKLVSIDSKAIVDGNLKLILGLVWTLILHYSISMPVWEDE-----KKQTPKQRLLGRIQNKIPYLPITNFNQNWQDGKALGALVDSCAPGLCPDWESWDPQKPVDNAREAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK 239
                                    17        27        37        47        57        67        77        87        97       107       117       127   |   137       147       157       167       177       187       197       207       217       227       237  
                                                                                                                                                     131   137                                                                                                      

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CH (43)
(-)
Family: CH (43)
1aCH-2wa6A01A:142-239
1bCH-2wa6A02A:142-239

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FLNB_HUMAN | O75369)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    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:0007016    cytoskeletal anchoring at plasma membrane    A cytoskeleton organization process that directly or indirectly links cytoskeletal filaments to the plasma membrane.
    GO:0003382    epithelial cell morphogenesis    The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state.
    GO:0003334    keratinocyte development    The process whose specific outcome is the progression of a keratinocyte 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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007519    skeletal muscle tissue development    The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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: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:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FLNB_HUMAN | O753692di8 2di9 2dia 2dib 2dic 2dj4 2dlg 2dmb 2dmc 2e9i 2e9j 2ee6 2ee9 2eea 2eeb 2eec 2eed 2wa5 2wa7 3fer 4b7l 5dcp

(-) Related Entries Specified in the PDB File

2di8 SOLUTION STRUCTURE OF THE 19TH FILAMIN DOMAIN FROM HUMANFILAMIN-B
2di9 SOLUTION STRUCTURE OF THE 9TH FILAMIN DOMAIN FROM HUMANFILAMIN-B
2dia SOLUTION STRUCTURE OF THE 10TH FILAMIN DOMAIN FROM HUMANFILAMIN-B
2dib SOLUTION STRUCTURE OF THE 11TH FILAMIN DOMAIN FROM HUMANFILAMIN-B
2dic SOLUTION STRUCTURE OF THE 12TH FILAMIN DOMAIN FROM HUMANFILAMIN-B
2dj4 SOLUTION STRUCTURE OF THE 13TH FILAMIN DOMAIN FROM HUMANFILAMIN-B
2wa5 CRYSTAL STRUCTURE OF HUMAN FILAMIN B ACTIN BINDING DOMAIN AT 1.9 ANGSTROM RESOLUTION
2wa7 STRUCTURE OF THE M202V MUTANT OF HUMAN FILAMIN B ACTIN BINDING DOMAIN AT 1.85 ANGSTROMS RESOLUTION