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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN BINDING DOMAIN)
 
Authors :  J. J. Ipsaro, A. Mondragon
Date :  03 Nov 08  (Deposition) - 24 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Spectrin, Spectrin Repeat, Three-Helix-Bundle, Ankyrin Binding, Actin Capping, Actin-Binding, Cytoskeleton, Disease Mutation, Elliptocytosis, Hereditary Hemolytic Anemia, Phosphoprotein, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Ipsaro, L. Huang, A. Mondragon
Structures Of The Spectrin-Ankyrin Interaction Binding Domains.
Blood V. 113 5385 2009
PubMed-ID: 19141864  |  Reference-DOI: 10.1182/BLOOD-2008-10-184358

(-) Compounds

Molecule 1 - SPECTRIN BETA CHAIN, ERYTHROCYTE
    Binding Domain)UNP RESIDUES 1686-1907
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN
    GeneSPTB, SPTB1
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-I SPECTRIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3F57)

(-) Sites  (0, 0)

(no "Site" information available for 3F57)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F57)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:1763 -Glu A:1764

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F57)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003897211ENSE00002200989chr14:65289866-65289665202SPTB1_HUMAN1-50500--
1.2ENST000003897212ENSE00001692272chr14:65271808-65271657152SPTB1_HUMAN50-100510--
1.3ENST000003897213ENSE00001642694chr14:65270498-65270325174SPTB1_HUMAN101-158580--
1.4ENST000003897214ENSE00001647147chr14:65269035-6526894492SPTB1_HUMAN159-189310--
1.5ENST000003897215ENSE00001592915chr14:65268552-6526847281SPTB1_HUMAN189-216280--
1.6ENST000003897216ENSE00001601006chr14:65268118-65268003116SPTB1_HUMAN216-255400--
1.7ENST000003897217ENSE00001788289chr14:65267586-65267474113SPTB1_HUMAN255-292380--
1.8ENST000003897218ENSE00001643410chr14:65266652-65266465188SPTB1_HUMAN293-355630--
1.9ENST000003897219ENSE00001793364chr14:65264564-65264447118SPTB1_HUMAN355-394400--
1.10ENST0000038972110ENSE00001786358chr14:65263433-65263275159SPTB1_HUMAN395-447530--
1.11ENST0000038972111ENSE00001689221chr14:65262357-65262055303SPTB1_HUMAN448-5481010--
1.12ENST0000038972112ENSE00001643743chr14:65261335-65261185151SPTB1_HUMAN549-599510--
1.13ENST0000038972113ENSE00001699666chr14:65260585-65259715871SPTB1_HUMAN599-8892910--
1.14ENST0000038972114ENSE00001604309chr14:65258574-65258437138SPTB1_HUMAN889-935470--
1.15ENST0000038972115ENSE00001594267chr14:65253878-65253122757SPTB1_HUMAN935-11872530--
1.16ENST0000038972116ENSE00001597703chr14:65252669-65252467203SPTB1_HUMAN1188-1255680--
1.17ENST0000038972117ENSE00000392073chr14:65252345-6525225591SPTB1_HUMAN1255-1285310--
1.18ENST0000038972118ENSE00000867578chr14:65251111-65250965147SPTB1_HUMAN1286-1334490--
1.19ENST0000038972119ENSE00001506737chr14:65249271-65249008264SPTB1_HUMAN1335-1422880--
1.20ENST0000038972120ENSE00001506736chr14:65246649-65246443207SPTB1_HUMAN1423-1491690--
1.21ENST0000038972121ENSE00000902497chr14:65245964-6524587590SPTB1_HUMAN1492-1521300--
1.22ENST0000038972122ENSE00000658448chr14:65242121-65241843279SPTB1_HUMAN1522-1614930--
1.23ENST0000038972123ENSE00000392079chr14:65241245-65241115131SPTB1_HUMAN1615-1658440--
1.24ENST0000038972124ENSE00000867584chr14:65240142-65239938205SPTB1_HUMAN1658-1726692A:1684-1726
B:1684-1726
43
43
1.25ENST0000038972125ENSE00000867585chr14:65239672-65239298375SPTB1_HUMAN1727-18511252A:1727-1851 (gaps)
B:1727-1851 (gaps)
125
125
1.26ENST0000038972126ENSE00000902494chr14:65237847-65237603245SPTB1_HUMAN1852-1933822A:1852-1896
B:1852-1891
45
40
1.27ENST0000038972127ENSE00000902493chr14:65236446-65236308139SPTB1_HUMAN1933-1979470--
1.28ENST0000038972128ENSE00000392084chr14:65235836-6523575285SPTB1_HUMAN1980-2008290--
1.29ENST0000038972129ENSE00000867589chr14:65234577-65234381197SPTB1_HUMAN2008-2073660--
1.30ENST0000038972130ENSE00000658438chr14:65234070-6523402150SPTB1_HUMAN2074-2090170--
1.31cENST0000038972131cENSE00001506734chr14:65233519-65233148372SPTB1_HUMAN2090-2137480--

(-) Sequences/Alignments

Asymmetric 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:190
 aligned with SPTB1_HUMAN | P11277 from UniProtKB/Swiss-Prot  Length:2137

    Alignment length:213
                                  1693      1703      1713      1723      1733      1743      1753      1763      1773      1783      1793      1803      1813      1823      1833      1843      1853      1863      1873      1883      1893   
         SPTB1_HUMAN   1684 RKLENMYHLFQLKRETDDLEQWISEKELVASSPEMGQDFDHVTLLRDKFRDFARETGAIGQERVDNVNAFIERLIDAGHSEAATIAEWKDGLNEMWADLLELIDTRMQLLAASYDLHRYFYTGAEILGLIDEKHRELPEDVGLDASTAESFHRVHTAFERELHLLGVQVQQFQDVATRLQTAYAGEKAEAIQNKEQEVSAAWQALLDACAGRR 1896
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----------------------...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.24  PDB: A:1684-1726 [INCOMPLETE]   Exon 1.25  PDB: A:1727-1851 (gaps) UniProt: 1727-1851                                                                        Exon 1.26  PDB: A:1852-1896 [INCOMPLETE]      Transcript 1
                3f57 A 1684 NALENMYHLFQLKRETDDLEQWISEKELVASSPEMGQDFDHVTLLRDKFRDFARETGAIGQERVDNVNAFIERLIDAGHSEAATIAEWKDGLNEMWADLLELIDTRMQLLAASYDLHRYFYTGAEILGLIDEKH-----------------------FERDVHLLGVQVQQFQDVATRLQTAYAGEKAEAIQNKEQEVSAAWQALLDACAGRR 1896
                                  1693      1703      1713      1723      1733      1743      1753      1763      1773      1783      1793      1803      1813   |     -         -      1843      1853      1863      1873      1883      1893   
                                                                                                                                                              1817                    1841                                                       

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with SPTB1_HUMAN | P11277 from UniProtKB/Swiss-Prot  Length:2137

    Alignment length:208
                                  1693      1703      1713      1723      1733      1743      1753      1763      1773      1783      1793      1803      1813      1823      1833      1843      1853      1863      1873      1883        
         SPTB1_HUMAN   1684 RKLENMYHLFQLKRETDDLEQWISEKELVASSPEMGQDFDHVTLLRDKFRDFARETGAIGQERVDNVNAFIERLIDAGHSEAATIAEWKDGLNEMWADLLELIDTRMQLLAASYDLHRYFYTGAEILGLIDEKHRELPEDVGLDASTAESFHRVHTAFERELHLLGVQVQQFQDVATRLQTAYAGEKAEAIQNKEQEVSAAWQALLDA 1891
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----------------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.24  PDB: B:1684-1726 [INCOMPLETE]   Exon 1.25  PDB: B:1727-1851 (gaps) UniProt: 1727-1851                                                                        Exon 1.26  PDB: B:1852-1891 [INCOMPLETE] Transcript 1
                3f57 B 1684 NALENMYHLFQLKRETDDLEQWISEKELVASSPEMGQDFDHVTLLRDKFRDFARETGAIGQERVDNVNAFIERLIDAGHSEAATIAEWKDGLNEMWADLLELIDTRMQLLAASYDLHRYFYTGAEILGLIDEKH----------------------AFERDVHLLGVQVQQFQDVATRLQTAYAGEKAEAIQNKEQEVSAAWQALLDA 1891
                                  1693      1703      1713      1723      1733      1743      1753      1763      1773      1783      1793      1803      1813   |     -         -      1843      1853      1863      1873      1883        
                                                                                                                                                              1817                   1840                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 3F57)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F57)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SPTB1_HUMAN | P11277)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0030506    ankyrin binding    Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane 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).
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0051693    actin filament capping    The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
cellular component
    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: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: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: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:0031235    intrinsic component of the cytoplasmic side of the plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that have some covalently attached part (e.g. peptide sequence or GPI anchor) which is embedded in the cytoplasmic side of the plasma membrane only.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0008091    spectrin    Membrane associated dimeric protein (240 and 220 kDa) of erythrocytes. Forms a complex with ankyrin, actin and probably other components of the membrane cytoskeleton, so that there is a mesh of proteins underlying the plasma membrane, potentially restricting the lateral mobility of integral proteins.
    GO:0014731    spectrin-associated cytoskeleton    The part of the cytoskeleton composed of spectrin, protein 4.1 and ankyrin. Spectrin-associated cytoskeleton is associated with the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPTB1_HUMAN | P112771s35 3edu 3kbt 3kbu 3lbx

(-) Related Entries Specified in the PDB File

1cun CHICKEN BRAIN ALPHA SPECTRIN REPEATS 16 AND 17
1s35 HUMAN ERYTHROID BETA SPECTRIN REPEATS 8 AND 9
1u4q CHICKEN BRAIN ALPHA SPECTRIN REPEATS 15, 16 AND 17
1u5p CHICKEN BRAIN ALPHA SPECTRIN REPEATS 15 AND 16
3f59 CRYSTAL STRUCTURE OF ZU5-ANK, THE SPECTRIN BINDING REGION OF HUMAN ERYTHROID ANKYRIN