Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PRIMITIVE-MONOCLINIC CRYSTAL STRUCTURE OF THE FERM DOMAIN OF PROTEIN 4.1R
 
Authors :  L. Nedyalkova, N. Zhong, Y. Tong, W. Tempel, C. H. Arrowsmith, A. M. Edwa C. Bountra, J. Weigelt, H. Park, Structural Genomics Consortium (
Date :  27 Jan 11  (Deposition) - 09 Feb 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytoskeleton, Structural Genomics, Structural Genomics Consortium, Sgc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Nedyalkova, N. Zhong, Y. Tong, W. Tempel, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park
Primitive-Monoclinic Crystal Structure Of The Ferm Domain O Protein 4. 1R
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN 4.1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneEPB41, E41P
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP4.1, 4.1R, BAND 4.1, EPB4.1

 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  (1, 19)

Asymmetric Unit (1, 19)
No.NameCountTypeFull Name
1UNX19Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1UNX10Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1UNX9Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3QIJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val B:278 -Pro B:279

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009122V214I41_HUMANPolymorphism111642750A/BV214I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009122V214I41_HUMANPolymorphism111642750AV214I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009122V214I41_HUMANPolymorphism111642750BV214I

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERM_3PS50057 FERM domain profile.41_HUMAN210-491
 
  2A:211-488
B:211-488
2FERM_1PS00660 FERM domain signature 1.41_HUMAN264-292
 
  2A:264-292
B:264-292
3FERM_2PS00661 FERM domain signature 2.41_HUMAN371-400
 
  2A:371-400
B:371-400
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERM_3PS50057 FERM domain profile.41_HUMAN210-491
 
  1A:211-488
-
2FERM_1PS00660 FERM domain signature 1.41_HUMAN264-292
 
  1A:264-292
-
3FERM_2PS00661 FERM domain signature 2.41_HUMAN371-400
 
  1A:371-400
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERM_3PS50057 FERM domain profile.41_HUMAN210-491
 
  1-
B:211-488
2FERM_1PS00660 FERM domain signature 1.41_HUMAN264-292
 
  1-
B:264-292
3FERM_2PS00661 FERM domain signature 2.41_HUMAN371-400
 
  1-
B:371-400

(-) Exons   (0, 0)

(no "Exon" information available for 3QIJ)

(-) 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:270
 aligned with 41_HUMAN | P11171 from UniProtKB/Swiss-Prot  Length:864

    Alignment length:317
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       
             41_HUMAN   172 EGEGLEECSKIEVKEESPQSKAETELKASQKPIRKHRNMHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVAGRLPCSFATLALLGSYTIQSELGDYDPELHGVDYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLENAKKLSMYGVDLHKAKDLEGVDIILGVCSSGLLVYKDKLRINRFPWPKVLKISYKRSSFFIKIRPGEQEQYESTIGFKLPSYRAAKKLWKVCVEHHTFFR 488
               SCOP domains d3                                     qija1 A:209-290 automated matches                                               d3qija2 A:291-396 automated matches                                                                       d3qija3 A:397-488 automated matches                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------------------------------eeeee.....eeeee.....hhhhhhhhhhhhhh..hhh.eeeeeeee..eeee.....hhhhhh---..eeeeee.....hhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhh.............hhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......eeeeee.....eeeeee...eeeeee..eeeeeee...eeeeeee..eeeeee.-------.eeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------FERM_3  PDB: A:211-488 UniProt: 210-491                                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------FERM_1  PDB: A:264-292       ------------------------------------------------------------------------------FERM_2  PDB: A:371-400        ---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qij A 209 QG-------------------------------------HCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQV---PWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVAGRLPCSFATLALLGSYTIQSELGDYDPELHGVDYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLENAKKLSMYGVDLHKAKDLEGVDIILGVCSSGLLVYKDKLRINRFPWPKVLKISYKRSSFFIKIR-------ESTIGFKLPSYRAAKKLWKVCVEHHTFFR 488
                             |       -         -         -       211       221       231       241       251       261       271   |   281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451|      461       471       481       
                             |                                   211                                                             275 279                                                                                                                                                                          452     460                            
                           210                                                                                                                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with 41_HUMAN | P11171 from UniProtKB/Swiss-Prot  Length:864

    Alignment length:292
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486  
             41_HUMAN   197 LKASQKPIRKHRNMHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVAGRLPCSFATLALLGSYTIQSELGDYDPELHGVDYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLENAKKLSMYGVDLHKAKDLEGVDIILGVCSSGLLVYKDKLRINRFPWPKVLKISYKRSSFFIKIRPGEQEQYESTIGFKLPSYRAAKKLWKVCVEHHTFFR 488
               SCOP domains d3q           ijb1 B:208-290 automated matches                                                d3qijb2 B:291-396 automated matches                                                                       d3qijb3 B:397-488 automated matches                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---           ---FERM_N-3qijB03 B:214-290                                                     -FERM_M-3qijB05 B:292-401                                                                                      ---FERM_C-3qijB01 B:405-488                                                             Pfam domains (1)
           Pfam domains (2) ---           ---FERM_N-3qijB04 B:214-290                                                     -FERM_M-3qijB06 B:292-401                                                                                      ---FERM_C-3qijB02 B:405-488                                                             Pfam domains (2)
         Sec.struct. author ...-----------eeeee.....eeeee.....hhhhhhhhhhhhhh..hhh.eeeee..----.ee...............eeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......eeeeee.....eeeeee...eeeeee..eeeeeee...eeeeeee..eeeeee..----...eeeeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------FERM_3  PDB: B:211-488 UniProt: 210-491                                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------FERM_1  PDB: B:264-292       ------------------------------------------------------------------------------FERM_2  PDB: B:371-400        ---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qij B 208 FQG-----------HCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWD----KTWLDSAKEIKKQVRGVPWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVAGRLPCSFATLALLGSYTIQSELGDYDPELHGVDYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLENAKKLSMYGVDLHKAKDLEGVDIILGVCSSGLLVYKDKLRINRFPWPKVLKISYKRSSFFIKIRP----QYESTIGFKLPSYRAAKKLWKVCVEHHTFFR 488
                              |      -    |  216       226       236       246       256|    | 266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446      |  - |     466       476       486  
                            210         211                                           257  262                                                                                                                                                                                            453  458                              

   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  (3, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: PH (111)
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (41_HUMAN | P11171)
molecular function
    GO:0005545    1-phosphatidylinositol binding    Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    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:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
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:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    GO:0030866    cortical 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 actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
cellular component
    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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0030863    cortical cytoskeleton    The portion of the cytoskeleton that lies just beneath the 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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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: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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3qij)
 
  Cis Peptide Bonds
    Val B:278 - Pro B:279   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3qij
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  41_HUMAN | P11171
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  41_HUMAN | P11171
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        41_HUMAN | P111711gg3 2rq1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QIJ)