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(-) Description

Title :  COMPLEX OF BARRIER-TO-AUTOINTEGRATION FACTOR AND LEM-DOMAIN OF EMERIN
 
Authors :  G. M. Clore, M. Cai
Date :  22 Dec 06  (Deposition) - 13 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Inner Nuclear Membrane Protein, Lem-Domain Baf Multidimensional Nmr Dipolar Couplings, Membrane Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Cai, Y. Huang, J. Y. Suh, J. M. Louis, R. Ghirlando, R. Craigie, G. M. Clore
Solution Nmr Structure Of The Barrier-To-Autointegration Factor-Emerin Complex.
J. Biol. Chem. V. 282 14525 2007
PubMed-ID: 17355960  |  Reference-DOI: 10.1074/JBC.M700576200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BARRIER-TO-AUTOINTEGRATION FACTOR
    Cellular LocationNUCLEUS
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 1-89
    GeneBANF1, BAF, BCRG1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBREAKPOINT CLUSTER REGION PROTEIN 1
 
Molecule 2 - EMERIN
    Cellular LocationNUCLEUS
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 2-47
    GeneEMD, EDMD, STA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2ODG)

(-) Sites  (0, 0)

(no "Site" information available for 2ODG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

NMR Structure (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065954A12TBAF_HUMANDisease (NGPS)387906871A/BA12T

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LEMPS50954 LEM domain profile.EMD_HUMAN1-45  1C:2-45

(-) Exons   (4, 6)

NMR Structure (4, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003121751aENSE00001189984chr11:65769550-65770041492BAF_HUMAN-00--
1.3bENST000003121753bENSE00001189976chr11:65770706-65770844139BAF_HUMAN1-41412A:1-41
B:1-41
41
41
1.4fENST000003121754fENSE00002191965chr11:65771097-65771620524BAF_HUMAN42-89482A:42-89
B:42-89
48
48

2.1aENST000003698421aENSE00001925261X:153607557-153607926370EMD_HUMAN1-28281C:1-2828
2.2bENST000003698422bENSE00001669344X:153608050-153608154105EMD_HUMAN28-63361C:28-4720
2.3aENST000003698423aENSE00001626504X:153608302-15360837978EMD_HUMAN63-89270--
2.3dENST000003698423dENSE00001687247X:153608594-153608727134EMD_HUMAN89-133450--
2.4bENST000003698424bENSE00001605338X:153609113-15360916250EMD_HUMAN134-150170--
2.4jENST000003698424jENSE00000868367X:153609242-153609883642EMD_HUMAN150-2541050--

(-) Sequences/Alignments

NMR Structure
   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:89
 aligned with BAF_HUMAN | O75531 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
             BAF_HUMAN    1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTCGANAKQSRDCFGCLREWCDAFL 89
               SCOP domains d2odga_ A: Barrier-to-autointegration factor, BAF                                         SCOP domains
               CATH domains 2odgA00 A:1-89  [code=1.10.150.40, no name defined]                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.......hhhhh...hhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------T----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:1-41 UniProt: 1-41     Exon 1.4f  PDB: A:42-89 UniProt: 42-89           Transcript 1
                  2odg A  1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTCGANAKQSRDCFGCLREWCDAFL 89
                                    10        20        30        40        50        60        70        80         

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with BAF_HUMAN | O75531 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
             BAF_HUMAN    1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTCGANAKQSRDCFGCLREWCDAFL 89
               SCOP domains d2odgb_ B: Barrier-to-autointegration factor, BAF                                         SCOP domains
               CATH domains 2odgB00 B:1-89  [code=1.10.150.40, no name defined]                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.......hhhhh...hhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------T----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: B:1-41 UniProt: 1-41     Exon 1.4f  PDB: B:42-89 UniProt: 42-89           Transcript 1
                  2odg B  1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTCGANAKQSRDCFGCLREWCDAFL 89
                                    10        20        30        40        50        60        70        80         

Chain C from PDB  Type:PROTEIN  Length:47
 aligned with EMD_HUMAN | P50402 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:47
                                    10        20        30        40       
             EMD_HUMAN    1 MDNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQRRR 47
               SCOP domains d2odgc_ C:                                      SCOP domains
               CATH domains 2odgC00 C:1-47                                  CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE LEM  PDB: C:2-45 UniProt: 1-45               -- PROSITE
           Transcript 2 (1) Exon 2.1a  PDB: C:1-28      ------------------- Transcript 2 (1)
           Transcript 2 (2) ---------------------------Exon 2.2b            Transcript 2 (2)
                  2odg C  1 HDNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQRRR 47
                                    10        20        30        40       

   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  (2, 3)

NMR Structure

(-) CATH Domains  (2, 3)

NMR Structure

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 39)

NMR Structure(hide GO term definitions)
Chain A,B   (BAF_HUMAN | O75531)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0007084    mitotic nuclear envelope reassembly    The cell cycle process that results in reformation of the nuclear envelope during mitotic cell division.
    GO:0051169    nuclear transport    The directed movement of substances into, out of, or within the nucleus.
    GO:0009615    response to virus    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 stimulus from a virus.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain C   (EMD_HUMAN | P50402)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    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:0071363    cellular response to growth factor 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 growth factor stimulus.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0007084    mitotic nuclear envelope reassembly    The cell cycle process that results in reformation of the nuclear envelope during mitotic cell division.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    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:0035414    negative regulation of catenin import into nucleus    Any process that decreases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
    GO:0048147    negative regulation of fibroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:0060828    regulation of canonical Wnt signaling pathway    Any process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005637    nuclear inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005640    nuclear outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAF_HUMAN | O755311ci4 1qck 2bzf 2ezx 2ezy 2ezz
        EMD_HUMAN | P504021jei 2odc

(-) Related Entries Specified in the PDB File

2odc LEM-DOMAIN OF THE NUCLEAR ENVELOPE PROTEIN EMERIN