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(-) Description

Title :  NEMO CC2-LZ DOMAIN - 1D5 DARPIN COMPLEX
 
Authors :  O. Grubisha, S. Duquerroy, F. Cordier, A. Haouz, M. Delepierre, M. Vero
Date :  22 Sep 08  (Deposition) - 03 Nov 09  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Transcription, Metal-Binding, Nemo - Ikk Gamma - Nfkb Pathway - Darpin, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Grubisha, M. Kaminska, S. Duquerroy, E. Fontan, F. Cordier, A. Haouz, B. Raynal, J. Chiaravalli, M. Delepierre, A. Israel, M. Veron, F. Agou
Darpin-Assisted Crystallography Of The Cc2-Lz Domain Of Nemo Reveals A Coupling Between Dimerization And Ubiquitin-Binding.
J. Mol. Biol. V. 395 89 2010
PubMed-ID: 19854204  |  Reference-DOI: 10.1016/J.JMB.2009.10.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NF-KAPPA-B ESSENTIAL MODULATOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentCC2-LZ DOMAIN, RESIDUES 251-337
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymNF-KAPPA-B ESSENTIAL MODIFIER, INHIBITOR OF NUCLEAR FACTOR KAPPA-B KINASE SUBUNIT GAMMA, IKB KINASE-ASSOCIATED PROTEIN 1, NEMO
 
Molecule 2 - 1D5 DARPIN
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-30
    Expression System StrainXL1-BLUE
    Expression System Taxid562
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsSEE SECONDARY REFERENCE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2V4H)

(-) Sites  (0, 0)

(no "Site" information available for 2V4H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V4H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V4H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V4H)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENSMUST000001141332cENSMUSE00000450177X:71669951-71670054104NEMO_MOUSE-00--
1.3bENSMUST000001141333bENSMUSE00000908250X:71673101-71673241141NEMO_MOUSE-00--
1.6bENSMUST000001141336bENSMUSE00000209243X:71678144-71678345202NEMO_MOUSE1-63630--
1.7bENSMUST000001141337bENSMUSE00000209248X:71679142-71679353212NEMO_MOUSE63-133710--
1.8bENSMUST000001141338bENSMUSE00000209244X:71682503-71682621119NEMO_MOUSE134-173400--
1.9bENSMUST000001141339bENSMUSE00000209240X:71684246-71684398153NEMO_MOUSE173-224520--
1.10bENSMUST0000011413310bENSMUSE00000898654X:71685214-7168528976NEMO_MOUSE224-249262A:240-250 (gaps)
B:247-250
12
4
1.11bENSMUST0000011413311bENSMUSE00000891147X:71688684-71688827144NEMO_MOUSE250-297482A:251-297
B:251-297
47
47
1.12bENSMUST0000011413312bENSMUSE00000209247X:71689111-71689253143NEMO_MOUSE298-345482A:298-337
B:298-337
40
40
1.13ENSMUST0000011413313ENSMUSE00000209245X:71693198-7169325962NEMO_MOUSE345-366220--
1.14gENSMUST0000011413314gENSMUSE00000698234X:71693556-716991935638NEMO_MOUSE366-412470--

(-) 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:98
 aligned with NEMO_MOUSE | O88522 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:102
                                   245       255       265       275       285       295       305       315       325       335  
           NEMO_MOUSE   236 QLFQDYDSHIKSSKGMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK 337
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2v4hA 00 A:2   40-337 Nemo cc2-lz domain - 1d5 darpin complex                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....-......---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.10b    Exon 1.11b  PDB: A:251-297 UniProt: 250-297     Exon 1.12b  PDB: A:298-337 [INCOMPLETE]  Transcript 1
                 2v4h A 240 GLVPR-GSHMAS---MQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK 337
                                | |248 |   | 255       265       275       285       295       305       315       325       335  
                              244 |  250 251                                                                                      
                                245                                                                                               

Chain B from PDB  Type:PROTEIN  Length:91
 aligned with NEMO_MOUSE | O88522 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:94
                                   253       263       273       283       293       303       313       323       333    
           NEMO_MOUSE   244 HIKSSKGMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK 337
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v4h   B00 B:247-337 Nemo cc2-lz domain - 1d5 darpin complex                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 1.10b Exon 1.11b  PDB: B:251-297 UniProt: 250-297     Exon 1.12b  PDB: B:298-337 [INCOMPLETE]  Transcript 1
                 2v4h B 247 HMAS---MQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK 337
                               |   253       263       273       283       293       303       313       323       333    
                             250 251                                                                                      

Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v4hC00 C:12-136  [code=1.25.40.20, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4h C  12 SDLGKKLLEAARAGQDDEVRILMANGADVNANDRKGNTPLHLAADYDHLEIVEVLLKHGADVNAHDNDGSTPLHLAALFGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN 136
                                    21        31        41        51        61        71        81        91       101       111       121       131     

Chain D from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v4hD00 D:9-136  [code=1.25.40.20, no name defined]                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v4h D   9 HHGSDLGKKLLEAARAGQDDEVRILMANGADVNANDRKGNTPLHLAADYDHLEIVEVLLKHGADVNAHDNDGSTPLHLAALFGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN 136
                                    18        28        38        48        58        68        78        88        98       108       118       128        

   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 2V4H)

(-) CATH Domains  (2, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V4H)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NEMO_MOUSE | O88522)
molecular function
    GO:0070530    K63-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein.
    GO:1990450    linear polyubiquitin binding    Interacting selectively and non-covalently with a linear polymer of ubiquitin. Linear ubiquitin polymers are formed by linking the amino-terminal methionine (M1) of one ubiquitin molecule to the carboxy-terminal glycine (G76) of the next.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0001782    B cell homeostasis    The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0007250    activation of NF-kappaB-inducing kinase activity    The stimulation of the activity of NF-kappaB-inducing kinase through phosphorylation at specific residues.
    GO:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0051650    establishment of vesicle localization    The directed movement of a vesicle to a specific location.
    GO:1902236    negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0008385    IkappaB kinase complex    A trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    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:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEMO_MOUSE | O885222zvn 2zvo 3f89 3jsv 4owf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2V4H)