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 :  STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A CDC27 PHOSPHOPEPTIDE
 
Authors :  N. Singh, J. R. Thompson, G. Mer
Date :  22 Jul 11  (Deposition) - 30 Nov 11  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Tandem Brct Domains, Cell Cycle Regulation, Dna Repair, Mitosis, Phosphorylation, Cell Cycle-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Singh, T. D. Wiltshire, J. R. Thompson, G. Mer, F. J. Couch
Molecular Basis For The Association Of Microcephalin (Mcph1 Protein With The Cell Division Cycle Protein 27 (Cdc27) Subunit Of The Anaphase-Promoting Complex.
J. Biol. Chem. V. 287 2854 2012
PubMed-ID: 22139841  |  Reference-DOI: 10.1074/JBC.M111.307868

(-) Compounds

Molecule 1 - MICROCEPHALIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTEV
    Expression System StrainBL21 ROSETTA (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL TANDEM BRCT DOMAINS, UNP RESIDUES 640-835
    GeneMCPH1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - CDC27 PEPTIDE
    ChainsC, D
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHETIC PEPTIDE CORRESPONDING TO THE LAST FOUR RESIDUES OF HUMAN CDC27 (SER821 TO PHE824). SER821 IS PHOSPHORYLATED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 3T1N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T1N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:769 -Pro A:770
2Ser B:769 -Pro B:770

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046755T682NMCPH1_HUMANPolymorphism12674488A/BT682N
2UniProtVAR_046756A761VMCPH1_HUMANPolymorphism1057090A/BV761V
3UniProtVAR_046757P828SMCPH1_HUMANPolymorphism1057091A/BP828S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046755T682NMCPH1_HUMANPolymorphism12674488AT682N
2UniProtVAR_046756A761VMCPH1_HUMANPolymorphism1057090AV761V
3UniProtVAR_046757P828SMCPH1_HUMANPolymorphism1057091AP828S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046755T682NMCPH1_HUMANPolymorphism12674488BT682N
2UniProtVAR_046756A761VMCPH1_HUMANPolymorphism1057090BV761V
3UniProtVAR_046757P828SMCPH1_HUMANPolymorphism1057091BP828S

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.MCPH1_HUMAN1-93
672-730
 
751-833
 
  4-
A:672-730
B:672-730
A:751-833
B:751-833
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.MCPH1_HUMAN1-93
672-730
 
751-833
 
  2-
A:672-730
-
A:751-833
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.MCPH1_HUMAN1-93
672-730
 
751-833
 
  2-
-
B:672-730
-
B:751-833

(-) Exons   (0, 0)

(no "Exon" information available for 3T1N)

(-) 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:191
 aligned with MCPH1_HUMAN | Q8NEM0 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:191
                                   653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833 
          MCPH1_HUMAN   644 KKPTRTLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIARGCWVLSYDWVLWSLELGHWISEEPFELSHHFPAAPLCRSECHLSAGPYRGTLFADQPAMFVSPASSPPVAKLCELVHLCGGRVSQVPRQASIVIGPYSGKKKATVKYLSEKWVLDSITQHKVCAPENYLLS 834
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhhh...........eeeeee.....hhhhhhhhhhh.eeeehhhhhhhhhhh....hhhhh......hhhhhhhhhhh.......hhhhhh.eeee......hhhhhhhhhhhhh.ee..hhhhh.eee...........eeehhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------N------------------------------------------------------------------------------V------------------------------------------------------------------S------ SAPs(SNPs)
                    PROSITE ----------------------------BRCT  PDB: A:672-730 UniProt: 672-730                      --------------------BRCT  PDB: A:751-833 UniProt: 751-833                                              - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t1n A 644 KKPTRTLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIARGCWVLSYDWVLWSLELGHWISEEPFELSHHFPAAPLCRSECHLSAGPYRGTLFADQPVMFVSPASSPPVAKLCELVHLCGGRVSQVPRQASIVIGPYSGKKKATVKYLSEKWVLDSITQHKVCAPENYLLS 834
                                   653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833 

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with MCPH1_HUMAN | Q8NEM0 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:190
                                   654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834
          MCPH1_HUMAN   645 KPTRTLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIARGCWVLSYDWVLWSLELGHWISEEPFELSHHFPAAPLCRSECHLSAGPYRGTLFADQPAMFVSPASSPPVAKLCELVHLCGGRVSQVPRQASIVIGPYSGKKKATVKYLSEKWVLDSITQHKVCAPENYLLS 834
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhhh..ee.......eeeeee.....hhhhhhhhhhh.eee.hhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhh..............eee......hhhhhhhhhhhh...ee.......eee...........eeehhhhhhhhhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------N------------------------------------------------------------------------------V------------------------------------------------------------------S------ SAPs(SNPs)
                    PROSITE ---------------------------BRCT  PDB: B:672-730 UniProt: 672-730                      --------------------BRCT  PDB: B:751-833 UniProt: 751-833                                              - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t1n B 645 KPTRTLVMTSMPSEKQNVVIQVVDKLKGFSIAPDVCETTTHVLSGKPLRTLNVLLGIARGCWVLSYDWVLWSLELGHWISEEPFELSHHFPAAPLCRSECHLSAGPYRGTLFADQPVMFVSPASSPPVAKLCELVHLCGGRVSQVPRQASIVIGPYSGKKKATVKYLSEKWVLDSITQHKVCAPENYLLS 834
                                   654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834

Chain C from PDB  Type:PROTEIN  Length:4
 aligned with CDC27_HUMAN | P30260 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:4
          CDC27_HUMAN   821 SDEF 824
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3t1n C 821 sDEF 824
                            |   
                            |   
                          821-SEP

Chain D from PDB  Type:PROTEIN  Length:4
 aligned with CDC27_HUMAN | P30260 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:4
          CDC27_HUMAN   821 SDEF 824
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3t1n D 821 sDEF 824
                            |   
                            |   
                          821-SEP

   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 3T1N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T1N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T1N)

(-) Gene Ontology  (25, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCPH1_HUMAN | Q8NEM0)
molecular function
    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:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0071850    mitotic cell cycle arrest    The process in which the mitotic cell cycle is halted during one of the normal phases (G1, S, G2, M).
cellular component
    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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

Chain C,D   (CDC27_HUMAN | P30260)
molecular function
    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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
biological process
    GO:0031145    anaphase-promoting complex-dependent catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007091    metaphase/anaphase transition of mitotic cell cycle    The cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
    GO:0051436    negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    GO:0051437    positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition    Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0070979    protein K11-linked ubiquitination    A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0051439    regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    A cell cycle process that modulates the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
cellular component
    GO:0005680    anaphase-promoting complex    A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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: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.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0005876    spindle microtubule    Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.

 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
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3t1n)
 
  Cis Peptide Bonds
    Ser A:769 - Pro A:770   [ RasMol ]  
    Ser B:769 - Pro B:770   [ 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
  3t1n
    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
  CDC27_HUMAN | P30260
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  MCPH1_HUMAN | Q8NEM0
    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
  CDC27_HUMAN | P30260
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MCPH1_HUMAN | Q8NEM0
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CDC27_HUMAN | P302604rg6 4rg7 4rg9 4ui9 5a31 5g04 5g05 5khr 5khu 5l9t 5l9u 5lcw
        MCPH1_HUMAN | Q8NEM02wt8 3ktf 3pa6 3sht 3shv 3szm 3u3z

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3T1N)