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

(-) Description

Title :  STRUCTURE OF CSM1 C-TERMINAL DOMAIN, P21212 FORM
 
Authors :  K. D. Corbett, S. C. Harrison
Date :  22 May 10  (Deposition) - 01 Sep 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Meiosis, Rdna, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. D. Corbett, C. K. Yip, L. S. Ee, T. Walz, A. Amon, S. C. Harrison
The Monopolin Complex Crosslinks Kinetochore Components To Regulate Chromosome-Microtubule Attachments.
Cell(Cambridge, Mass. ) V. 142 556 2010
PubMed-ID: 20723757  |  Reference-DOI: 10.1016/J.CELL.2010.07.017

(-) Compounds

Molecule 1 - MONOPOLIN COMPLEX SUBUNIT CSM1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainROSETTA 2 PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN (RESIDUES 69-181)
    GeneCSM1, SPO86, YCR086W, YCR86W
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymCHROMOSOME SEGREGATION IN MEIOSIS PROTEIN 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
11PE10Ligand/IonPENTAETHYLENE GLYCOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
11PE7Ligand/IonPENTAETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR B:156 , SER B:167 , GLN B:170 , PHE B:171 , LYS B:174BINDING SITE FOR RESIDUE 1PE B 6
02AC2SOFTWAREASN A:173 , ALA A:176 , LYS A:177 , ASN B:173 , ALA B:176 , LYS B:177 , HOH B:200BINDING SITE FOR RESIDUE 1PE B 7
03AC3SOFTWARETYR A:80 , GLY B:95 , PHE B:98 , PHE B:122 , THR B:130 , LEU B:165 , GLU D:155BINDING SITE FOR RESIDUE 1PE B 9
04AC4SOFTWARELYS A:139 , GLN A:150 , TYR C:147 , GLN C:150 , HOH C:185BINDING SITE FOR RESIDUE 1PE C 2
05AC5SOFTWAREGLU C:79 , ASN C:83 , ARG C:85BINDING SITE FOR RESIDUE 1PE C 10
06AC6SOFTWAREGLU B:91 , LYS B:119 , LYS B:139 , GLU D:91 , TRP D:97 , LYS D:119 , VAL D:137 , LYS D:139 , HOH D:193 , HOH D:207BINDING SITE FOR RESIDUE 1PE D 1
07AC7SOFTWARETYR C:80 , GLY D:95 , PHE D:122 , LYS D:124 , LEU D:165BINDING SITE FOR RESIDUE 1PE D 3
08AC8SOFTWAREASN C:173 , LYS C:177 , ASN C:180 , ASN D:173 , ALA D:176 , LYS D:177BINDING SITE FOR RESIDUE 1PE D 4
09AC9SOFTWARETYR D:156 , SER D:167 , GLN D:170 , PHE D:171 , LYS D:174BINDING SITE FOR RESIDUE 1PE D 5
10BC1SOFTWAREHOH B:18 , HOH D:23 , VAL D:123 , VAL D:129 , GLU D:131 , SER D:162 , PHE D:163 , HOH D:192BINDING SITE FOR RESIDUE 1PE D 8

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N4S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N4S)

(-) Exons   (0, 0)

(no "Exon" information available for 3N4S)

(-) 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 CSM1_YEAST | P25651 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:112
                                    79        89        99       109       119       129       139       149       159       169       179  
           CSM1_YEAST    70 NSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLNK 181
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheeeeeeee.-..eeeeeee..-------....eeeeeee.------.eeeeeee....hhhhhhhhhh..hhhhhh.eeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3n4s A  70 NSEVIKDLYEYLCNVRVHKSYED-SGLWFDISQGT-------DYSIMDYKLGFV------TEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLNK 181
                                    79        89  | |   99    |    -  |    119   |     -|      139       149       159       169       179  
                                                 92 |       104     112        123    130                                                   
                                                   94                                                                                       

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with CSM1_YEAST | P25651 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:111
                                    79        89        99       109       119       129       139       149       159       169       179 
           CSM1_YEAST    70 NSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLN 180
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhheeeee........eeeeee..---------..eeeeeeee.......eeeeeee....hhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3n4s B  70 NSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGT---------SIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLN 180
                                    79        89        99    |    -    |  119       129       139       149       159       169       179 
                                                            104       114                                                                  

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with CSM1_YEAST | P25651 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:111
                                    79        89        99       109       119       129       139       149       159       169       179 
           CSM1_YEAST    70 NSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLN 180
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheeeeeeee....eeeeeeee.--------..eeeeeeeee-----..eeeeee.....hhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3n4s C  70 NSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGT--------YSIMDYKLGFV-----VTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLN 180
                                    79        89        99    |    -   |   119   |   129       139       149       159       169       179 
                                                            104      113       123   129                                                   

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with CSM1_YEAST | P25651 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:110
                                    80        90       100       110       120       130       140       150       160       170       180
           CSM1_YEAST    71 SEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLN 180
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Csm1-3n4sD01 D:71-167                                                                            ------------- Pfam domains (1)
           Pfam domains (2) Csm1-3n4sD02 D:71-167                                                                            ------------- Pfam domains (2)
           Pfam domains (3) Csm1-3n4sD03 D:71-167                                                                            ------------- Pfam domains (3)
           Pfam domains (4) Csm1-3n4sD04 D:71-167                                                                            ------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhheeeee........eeeeeee.-------...eeeeeeeee.---...eeeeeee....hhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3n4s D  71 SEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGT-------DYSIMDYKLGFVK---QVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLN 180
                                    80        90       100   |     - |     120   |   130       140       150       160       170       180
                                                           104     112         124 128                                                    

   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 3N4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N4S)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CSM1_YEAST | P25651)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:1990644    microtubule site clamp    The binding activity of a molecule that attaches the spindle microtubules to the kinetochore.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0051315    attachment of mitotic spindle microtubules to kinetochore    The cell cycle process in which spindle microtubules become physically associated with the proteins making up the kinetochore complex as part of mitotic metaphase plate congression.
    GO:0045143    homologous chromosome segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the first division of the meiotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner; this pairing off, referred to as synapsis, permits genetic recombination. One homolog (both sister chromatids) of each morphologic type goes into each of the resulting chromosome sets.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0045132    meiotic chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle.
    GO:0045144    meiotic sister chromatid segregation    The cell cycle process in which sister chromatids are organized and then physically separated and randomly apportioned to two sets during the second division of the meiotic cell cycle.
    GO:0034503    protein localization to nucleolar rDNA repeats    Any process in which a protein is transported to, or maintained at, the rDNA repeats on a chromosome in the nucleolus.
    GO:0070550    rDNA condensation    The process in which the chromatin structure of the rDNA repeats is compacted. In S. cerevisiae, condensation and resolution of the rDNA occurs during anaphase.
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:0034506    chromosome, centromeric core domain    The innermost portion of the centromeric region of a chromosome, encompassing the core region of a chromosome centromere and the proteins that bind to it.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000778    condensed nuclear chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
    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:0033551    monopolin complex    A protein complex required for clamping microtubule binding sites, ensuring orientation of sister kinetochores to the same pole (mono-orientation) during meiosis I. In the yeast S. cerevisiae this complex consists of Csm1p, Lrs4p, Hrr25p and Mam1p; in S. pombe Psc1 and Mde4 have been identified as subunits.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3n4s)
 
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
  3n4s
    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
  CSM1_YEAST | P25651
    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
  CSM1_YEAST | P25651
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CSM1_YEAST | P256513n4r 3n4x 3n7n 5ktb 5v1a 5v3n

(-) Related Entries Specified in the PDB File

3n4r STRUCTURE OF CSM1 C-TERMINAL DOMAIN, R3 FORM
3n4x STRUCTURE OF CSM1 FULL-LENGTH