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Complex Overview

From Publication: Ho Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002 Jan 10;415(6868):180-3.
Notes: This molecular complex record represents a population of complexes co-purified by immunoprecipitation of FLAG-tagged Rad3. The topolgies of protein complexes in this experiment are unknown.
Complex Size: 12 proteins

Complex Member Proteins

Protein

 GO Cellular Component GO Biological Process GO Molecular Function
AAC1
  • mitochondrion
  • mitochondrial inner membrane
    		•
  • mitochondrial transport
  • aerobic respiration
    		•
  • ATP:ADP antiporter activity
    		•
    AAC3
  • mitochondrion
  • mitochondrial inner membrane
    		•
  • anaerobic respiration
    		•
  • ATP:ADP antiporter activity
    		•
    ATP3
  • mitochondrial proton-transporting ATP synthase, central stalk
  • mitochondrion
    		•
  • ATP synthesis coupled proton transport
    		•
  • hydrogen ion transporting ATP synthase activity, rotational mechanism
    		•
    IDH2
  • mitochondrial matrix
  • mitochondrion
    		•
  • glutamate biosynthetic process
  • isocitrate metabolic process
  • tricarboxylic acid cycle
    		•
  • isocitrate dehydrogenase (NAD+) activity
    		•
    KIN28
  • holo TFIIH complex
    		•
  • protein amino acid phosphorylation
  • positive regulation of transcription from RNA polymerase II promoter
  • transcription initiation from RNA polymerase II promoter
    		•
  • cyclin-dependent protein kinase activating kinase activity
  • RNA polymerase II carboxy-terminal domain kinase activity
  • general RNA polymerase II transcription factor activity
  • cyclin-dependent protein kinase activity
    		•
    MDH1
  • mitochondrial matrix
  • mitochondrion
    		•
  • malate metabolic process
  • tricarboxylic acid cycle
    		•
  • L-malate dehydrogenase activity
    		•
    MET18
  • nucleoplasm
    		•
  • telomere maintenance
  • nucleotide-excision repair
  • transcription from RNA polymerase II promoter
  • methionine metabolic process
    		•
  • RNA polymerase II transcription factor activity
    		•
    RAD3
  • holo TFIIH complex
  • nucleotide-excision repair factor 3 complex
    		•
  • negative regulation of transcription from RNA polymerase II promoter, mitotic
  • nucleotide-excision repair, DNA duplex unwinding
  • nucleotide-excision repair
  • transcription initiation from RNA polymerase II promoter
    		•
  • DNA helicase activity
  • general RNA polymerase II transcription factor activity
    		•
    RPN8
  • proteasome regulatory particle, lid subcomplex
    		•
  • ubiquitin-dependent protein catabolic process
    		•
  • molecular_function
    		•
    TFB3
  • holo TFIIH complex
  • nucleotide-excision repair factor 3 complex
    		•
  • negative regulation of transcription from RNA polymerase II promoter, mitotic
  • nucleotide-excision repair, DNA duplex unwinding
  • nucleotide-excision repair
  • transcription initiation from RNA polymerase II promoter
    		•
  • general RNA polymerase II transcription factor activity
    		•
    TFP1
  • vacuolar proton-transporting V-type ATPase, V1 domain
  • fungal-type vacuole membrane
    		•
  • protein metabolic process
  • vacuolar acidification
  • intron homing
    		•
  • proton-transporting ATPase activity, rotational mechanism
  • endodeoxyribonuclease activity
    		•
    YBR184W
  • cellular_component
    		•
  • biological_process
    		•
  • molecular_function
    		•

    Cellular Component Analysis

    Given the number of proteins in the complex (A), total proteins annotated with a given GO term (B), and the total number of annotated proteins (T); the p-value represents the chances of randomly having the number of proteins in the complex annotated with a specific GO term (I).

    Only showing terms with a p-value less than or equal to 0.01.

    GO Term

    		 P-value

    		 A

    		 B

    		 I

    		 T
    holo TFIIH complex 6.3144E-7 12 10 3 6292
    nucleotide-excision repair factor 3 complex 6.966E-5 12 7 2 6292
    DNA-directed RNA polymerase II, holoenzyme 1.3882E-4 12 56 3 6292
    proton-transporting two-sector ATPase complex, catalytic domain 2.571E-4 12 13 2 6292
    transcription factor complex 2.8164E-4 12 71 3 6292
    nucleotide-excision repair complex 6.8633E-4 12 21 2 6292
    organelle lumen 6.9054E-4 12 660 6 6292
    intracellular organelle lumen 6.9054E-4 12 660 6 6292
    membrane-enclosed lumen 9.4976E-4 12 700 6 6292
    nucleoplasm 1.1483E-3 12 264 4 6292
    intracellular organelle part 1.1585E-3 12 2282 10 6292
    organelle part 1.1585E-3 12 2282 10 6292
    mitochondrial part 1.2171E-3 12 475 5 6292
    proton-transporting two-sector ATPase complex 1.916E-3 12 35 2 6292
    mitochondrial inner membrane 3.8043E-3 12 174 3 6292
    organelle inner membrane 4.5228E-3 12 185 3 6292
    mitochondrial proton-transporting ATP synthase, central stalk 5.7116E-3 12 3 1 6292
    proton-transporting ATP synthase, central stalk 5.7116E-3 12 3 1 6292
    nuclear lumen 8.2402E-3 12 453 4 6292
    proton-transporting ATP synthase complex, catalytic core F(1) 9.5026E-3 12 5 1 6292
    mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) 9.5026E-3 12 5 1 6292
    nucleoplasm part 9.8819E-3 12 245 3 6292

    Biological Process Analysis

    Given the number of proteins in the complex (A), total proteins annotated with a given GO term (B), and the total number of annotated proteins (T); the p-value represents the chances of randomly having the number of proteins in the complex annotated with a specific GO term (I).

    Only showing terms with a p-value less than or equal to 0.01.

    GO Term

    		 P-value

    		 A

    		 B

    		 I

    		 T
    generation of precursor metabolites and energy 1.8022E-5 12 195 5 6292
    cellular respiration 2.3903E-5 12 97 4 6292
    nucleotide-excision repair 4.3074E-5 12 38 3 6292
    nucleotide-excision repair, DNA duplex unwinding 4.981E-5 12 6 2 6292
    transcription initiation from RNA polymerase II promoter 8.1995E-5 12 47 3 6292
    regulation of transcription from RNA polymerase II promoter, mitotic 9.2781E-5 12 8 2 6292
    negative regulation of transcription from RNA polymerase II promoter, mitotic 9.2781E-5 12 8 2 6292
    regulation of transcription, mitotic 1.1916E-4 12 9 2 6292
    negative regulation of transcription, mitotic 1.1916E-4 12 9 2 6292
    energy derivation by oxidation of organic compounds 1.2896E-4 12 149 4 6292
    transcription initiation 1.5419E-4 12 58 3 6292
    tricarboxylic acid cycle 3.4536E-4 12 15 2 6292
    acetyl-CoA catabolic process 3.4536E-4 12 15 2 6292
    aerobic respiration 4.4694E-4 12 83 3 6292
    acetyl-CoA metabolic process 6.2163E-4 12 20 2 6292
    coenzyme catabolic process 6.2163E-4 12 20 2 6292
    DNA geometric change 6.2163E-4 12 20 2 6292
    DNA duplex unwinding 6.2163E-4 12 20 2 6292
    cofactor catabolic process 7.5417E-4 12 22 2 6292
    cellular metabolic process 2.1697E-3 12 3033 11 6292
    protein complex biogenesis 2.7392E-3 12 155 3 6292
    protein complex assembly 2.7392E-3 12 155 3 6292
    transcription from RNA polymerase II promoter 2.7777E-3 12 335 4 6292
    metabolic process 3.2647E-3 12 3157 11 6292
    anaerobic respiration 3.811E-3 12 2 1 6292
    DNA repair 5.0207E-3 12 192 3 6292
    DNA conformation change 5.1947E-3 12 58 2 6292
    negative regulation of transcription from RNA polymerase II promoter 5.5506E-3 12 60 2 6292
    malate metabolic process 7.6087E-3 12 4 1 6292
    regulation of transcription from RNA polymerase II promoter 8.1053E-3 12 228 3 6292
    response to DNA damage stimulus 8.915E-3 12 236 3 6292
    isocitrate metabolic process 9.5026E-3 12 5 1 6292

    Molecular Function Analysis

    Given the number of proteins in the complex (A), total proteins annotated with a given GO term (B), and the total number of annotated proteins (T); the p-value represents the chances of randomly having the number of proteins in the complex annotated with a specific GO term (I).

    Only showing terms with a p-value less than or equal to 0.01.

    GO Term

    		 P-value

    		 A

    		 B

    		 I

    		 T
    ATP:ADP antiporter activity 9.9937E-6 12 3 2 6292
    RNA polymerase II transcription factor activity 7.5748E-5 12 130 4 6292
    solute:solute antiporter activity 9.2781E-5 12 8 2 6292
    antiporter activity 1.1916E-4 12 9 2 6292
    general RNA polymerase II transcription factor activity 2.0686E-4 12 64 3 6292
    secondary active transmembrane transporter activity 1.0566E-3 12 26 2 6292
    active transmembrane transporter activity 1.3445E-3 12 121 3 6292
    RNA polymerase II carboxy-terminal domain kinase activity 1.9072E-3 12 1 1 6292
    transmembrane transporter activity 1.9899E-3 12 306 4 6292
    transcription regulator activity 2.9012E-3 12 339 4 6292
    cyclin-dependent protein kinase activating kinase activity 3.811E-3 12 2 1 6292
    isocitrate dehydrogenase (NAD+) activity 3.811E-3 12 2 1 6292
    hydrogen ion transmembrane transporter activity 4.5161E-3 12 54 2 6292
    monovalent inorganic cation transmembrane transporter activity 5.3712E-3 12 59 2 6292
    transporter activity 5.481E-3 12 404 4 6292
    L-malate dehydrogenase activity 7.6087E-3 12 4 1 6292
    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 8.1285E-3 12 73 2 6292
    malate dehydrogenase activity 9.5026E-3 12 5 1 6292
    isocitrate dehydrogenase activity 9.5026E-3 12 5 1 6292
    oxidoreductase activity, acting on CH-OH group of donors 9.9369E-3 12 81 2 6292
    YRC Informatics Platform - Version 3.0
    Created and Maintained by: Michael Riffle