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(-) Description

Title :  STRUCTURE OF THE RB C-TERMINAL DOMAIN BOUND TO AN E2F1-DP1 HETERODIMER
 
Authors :  S. M. Rubin, A. L. Gall, N. Zheng, N. P. Pavletich
Date :  10 Sep 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Coiled Coil, Beta Sandwich, Cell Cycle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Rubin, A. L. Gall, N. Zheng, N. P. Pavletich
Structure Of The Rb C-Terminal Domain Bound To E2F1-Dp1: A Mechanism For Phosphorylation-Induced E2F Release.
Cell(Cambridge, Mass. ) V. 123 1093 2005
PubMed-ID: 16360038  |  Reference-DOI: 10.1016/J.CELL.2005.09.044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR DP-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCOILED COIL AND MARKED BOX DOMAINS (RESIDUES 199- 350)
    GeneTFDP1, DP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE2F DIMERIZATION PARTNER 1, DRTF1-POLYPEPTIDE-1, DRTF1
 
Molecule 2 - TRANSCRIPTION FACTOR E2F1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCOILED COIL AND MARKED BOX DOMAINS (RESIDUES 200- 301)
    GeneE2F1, RBBP3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE2F-1, RETINOBLASTOMA BINDING PROTEIN 3, RBBP-3, PRB-BINDING PROTEIN E2F-1, PBR3, RETINOBLASTOMA-ASSOCIATED PROTEIN 1, RBAP-1
 
Molecule 3 - RETINOBLASTOMA-ASSOCIATED PROTEIN
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC-TERMINAL CORE DOMAIN (RESIDUES 829-874)
    GeneRB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPP110, P105-RB, RB

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC
Biological Unit 2 (2x)ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2AZE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:259 -Pro A:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013607R252HE2F1_HUMANPolymorphism3213172BR252H
2UniProtVAR_013608V276ME2F1_HUMANPolymorphism3213173BV276M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013607R252HE2F1_HUMANPolymorphism3213172BR252H
2UniProtVAR_013608V276ME2F1_HUMANPolymorphism3213173BV276M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013607R252HE2F1_HUMANPolymorphism3213172BR252H
2UniProtVAR_013608V276ME2F1_HUMANPolymorphism3213173BV276M

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (11, 11)

Asymmetric Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002671631bENSE00002199946chr13:48877911-48878185275RB_HUMAN1-46460--
1.2ENST000002671632ENSE00000939664chr13:48881416-48881542127RB_HUMAN46-88430--
1.3ENST000002671633ENSE00000939665chr13:48916735-48916850116RB_HUMAN89-127390--
1.4ENST000002671634ENSE00000939666chr13:48919216-48919335120RB_HUMAN127-167410--
1.5ENST000002671635ENSE00000939667chr13:48921961-4892199939RB_HUMAN167-180140--
1.6ENST000002671636ENSE00000939668chr13:48923092-4892315968RB_HUMAN180-203240--
1.7aENST000002671637aENSE00000939669chr13:48934153-48934263111RB_HUMAN203-240380--
1.8bENST000002671638bENSE00000939670chr13:48936951-48937093143RB_HUMAN240-287480--
1.9ENST000002671639ENSE00000939671chr13:48939030-4893910778RB_HUMAN288-313260--
1.10ENST0000026716310ENSE00000939672chr13:48941630-48941739110RB_HUMAN314-350370--
1.11ENST0000026716311ENSE00000939673chr13:48942663-4894274078RB_HUMAN350-376270--
1.12ENST0000026716312ENSE00000939674chr13:48947541-4894762888RB_HUMAN376-405300--
1.13ENST0000026716313ENSE00000939675chr13:48951054-48951170117RB_HUMAN406-444390--
1.14ENST0000026716314ENSE00000939676chr13:48953730-4895378657RB_HUMAN445-463190--
1.15ENST0000026716315ENSE00000939677chr13:48954189-4895422032RB_HUMAN464-474110--
1.16ENST0000026716316ENSE00000939678chr13:48954301-4895437777RB_HUMAN474-500270--
1.17ENST0000026716317ENSE00000939679chr13:48955383-48955579197RB_HUMAN500-565660--
1.19ENST0000026716319ENSE00000939680chr13:49027129-49027247119RB_HUMAN566-605400--
1.20bENST0000026716320bENSE00000939681chr13:49030340-49030485146RB_HUMAN605-654500--
1.21ENST0000026716321ENSE00000939682chr13:49033824-49033969146RB_HUMAN654-702490--
1.22ENST0000026716322ENSE00000939683chr13:49037867-49037971105RB_HUMAN703-737350--
1.23ENST0000026716323ENSE00000939684chr13:49039134-49039247114RB_HUMAN738-775380--
1.24ENST0000026716324ENSE00000939685chr13:49039341-49039504164RB_HUMAN776-830551C:829-8302
1.25ENST0000026716325ENSE00001003962chr13:49047496-4904752631RB_HUMAN830-840111C:830-84011
1.26cENST0000026716326cENSE00000939686chr13:49050837-49050979143RB_HUMAN841-888481C:841-87232
1.27ENST0000026716327ENSE00000939687chr13:49051491-4905154050RB_HUMAN888-905180--
1.28cENST0000026716328cENSE00001241067chr13:49054134-490561221989RB_HUMAN905-928240--

2.1aENST000003433801aENSE00001667355chr20:32274210-32273810401E2F1_HUMAN1-87870--
2.2ENST000003433802ENSE00000661346chr20:32268222-3226813291E2F1_HUMAN88-118310--
2.3ENST000003433803ENSE00000661345chr20:32267780-32267561220E2F1_HUMAN118-191740--
2.4aENST000003433804aENSE00001387594chr20:32266159-32266007153E2F1_HUMAN191-242521B:201-24242
2.5aENST000003433805aENSE00000860058chr20:32265346-32265232115E2F1_HUMAN242-280391B:242-28039
2.6ENST000003433806ENSE00000661342chr20:32265136-32264911226E2F1_HUMAN281-356761B:281-30121
2.7ENST000003433807ENSE00001386402chr20:32264785-322634891297E2F1_HUMAN356-437820--

3.1cENST000003753701cENSE00001466880chr13:114239056-114239203148TFDP1_HUMAN-00--
3.3ENST000003753703ENSE00002175315chr13:114240089-11424016476TFDP1_HUMAN1-440--
3.5ENST000003753705ENSE00001385204chr13:114265311-11426537767TFDP1_HUMAN5-27230--
3.6ENST000003753706ENSE00000862637chr13:114277495-114277601107TFDP1_HUMAN27-62360--
3.7aENST000003753707aENSE00000862639chr13:114285938-114286059122TFDP1_HUMAN63-103410--
3.8aENST000003753708aENSE00001325757chr13:114287435-114287600166TFDP1_HUMAN103-158560--
3.9bENST000003753709bENSE00001618735chr13:114288205-114288348144TFDP1_HUMAN159-206481A:198-2069
3.10ENST0000037537010ENSE00000862642chr13:114288849-11428891769TFDP1_HUMAN207-229231A:207-22923
3.11bENST0000037537011bENSE00001290461chr13:114290292-114290443152TFDP1_HUMAN230-280511A:230-28051
3.12ENST0000037537012ENSE00000862645chr13:114290849-114291015167TFDP1_HUMAN280-336571A:280-33657
3.14ENST0000037537014ENSE00000862648chr13:114292133-11429221179TFDP1_HUMAN336-362271A:336-34611
3.15bENST0000037537015bENSE00001433161chr13:114294435-1142955041070TFDP1_HUMAN362-410490--

(-) 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:149
 aligned with TFDP1_HUMAN | Q14186 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:149
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337         
          TFDP1_HUMAN   198 SAQECQNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVF 346
               SCOP domains -d2azea1 A:199-346 Transcription factor DP-1                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eee...eeeeee....eeeee.....eeeeee...eeeeehhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 3 (1) Exon 3.9bExon 3.10              Exon 3.11b  PDB: A:230-280 UniProt: 230-280        -------------------------------------------------------Exon 3.14   Transcript 3 (1)
           Transcript 3 (2) ----------------------------------------------------------------------------------Exon 3.12  PDB: A:280-336 UniProt: 280-336               ---------- Transcript 3 (2)
                 2aze A 198 FAQECQNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVF 346
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337         

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with E2F1_HUMAN | Q01094 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:101
                                   210       220       230       240       250       260       270       280       290       300 
           E2F1_HUMAN   201 GRLEGLTQDLRQLQESEQQLDHLMNICTTQLRLLSEDTDSQRLAYVTCQDLRSIADPAEQMVMVIKAPPETQLQAVDSSENFQISLKSKQGPIDVFLCPEE 301
               SCOP domains d2azeb1 B:201-301 Transcription factor E2F1                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhh......eeeeeee.....eeeeee....eeeeee......eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------H-----------------------M------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.4a  PDB: B:201-242 UniProt: 191-242--------------------------------------Exon 2.6 [INCOMPLETE] Transcript 2 (1)
           Transcript 2 (2) -----------------------------------------Exon 2.5a  PDB: B:242-280              --------------------- Transcript 2 (2)
                 2aze B 201 GRLEGLTQDLRQLQESEQQLDHLMNICTTQLRLLSEDTDSQRLAYVTCQDLRSIADPAEQMVMVIKAPPETQLQAVDSSENFQISLKSKQGPIDVFLCPEE 301
                                   210       220       230       240       250       260       270       280       290       300 

Chain C from PDB  Type:PROTEIN  Length:44
 aligned with RB_HUMAN | P06400 from UniProtKB/Swiss-Prot  Length:928

    Alignment length:44
                                   838       848       858       868    
             RB_HUMAN   829 SRILVSIGESFGTSEKFQKINQMVCNSDRVLKRSAEGSNPPKPL 872
               SCOP domains d2azec1 C:829-872                            SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
           Transcript 1 (1) 1.----------Exon 1.26c  PDB: C:841-872       Transcript 1 (1)
           Transcript 1 (2) -Exon 1.25  -------------------------------- Transcript 1 (2)
                 2aze C 829 SRILVSIGESFGTSEKFQKINQMVCNSDRVLKRSAEGSNPPKPL 872
                                   838       848       858       868    

   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  (3, 3)

Asymmetric Unit
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AZE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (105, 142)

Asymmetric Unit(hide GO term definitions)
Chain A   (TFDP1_HUMAN | Q14186)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0070345    negative regulation of fat cell proliferation    Any process that stops or decreases the rate or extent of fat cell proliferation.
    GO:1900740    positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain B   (E2F1_HUMAN | Q01094)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0000077    DNA damage checkpoint    A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0043276    anoikis    Apoptosis triggered by inadequate or inappropriate adherence to substrate e.g. after disruption of the interactions between normal epithelial cells and the extracellular matrix.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0071398    cellular response to fatty acid    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 fatty acid stimulus.
    GO:0071456    cellular response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:1990090    cellular response to nerve growth factor stimulus    A 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 nerve growth factor stimulus.
    GO:0071466    cellular response to xenobiotic 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 xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0072332    intrinsic apoptotic signaling pathway by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:1990086    lens fiber cell apoptotic process    Any apoptotic process in a lens fiber cell. Lens fiber cells are elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye.
    GO:0048255    mRNA stabilization    Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    GO:0070345    negative regulation of fat cell proliferation    Any process that stops or decreases the rate or extent of fat cell proliferation.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0071930    negative regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that stop, prevents or decreases transcription as part of the G1/S transition of the mitotic cell cycle.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048146    positive regulation of fibroblast proliferation    Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    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:1900740    positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:2000045    regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0035189    Rb-E2F complex    A multiprotein complex containing a heterodimeric E2F transcription factor and a Retinoblastoma (Rb) family member. This complex is capable of repressing transcription of E2F-regulated genes in order to regulate cell cycle progression.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain C   (RB_HUMAN | P06400)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0030521    androgen receptor signaling pathway    Any series of molecular signals generated as a consequence of an androgen binding to its receptor.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0000075    cell cycle checkpoint    A cell cycle process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0048667    cell morphogenesis involved in neuron differentiation    The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron.
    GO:0071466    cellular response to xenobiotic 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 xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0043353    enucleate erythrocyte differentiation    The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
    GO:0034349    glial cell apoptotic process    Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system.
    GO:0097284    hepatocyte apoptotic process    Any apoptotic process in a hepatocyte, the main structural component of the liver.
    GO:0034088    maintenance of mitotic sister chromatid cohesion    The process in which the association between sister chromatids of a replicated chromosome is maintained as chromosomes condense, attach to the spindle in a bipolar orientation, and congress to the metaphase plate during a mitotic cell cycle.
    GO:0007093    mitotic cell cycle checkpoint    A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
    GO:0045445    myoblast differentiation    The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0050680    negative regulation of epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
    GO:0010629    negative regulation of gene expression    Any process that decreases 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:0045930    negative regulation of mitotic cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045879    negative regulation of smoothened signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0007070    negative regulation of transcription from RNA polymerase II promoter during mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle.
    GO:0071930    negative regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that stop, prevents or decreases transcription as part of the G1/S transition of the mitotic cell cycle.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0042551    neuron maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0045651    positive regulation of macrophage differentiation    Any process that activates or increases the frequency, rate or extent of macrophage differentiation.
    GO:0045842    positive regulation of mitotic metaphase/anaphase transition    Any process that activates or increases the frequency, rate or extent of 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: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:2000679    positive regulation of transcription regulatory region DNA binding    Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0071459    protein localization to chromosome, centromeric region    Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0090230    regulation of centromere complex assembly    Any process that modulates the rate, frequency, or extent of centromere complex assembly, the aggregation, arrangement and bonding together of proteins and centromeric DNA molecules to form a centromeric protein-DNA complex.
    GO:0071922    regulation of cohesin loading    Any process that modulates the frequency, rate or extent of a process in which a cohesin complex is transported to, or maintained at, a part of a chromosome that is organized into chromatin.
    GO:0043550    regulation of lipid kinase activity    Any process that modulates the frequency, rate or extent of lipid kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a simple or complex lipid.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031134    sister chromatid biorientation    The cell cycle process in which sister chromatids establish stable attachments to microtubules emanating from opposite spindle poles.
    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.
    GO:0051146    striated muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    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:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0035189    Rb-E2F complex    A multiprotein complex containing a heterodimeric E2F transcription factor and a Retinoblastoma (Rb) family member. This complex is capable of repressing transcription of E2F-regulated genes in order to regulate cell cycle progression.
    GO:0016514    SWI/SNF complex    A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components.
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0008024    cyclin/CDK positive transcription elongation factor complex    A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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        E2F1_HUMAN | Q010941h24 1o9k 5m9n 5m9o
        RB_HUMAN | P064001ad6 1gh6 1gux 1h25 1n4m 1o9k 1pjm 2qdj 2r7g 3n5u 3pom 4cri 4elj 4ell
        TFDP1_HUMAN | Q141865gow 5tuu 5tuv

(-) Related Entries Specified in the PDB File

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