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(-) Description

Title :  CRYSTAL STRUCTURE OF AN RB C-TERMINAL PEPTIDE BOUND TO THE CATALYTIC SUBUNIT OF PP1
 
Authors :  A. M. Hirschi, M. Cecchini, R. C. Steinhardt, F. A. Dick, S. M. Rubin
Date :  25 May 10  (Deposition) - 11 Aug 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Retinoblastoma, Prb, Rb, Protein Phosphatase-1, Pp1, Phosphatase, Hydrolase, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Hirschi, M. Cecchini, R. C. Steinhardt, M. R. Schamber, F. A. Dick, S. M. Rubin
An Overlapping Kinase And Phosphatase Docking Site Regulate Activity Of The Retinoblastoma Protein.
Nat. Struct. Mol. Biol. V. 17 1051 2010
PubMed-ID: 20694007  |  Reference-DOI: 10.1038/NSMB.1868

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-ALPHA CATALYTIC SUBUNIT
    ChainsA, B
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPFLAG-CTS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-300
    GenePPP1A, PPP1CA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPP-1A
 
Molecule 2 - RETINOBLASTOMA-ASSOCIATED PROTEIN
    ChainsC
    EngineeredYES
    FragmentUNP RESIDUES 870-882
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHETIC 13-MER PEPTIDE
    SynonymPRB, RB, PP110, P105-RB
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMN A:2 , ASP A:64 , HIS A:66 , ASP A:92 , TYR A:272 , CL A:301BINDING SITE FOR RESIDUE MN A 1
2AC2SOFTWAREMN A:1 , ASP A:64 , ASP A:92 , ASN A:124 , HIS A:173 , HIS A:248 , CL A:301BINDING SITE FOR RESIDUE MN A 2
3AC3SOFTWARECL B:2 , MN B:4 , ASP B:64 , HIS B:66 , ASP B:92 , TYR B:272BINDING SITE FOR RESIDUE MN B 3
4AC4SOFTWARECL B:2 , MN B:3 , ASP B:64 , ASP B:92 , ASN B:124 , HIS B:173 , HIS B:248BINDING SITE FOR RESIDUE MN B 4
5AC5SOFTWAREMN A:1 , MN A:2 , ARG A:96 , HIS A:125 , ARG A:221BINDING SITE FOR RESIDUE CL A 301
6AC6SOFTWAREMN B:3 , MN B:4 , ARG B:96 , ASN B:124 , HIS B:125 , ARG B:221BINDING SITE FOR RESIDUE CL B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N5U)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:57 -Pro A:58
2Pro A:82 -Pro A:83
3Arg A:191 -Pro A:192
4Ala B:57 -Pro B:58
5Pro B:82 -Pro B:83
6Arg B:191 -Pro B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N5U)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SER_THR_PHOSPHATASEPS00125 Serine/threonine specific protein phosphatases signature.PP1A_HUMAN121-126
 
  2A:121-126
B:121-126
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SER_THR_PHOSPHATASEPS00125 Serine/threonine specific protein phosphatases signature.PP1A_HUMAN121-126
 
  2A:121-126
B:121-126
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SER_THR_PHOSPHATASEPS00125 Serine/threonine specific protein phosphatases signature.PP1A_HUMAN121-126
 
  1A:121-126
-

(-) Exons   (8, 15)

Asymmetric Unit (8, 15)
 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_HUMAN776-830550--
1.25ENST0000026716325ENSE00001003962chr13:49047496-4904752631RB_HUMAN830-840110--
1.26cENST0000026716326cENSE00000939686chr13:49050837-49050979143RB_HUMAN841-888481C:873-8797
1.27ENST0000026716327ENSE00000939687chr13:49051491-4905154050RB_HUMAN888-905180--
1.28cENST0000026716328cENSE00001241067chr13:49054134-490561221989RB_HUMAN905-928240--

2.3aENST000003767453aENSE00001471548chr11:67169402-67169199204PP1A_HUMAN1-19192A:7-19
B:7-19
13
13
2.4dENST000003767454dENSE00001212206chr11:67168670-67168539132PP1A_HUMAN19-63452A:19-63
B:19-63
45
45
2.4fENST000003767454fENSE00001741927chr11:67168390-67168160231PP1A_HUMAN63-140782A:63-140
B:63-140
78
78
2.5aENST000003767455aENSE00001186176chr11:67167136-67167032105PP1A_HUMAN140-175362A:140-175
B:140-175
36
36
2.6aENST000003767456aENSE00001186169chr11:67166634-67166411224PP1A_HUMAN175-249752A:175-249
B:175-249
75
75
2.6dENST000003767456dENSE00001707059chr11:67166327-67166193135PP1A_HUMAN250-294452A:250-294
B:250-294
45
45
2.7cENST000003767457cENSE00002183271chr11:67166116-67165672445PP1A_HUMAN295-330362A:295-300
B:295-300
6
6

(-) 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:294
 aligned with PP1A_HUMAN | P62136 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:294
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
           PP1A_HUMAN     7 LNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD 300
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..ee.....eeee.....hhhhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhh...eee......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeee...eee..........hhhhhhh.........hhhhhhhhhhee......eee......eeehhhhhhhhhhhh...eeee........eeee....eeee.............eeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------SER_TH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.3a    -------------------------------------------Exon 2.4f  PDB: A:63-140 UniProt: 63-140                                      ----------------------------------Exon 2.6a  PDB: A:175-249 UniProt: 175-249                                 Exon 2.6d  PDB: A:250-294 UniProt: 250-294   2.7c   Transcript 2 (1)
           Transcript 2 (2) ------------Exon 2.4d  PDB: A:19-63 UniProt: 19-63       ----------------------------------------------------------------------------Exon 2.5a  PDB: A:140-175           ----------------------------------------------------------------------------------------------------------------------------- Transcript 2 (2)
                 3n5u A   7 LNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD 300
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with PP1A_HUMAN | P62136 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:294
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
           PP1A_HUMAN     7 LNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD 300
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------------------------Metallophos-3n5uB01 B:57-252                                                                                                                                                                        ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------Metallophos-3n5uB02 B:57-252                                                                                                                                                                        ------------------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..ee.....eeee.....hhhhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhh...eee......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeee...eee..........hhhhhhh.........hhhhhhhhhhee......eee......eeehhhhhhhhhhhh...eeee........eeee....eeee.............eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------SER_TH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.3a    -------------------------------------------Exon 2.4f  PDB: B:63-140 UniProt: 63-140                                      ----------------------------------Exon 2.6a  PDB: B:175-249 UniProt: 175-249                                 Exon 2.6d  PDB: B:250-294 UniProt: 250-294   2.7c   Transcript 2 (1)
           Transcript 2 (2) ------------Exon 2.4d  PDB: B:19-63 UniProt: 19-63       ----------------------------------------------------------------------------Exon 2.5a  PDB: B:140-175           ----------------------------------------------------------------------------------------------------------------------------- Transcript 2 (2)
                 3n5u B   7 LNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD 300
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with RB_HUMAN | P06400 from UniProtKB/Swiss-Prot  Length:928

    Alignment length:7
             RB_HUMAN   873 KKLRFDI 879
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains Rb_C-3n Pfam domains
         Sec.struct. author ...ee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
               Transcript 1 1.26c   Transcript 1
                 3n5u C 873 KKLRFDI 879

   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 3N5U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N5U)

(-) Pfam Domains  (2, 3)

Asymmetric Unit

(-) Gene Ontology  (114, 119)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PP1A_HUMAN | P62136)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
    GO:0043021    ribonucleoprotein complex binding    Interacting selectively and non-covalently with any complex of RNA and protein.
biological process
    GO:1904886    beta-catenin destruction complex disassembly    The disaggregation of a beta-catenin destruction complex into its constituent components.
    GO:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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: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:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0043153    entrainment of circadian clock by photoperiod    The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
    GO:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:2001241    positive regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0060828    regulation of canonical Wnt signaling pathway    Any process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0005979    regulation of glycogen biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:0005981    regulation of glycogen catabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.
    GO:0036496    regulation of translational initiation by eIF2 alpha dephosphorylation    Any process that modulates the frequency, rate or extent of translation initiation in response to stress by the dephosphorylation of eIF2 alpha.
cellular component
    GO:0070688    MLL5-L complex    A protein complex that can methylate lysine-4 of histone H3 and plays an essential role in retinoic-acid-induced granulopoiesis. MLL5 is the catalytic methyltransferase subunit, and the complex also contains serine/threonine kinase 38 (STK38), protein phosphatase 1 catalytic subunits, the host cell factor-1 N-terminal subunit, beta-actin, and O-GlcNAc transferase; the human genes encoding the subunits are MLL5, STK38, PPP1CA, PPP1CB, PPP1CC, HCFC1, ACTB and OGT, respectively.
    GO:0072357    PTW/PP1 phosphatase complex    A protein serine/threonine phosphatase complex that contains a catalytic subunit (PPP1CA, PPP1CB or PPP1CC) and the regulatory subunits PPP1R10 (PNUTS), TOX4 and WDR82, and plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase.
    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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0042587    glycogen granule    Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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: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:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0000164    protein phosphatase type 1 complex    A protein complex that possesses magnesium-dependent protein serine/threonine phosphatase (AMD phosphatase) activity, and consists of a catalytic subunit and one or more regulatory subunits that dictates the phosphatase's substrate specificity, function, and activity.

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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        PP1A_HUMAN | P621361fjm 3e7a 3e7b 3egg 3egh 3hvq 3v4y 4g9j 4mov 4moy 4mp0 4xpn 5ioh
        RB_HUMAN | P064001ad6 1gh6 1gux 1h25 1n4m 1o9k 1pjm 2aze 2qdj 2r7g 3pom 4cri 4elj 4ell

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3N5U)