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(-) Description

Title :  STRUCTURAL BASIS FOR RBAP48 BINDING TO FOG-1
 
Authors :  S. Lejon, S. Y. Thong, A. Murthy, G. A. Blobel, J. P. Mackay, N. V. Murzina
Date :  15 Oct 10  (Deposition) - 03 Nov 10  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Transcription, Chromatin Remodelling, Histone Chaperone, Corepressor, Gata1-Mediated Repression, Nurd Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Lejon, S. Y. Thong, A. Murthy, S. Alqarni, N. V. Murzina, G. A. Blobel E. D. Laue, J. P. Mackay
Insights Into Association Of The Nurd Complex With Fog-1 From The Crystal Structure Of An Rbap48-Fog- 1 Complex.
J. Biol. Chem. V. 286 1196 2011
PubMed-ID: 21047798  |  Reference-DOI: 10.1074/JBC.M110.195842

(-) Compounds

Molecule 1 - HISTONE-BINDING PROTEIN RBBP4
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFBDM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHROMATIN ASSEMBLY FACTOR 1 SUBUNIT C, CAF-1 SUBUNIT C, NUCLEOSOME-REMODELING FACTOR SUBUNIT RBAP48, CAF-I 48 KDA SUBUNIT, CAF-I P48, RETINOBLASTOMA-BINDING PROTEIN 4, RBBP-4, RETINOBLASTOMA-BINDING PROTEIN P48
 
Molecule 2 - ZINC FINGER PROTEIN ZFPM1
    ChainsC, D
    FragmentRBAP48-BINDING FRAGMENT, RESIDUES 1-15
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFRIEND OF GATA PROTEIN 1, FOG-1, FRIEND OF GATA 1, ZINC FINGER PROTEIN MULTITYPE 1
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:318 , HOH A:2081BINDING SITE FOR RESIDUE PG4 A1411
2AC2SOFTWAREALA B:294 , LYS B:296 , ASP B:318 , GLU B:319BINDING SITE FOR RESIDUE PG4 B1411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XU7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XU7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XU7)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.RBBP4_HUMAN193-207
 
289-303
 
333-347
 
  6A:193-207
B:193-207
A:289-303
B:289-303
A:333-347
B:333-347
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.RBBP4_HUMAN193-207
 
289-303
 
333-347
 
  3A:193-207
-
A:289-303
-
A:333-347
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.RBBP4_HUMAN193-207
 
289-303
 
333-347
 
  3-
B:193-207
-
B:289-303
-
B:333-347

(-) Exons   (0, 0)

(no "Exon" information available for 2XU7)

(-) 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:360
 aligned with RBBP4_HUMAN | Q09028 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:395
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405     
          RBBP4_HUMAN    16 VINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYN 410
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhheeeeeeee........eeeeeee------.eeeeeeee........eeeeeeeee..-------------------------.eeeeeeee......eeeee..eeeeeeee.....eeeee.hhh.............eeee.....eeeeee......eeeeee....eeeee........eeee..eee......eeeeee......eeeeee...eeeeee..........eeee.....eeeeee......eeeeee...eeeeee........eeee.....eeeeee......eeeeee....eeeee.hhh.....----......eeeee......eeeeee......eeeeee...eeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   ---------------------------------------------------------------------------------WD_REPEATS_1   -----------------------------WD_REPEATS_1   --------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xu7 A  16 VINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVT------FSIHRLVLGTHTSDEQNHLVIASVQLPN-------------------------KIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQS----EDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYN 410
                                    25        35        45        |-     |  65        75        85  |      -         -       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    |  365       375       385       395       405     
                                                                 54     61                         88                       114                                                                                                                                                                                                                                              355  360                                                  

Chain B from PDB  Type:PROTEIN  Length:367
 aligned with RBBP4_HUMAN | Q09028 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:400
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
          RBBP4_HUMAN    11 AVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYN 410
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------CAF1C_H4-bd-2xu7B11 B:18-88                                            -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B01 B:364-403                  ------- Pfam domains (1)
           Pfam domains (2) -------CAF1C_H4-bd-2xu7B12 B:18-88                                            -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B02 B:364-403                  ------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B03 B:364-403                  ------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B04 B:364-403                  ------- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B05 B:364-403                  ------- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B06 B:364-403                  ------- Pfam domains (6)
           Pfam domains (7) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B07 B:364-403                  ------- Pfam domains (7)
           Pfam domains (8) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B08 B:364-403                  ------- Pfam domains (8)
           Pfam domains (9) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B09 B:364-403                  ------- Pfam domains (9)
          Pfam domains (10) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-2xu7B10 B:364-403                  ------- Pfam domains (10)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhheeeeeeee.......eee...........eeeeeeeee.......eeeeeeeeeee.-------------------------.eeeeeeeee.....eeeee..eeeeeeee.....eeeee.hhh.............eeee........eee......eeeee.....eeeee.........eee..eee......eeeeee......eeeeee...eeeeee..........eeee.....eeeeee......eeeeee...eeeeee.hhh....eeee.....eeeeee......eeeeee....eeeee.hhh..--------.....eeeee......eeeeee......eeeeee...eeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   ---------------------------------------------------------------------------------WD_REPEATS_1   -----------------------------WD_REPEATS_1   --------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xu7 B  11 AVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPN-------------------------KIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGE--------DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYN 410
                                    20        30        40        50        60        70        80       | -         -         -   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 |       -|      370       380       390       400       410
                                                                                                        88                       114                                                                                                                                                                                                                                           352      361                                                 

Chain C from PDB  Type:PROTEIN  Length:12
 aligned with FOG1_HUMAN | Q8IX07 from UniProtKB/Swiss-Prot  Length:1006

    Alignment length:12
                                    11  
           FOG1_HUMAN     2 SRRKQSNPRQIK  13
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2xu7 C   2 SRRKQSNPRQIK  13
                                    11  

Chain D from PDB  Type:PROTEIN  Length:13
 aligned with FOG1_HUMAN | Q8IX07 from UniProtKB/Swiss-Prot  Length:1006

    Alignment length:13
                                    10   
           FOG1_HUMAN     1 MSRRKQSNPRQIK  13
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2xu7 D   1 MSRRKQSNPRQIK  13
                                    10   

   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 2XU7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XU7)

(-) Pfam Domains  (2, 12)

Asymmetric Unit
(-)
Family: WD40 (64)
1aWD40-2xu7B01B:364-403
1bWD40-2xu7B02B:364-403
1cWD40-2xu7B03B:364-403
1dWD40-2xu7B04B:364-403
1eWD40-2xu7B05B:364-403
1fWD40-2xu7B06B:364-403
1gWD40-2xu7B07B:364-403
1hWD40-2xu7B08B:364-403
1iWD40-2xu7B09B:364-403
1jWD40-2xu7B10B:364-403

(-) Gene Ontology  (72, 77)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RBBP4_HUMAN | Q09028)
molecular function
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0034080    CENP-A containing nucleosome assembly    The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    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:0031497    chromatin assembly    The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
    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:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    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:0033186    CAF-1 complex    A conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). In many species the CAF-1 subunits are designated p150, p60, and p48.
    GO:0035098    ESC/E(Z) complex    A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.
    GO:0016589    NURF complex    An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.
    GO:0016581    NuRD complex    An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
    GO:0016580    Sin3 complex    A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Chain C,D   (FOG1_HUMAN | Q8IX07)
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:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0002295    T-helper cell lineage commitment    The process in which a CD4-positive, alpha-beta T cell becomes committed to becoming a T-helper cell, a CD4-positive, alpha-beta T cell specialized to promote various immunological processes.
    GO:0060413    atrial septum morphogenesis    The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another.
    GO:0003181    atrioventricular valve morphogenesis    The process in which the structure of the atrioventricular valve is generated and organized.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0055008    cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac muscle tissue are generated and organized.
    GO:0060318    definitive erythrocyte differentiation    Erythrocyte differentiation which occurs as part of the process of definitive hemopoiesis.
    GO:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0030851    granulocyte differentiation    The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0048872    homeostasis of number of cells    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
    GO:0035855    megakaryocyte development    The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
    GO:0030219    megakaryocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
    GO:0003192    mitral valve formation    The developmental process pertaining to the initial formation of the mitral valve from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable.
    GO:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    GO:0045403    negative regulation of interleukin-4 biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-4.
    GO:0060377    negative regulation of mast cell differentiation    Any process that decreases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    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:0003151    outflow tract morphogenesis    The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
    GO:0030220    platelet formation    The process in which platelets bud from long processes extended by megakaryocytes.
    GO:0045078    positive regulation of interferon-gamma biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
    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:0060319    primitive erythrocyte differentiation    Erythrocyte differentiation which occurs as part of the process of primitive hemopoiesis.
    GO:0032642    regulation of chemokine production    Any process that modulates the frequency, rate, or extent of chemokine production.
    GO:0010724    regulation of definitive erythrocyte differentiation    Any process that modulates the rate, frequency, or extent of definitive erythrocyte differentiation. Definitive erythrocyte differentiation occurs as part of the process of definitive hemopoiesis.
    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.
    GO:0071733    transcriptional activation by promoter-enhancer looping    The formation and maintenance of DNA loops that juxtapose the promoter and enhancer regions of RNA polymerase II-transcribed genes and activate transcription from an RNA polymerase II promoter.
    GO:0003195    tricuspid valve formation    The developmental process pertaining to the initial formation of the tricuspid valve from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable.
    GO:0060412    ventricular septum morphogenesis    The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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        RBBP4_HUMAN | Q090283gfc 4pby 4pbz 4pc0 4r7a 5fxy

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