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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN AAA DOMAIN CONTAINING 2B (ATAD2B)
 
Authors :  P. Filippakopoulos, T. Keates, S. Picaud, O. Fedorov, T. Krojer, M. Vol J. Muniz, A. C. W. Pike, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. W C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)
Date :  25 Feb 10  (Deposition) - 09 Mar 10  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Atpase Family, Aaa Domain Containing 2B, Atad2B, Bromodomain, Structural Genomics Consortium, Sgc, Atp-Binding, Nucleotide- Binding, Phosphoprotein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, S. Knapp
Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family.
Cell(Cambridge, Mass. ) V. 149 214 2012
PubMed-ID: 22464331  |  Reference-DOI: 10.1016/J.CELL.2012.02.013

(-) Compounds

Molecule 1 - ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2B
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBROMODOMAIN
    GeneATAD2B, KIAA1240
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1IPA5Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:1066 , ASP B:1068BINDING SITE FOR RESIDUE IPA B 3
2AC2SOFTWAREGLU D:1066 , ASP D:1068BINDING SITE FOR RESIDUE IPA D 1
3AC3SOFTWAREARG D:1049BINDING SITE FOR RESIDUE IPA D 5

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.ATD2B_HUMAN975-1038
 
 
 
  4A:975-1038
B:975-1038
C:975-1038
D:975-1038
2BROMODOMAIN_1PS00633 Bromodomain signature.ATD2B_HUMAN980-1037
 
 
 
  4A:980-1037
B:980-1037
C:980-1037
D:980-1037
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.ATD2B_HUMAN975-1038
 
 
 
  1A:975-1038
-
-
-
2BROMODOMAIN_1PS00633 Bromodomain signature.ATD2B_HUMAN980-1037
 
 
 
  1A:980-1037
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.ATD2B_HUMAN975-1038
 
 
 
  1-
B:975-1038
-
-
2BROMODOMAIN_1PS00633 Bromodomain signature.ATD2B_HUMAN980-1037
 
 
 
  1-
B:980-1037
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.ATD2B_HUMAN975-1038
 
 
 
  1-
-
C:975-1038
-
2BROMODOMAIN_1PS00633 Bromodomain signature.ATD2B_HUMAN980-1037
 
 
 
  1-
-
C:980-1037
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.ATD2B_HUMAN975-1038
 
 
 
  1-
-
-
D:975-1038
2BROMODOMAIN_1PS00633 Bromodomain signature.ATD2B_HUMAN980-1037
 
 
 
  1-
-
-
D:980-1037

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002387891aENSE00001558735chr2:24149984-24149425560ATD2B_HUMAN1-72720--
1.2ENST000002387892ENSE00001607011chr2:24118840-24118689152ATD2B_HUMAN73-123510--
1.3ENST000002387893ENSE00001707339chr2:24111269-2411122050ATD2B_HUMAN123-140180--
1.4ENST000002387894ENSE00001681974chr2:24110855-24110702154ATD2B_HUMAN140-191520--
1.5ENST000002387895ENSE00001654691chr2:24108699-24108597103ATD2B_HUMAN191-225350--
1.6ENST000002387896ENSE00001741373chr2:24107743-24107635109ATD2B_HUMAN226-262370--
1.8ENST000002387898ENSE00001686370chr2:24103625-24103509117ATD2B_HUMAN262-301400--
1.9ENST000002387899ENSE00001705994chr2:24098774-2409869976ATD2B_HUMAN301-326260--
1.10bENST0000023878910bENSE00001654093chr2:24092631-2409253399ATD2B_HUMAN326-359340--
1.12aENST0000023878912aENSE00001602331chr2:24090816-24090705112ATD2B_HUMAN359-396380--
1.13ENST0000023878913ENSE00001789499chr2:24087794-24087679116ATD2B_HUMAN397-435390--
1.14ENST0000023878914ENSE00001766749chr2:24086425-24086251175ATD2B_HUMAN435-493590--
1.15ENST0000023878915ENSE00001768269chr2:24080373-2408028589ATD2B_HUMAN494-523300--
1.17ENST0000023878917ENSE00001785541chr2:24056948-24056789160ATD2B_HUMAN523-576540--
1.19ENST0000023878919ENSE00001800581chr2:24051809-2405171991ATD2B_HUMAN577-607310--
1.21bENST0000023878921bENSE00001663711chr2:24046439-24046128312ATD2B_HUMAN607-7111050--
1.22aENST0000023878922aENSE00001287157chr2:24042752-24042617136ATD2B_HUMAN711-756460--
1.24ENST0000023878924ENSE00001034632chr2:24033372-24033186187ATD2B_HUMAN756-818630--
1.28ENST0000023878928ENSE00000721282chr2:24021193-24021008186ATD2B_HUMAN819-880620--
1.29ENST0000023878929ENSE00000721276chr2:24011517-24011382136ATD2B_HUMAN881-926460--
1.31bENST0000023878931bENSE00001487247chr2:24009093-24008897197ATD2B_HUMAN926-991664A:951-991
B:951-991
C:951-991
D:951-991
41
41
41
41
1.32ENST0000023878932ENSE00000721263chr2:24005898-24005739160ATD2B_HUMAN992-1045544A:992-1045
B:992-1045
C:992-1045
D:992-1045
54
54
54
54
1.33ENST0000023878933ENSE00001549457chr2:23988498-23988376123ATD2B_HUMAN1045-1086424A:1045-1085
B:1045-1085
C:1045-1085
D:1045-1084
41
41
41
40
1.34ENST0000023878934ENSE00000721253chr2:23985216-23985079138ATD2B_HUMAN1086-1132470--
1.35ENST0000023878935ENSE00000808809chr2:23980971-23980288684ATD2B_HUMAN1132-13602290--
1.36bENST0000023878936bENSE00000808808chr2:23977644-23977517128ATD2B_HUMAN1360-1402430--
1.37bENST0000023878937bENSE00000808807chr2:23977177-23977049129ATD2B_HUMAN1403-1445430--
1.38cENST0000023878938cENSE00000721122chr2:23974957-239715343424ATD2B_HUMAN1446-1458130--

(-) 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:135
 aligned with ATD2B_HUMAN | Q9ULI0 from UniProtKB/Swiss-Prot  Length:1458

    Alignment length:135
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080     
         ATD2B_HUMAN    951 RMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR 1085
               SCOP domains d3lxja_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------BROMODOMAIN_2  PDB: A:975-1038 UniProt: 975-1038                ----------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------BROMODOMAIN_1  PDB: A:980-1037 UniProt: 980-1037          ------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.31b  PDB: A:951-991 [INCOMPLETE]  Exon 1.32  PDB: A:992-1045 UniProt: 992-1045          ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.33  PDB: A:1045-1085 [INCOMPLETE]  Transcript 1 (2)
                3lxj A  951 SMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR 1085
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080     

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with ATD2B_HUMAN | Q9ULI0 from UniProtKB/Swiss-Prot  Length:1458

    Alignment length:135
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080     
         ATD2B_HUMAN    951 RMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR 1085
               SCOP domains d3lxjb_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------BROMODOMAIN_2  PDB: B:975-1038 UniProt: 975-1038                ----------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------BROMODOMAIN_1  PDB: B:980-1037 UniProt: 980-1037          ------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.31b  PDB: B:951-991 [INCOMPLETE]  Exon 1.32  PDB: B:992-1045 UniProt: 992-1045          ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.33  PDB: B:1045-1085 [INCOMPLETE]  Transcript 1 (2)
                3lxj B  951 SMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR 1085
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080     

Chain C from PDB  Type:PROTEIN  Length:135
 aligned with ATD2B_HUMAN | Q9ULI0 from UniProtKB/Swiss-Prot  Length:1458

    Alignment length:135
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080     
         ATD2B_HUMAN    951 RMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR 1085
               SCOP domains d3lxjc_ C: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------BROMODOMAIN_2  PDB: C:975-1038 UniProt: 975-1038                ----------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------BROMODOMAIN_1  PDB: C:980-1037 UniProt: 980-1037          ------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.31b  PDB: C:951-991 [INCOMPLETE]  Exon 1.32  PDB: C:992-1045 UniProt: 992-1045          ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.33  PDB: C:1045-1085 [INCOMPLETE]  Transcript 1 (2)
                3lxj C  951 SMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIKR 1085
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080     

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with ATD2B_HUMAN | Q9ULI0 from UniProtKB/Swiss-Prot  Length:1458

    Alignment length:134
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080    
         ATD2B_HUMAN    951 RMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIK 1084
               SCOP domains d3lxjd_ D: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------BROMODOMAIN_2  PDB: D:975-1038 UniProt: 975-1038                ---------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------BROMODOMAIN_1  PDB: D:980-1037 UniProt: 980-1037          ----------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.31b  PDB: D:951-991 [INCOMPLETE]  Exon 1.32  PDB: D:992-1045 UniProt: 992-1045          --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.33  PDB: D:1045-1084 [INCOMPLETE] Transcript 1 (2)
                3lxj D  951 SMEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKEARIK 1084
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080    

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LXJ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ATD2B_HUMAN | Q9ULI0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0031936    negative regulation of chromatin silencing    Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing.
    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.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATD2B_HUMAN | Q9ULI02dkw

(-) Related Entries Specified in the PDB File

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