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(-) Description

Title :  STRUCTURAL BASIS FOR HISTONE CODE RECOGNITION BY BRPF2-PHD1 FINGER
 
Authors :  S. Qin, J. Zhang, J. Wu, Y. Shi
Date :  01 Oct 10  (Deposition) - 31 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Phd Finger, Histone Code, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Qin, J. Zhang, J. Wu, Y. Shi
Recognition Of Unmodified Histone H3 By The First Phd Finge Of Bromodomain-Phd Finger Protein 2 Provides Insights Into The Regulation Of Histone Acetyltransferases Moz And Morf
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - N-TEMINAL DOMAIN FROM HISTONE H3.3, LINKER, PHD1 DOMAIN FROM BROMODOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: HUMAN, SYNTHETIC, HUMAN
    Organism Scientific: HOMO SAPIENS, SYNTHETIC, HOMO SAPIENS
    Organism Taxid: 9606, 32630, 9606
    Other Details: CHIMERIC PROTEIN OF HISTONE H3.3, LINKER, BRPF2 PHD1 DOMAIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:28 , CYS A:31 , HIS A:53 , CYS A:56BINDING SITE FOR RESIDUE ZN A 89
2AC2SOFTWARECYS A:45 , CYS A:48 , CYS A:69 , CYS A:72BINDING SITE FOR RESIDUE ZN A 90

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L43)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L43)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L43)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.BRD1_HUMAN214-264  1A:25-75
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.BRD1_HUMAN217-261  1A:28-72
3EPHDPS51805 Extended PHD (ePHD) domain profile.BRD1_HUMAN268-389  1A:79-80
NMR Structure * (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.BRD1_HUMAN214-264  1A:25-75
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.BRD1_HUMAN217-261  1A:28-72
3EPHDPS51805 Extended PHD (ePHD) domain profile.BRD1_HUMAN268-389  1A:79-80

(-) Exons   (0, 0)

(no "Exon" information available for 2L43)

(-) Sequences/Alignments

NMR Structure
   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:80
 aligned with BRD1_HUMAN | O95696 from UniProtKB/Swiss-Prot  Length:1058

    Alignment length:173
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266   
           BRD1_HUMAN    97 VKKKNEALPSAHGTPASASALPEPKVRIVEYSPPSAPRRPPVYYKFIEKSAEELDNEVEYDMDEEDYAWLEIVNEKRKGDCVPAVSQSMFEFLMDRFEKESHCENQKQGEQQSLIDEDAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPA 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........---------------------------------------------------------------------------------------------....................eeeeee........hhhhhh..........hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------ZF_PHD_2  PDB: A:25-75 UniProt: 214-264            ---EP PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------ZF_PHD_1  PDB: A:28-72 UniProt: 217-261      -------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2l43 A   1 ARTKQTARKSTGGSSGSS---------------------------------------------------------------------------------------------QSLIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPA  80
                                    10       | -         -         -         -         -         -         -         -         -         - |      27        37        47        57        67        77   
                                            18                                                                                            19
   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 2L43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L43)

(-) Gene Ontology  (37, 40)

NMR Structure(hide GO term definitions)
Chain A   (BRD1_HUMAN | O95696)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0051602    response to electrical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus.
    GO:0035902    response to immobilization stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of being rendered immobile.
cellular component
    GO:0070776    MOZ/MORF histone acetyltransferase complex    A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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.

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  H33_HUMAN | P84243
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 Related Entries

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

UniProtKB/Swiss-Prot
        BRD1_HUMAN | O95696: 2ku3 2lq6 3lyi 3rcw 4z02 5ame 5amf 5fg6 5gk9 5n49 5pnx 5pny 5pnz 5po0 5po1 5po2 5po3 5po4 5po5 5po6 5po7 5po8 5po9 5poa 5pob 5poc 5pod 5poe 5pof 5pog 5poh 5poi 5poj 5pok 5pol 5pom 5pon 5poo 5pop 5poq 5por 5pos 5pot 5pou 5pov 5pow 5pox 5poy 5poz 5pp0 5pp1 5pp2 5pp3 5pp4 5pp5 5pp6 5pp7 5pp8 5pp9 5ppa 5ppb 5ppc 5ppd 5ppe 5ppf 5ppg 5pph 5ppi 5ppj 5ppk 5ppl 5ppm 5ppn 5ppo 5ppp 5ppq 5ppr 5pps 5ppt 5ppu 5ppv 5ppw 5ppx 5ppy 5ppz 5pq0 5pq1 5pq2 5pq3 5pq4 5pq5 5pq6 5pq7 5pq8 5pq9 5pqa 5pqb 5pqc 5pqd 5pqe 5pqf 5pqg 5pqh 5pqi 5pqj 5pqk 5pql 5pqm 5pqn 5pqo 5pqp 5pqq 5pqr 5pqs 5pqt 5pqu 5pqv 5pqw 5pqx 5pqy 5pqz 5pr0 5pr1 5pr2 5pr4 5pr5 5pr6 5pr7 5pr8 5pr9 5pra 5prb 5prd 5pre 5prf 5prg 5prh 5pri 5prj 5prk 5prl 5prm 5pro 5prp 5prq 5prr 5prs 5prt 5pru 5prv 5prw 5prx 5pry 5prz 5ps0 5ps1 5ps2 5ps3 5ps4 5ps5 5ps6 5ps7 5ps8 5ps9 5psa 5psb 5psc 5psd 5pse 5psf 5psg 5psh 5psi 5psj 5psk 5psl 5psm 5psn 5pso 5psp 5psq 5psr 5pss 5pst 5psu 5psv 5psw 5psx 5psy 5psz 5pt0 5pt1 5pt2 5pt3 5pt4 5pt5 5pt6 5pt7 5pt8 5pt9 5pta 5ptb 5ptc 5pte 5ptf 5ptg 5pth 5ptj 5ptk 5ptl 5ptm 5ptn 5pto 5ptq 5ptr 5pts 5ptt 5ptu 5ptv 5ptw 5ptx 5pty 5ptz 5pu0 5pu1 5pu2 5pu3 5pu4 5pu5 5pu6 5pu7 5pu8 5pu9 5pua 5pub 5puc 5pud 5pue 5puf 5pug 5puh 5pui 5puj 5puk 5pul 5pum 5pun 5puo 5pup 5puq 5pur 5pus 5put 5puu 5puv 5puw 5pux 5puy 5puz 5pv0 5pv1 5pv2 5pv3 5pv4 5pv5 5pv6 5pv7 5pv8 5pv9 5pva 5pvb 5pvc 5pvd 5pve 5pvf 5pvg 5pvh 5pvi 5pvj 5pvk 5pvl 5pvm 5pvn 5pvo 5pvp 5pvq 5pvr 5pvs 5pvt 5pvu 5pvv 5pvw 5pvx 5pvy 5pvz 5pw0 5pw1 5pw2 5pw3 5pw4 5pw5 5pw6 5pw7 5pw8 5pw9 5pwa 5pwb
        H33_HUMAN | P84243: 1pdq 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5kdm 5x7x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2L43)