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(-) Description

Title :  CRYSTAL STRUCTURE OF PHD FINGER-LINKER-BROMODOMAIN FRAGMENT OF HUMAN BPTF IN THE FREE FORM
 
Authors :  H. Li, D. J. Patel
Date :  29 Nov 05  (Deposition) - 11 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phd Finger; Bromo Domain; Histone Tail Binding; Methylation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, S. Ilin, W. Wang, E. M. Duncan, J. Wysocka, C. D. Allis, D. J. Patel
Molecular Basis For Site-Specific Read-Out Of Histone H3K4Me3 By The Bptf Phd Finger Of Nurf.
Nature V. 442 91 2006
PubMed-ID: 16728978  |  Reference-DOI: 10.1038/NATURE04802
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BROMODOMAIN PHD FINGER TRANSCRIPTION FACTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P
    Expression System StrainROSETTA2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFINGER-LINKER-BROMODOMAIN (RESIDUES 2583-2751)
    GeneBPTF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:11 , CYS A:13 , HIS A:34 , CYS A:37BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARECYS A:26 , CYS A:29 , CYS A:53 , CYS A:56BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWARECYS B:11 , CYS B:13 , HIS B:34 , CYS B:37BINDING SITE FOR RESIDUE ZN B 1003
4AC4SOFTWARECYS B:26 , CYS B:29 , CYS B:53 , CYS B:56BINDING SITE FOR RESIDUE ZN B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F6N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F6N)

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.BPTF_HUMAN390-437
2867-2918
 
  2-
A:8-59
B:8-59
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.BPTF_HUMAN393-434
2870-2915
 
  2-
A:11-56
B:11-56
3BROMODOMAIN_2PS50014 Bromodomain profile.BPTF_HUMAN2944-3014
 
  2A:85-155
B:85-155
4BROMODOMAIN_1PS00633 Bromodomain signature.BPTF_HUMAN2949-3006
 
  2A:90-147
B:90-147

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003218921cENSE00001357454chr17:65821780-65822453674BPTF_HUMAN1-2052050--
1.2ENST000003218922ENSE00001148014chr17:65850056-65850878823BPTF_HUMAN205-4792750--
1.3ENST000003218923ENSE00001148007chr17:65862580-65862803224BPTF_HUMAN479-554760--
1.4ENST000003218924ENSE00001147999chr17:65870933-65871136204BPTF_HUMAN554-622690--
1.5ENST000003218925ENSE00001147993chr17:65871672-65871860189BPTF_HUMAN622-685640--
1.7ENST000003218927ENSE00001147984chr17:65882244-65882432189BPTF_HUMAN685-748640--
1.8ENST000003218928ENSE00001147980chr17:65887960-65888150191BPTF_HUMAN748-811640--
1.9ENST000003218929ENSE00001223583chr17:65889486-65889841356BPTF_HUMAN812-9301190--
1.10ENST0000032189210ENSE00001612408chr17:65890150-65890281132BPTF_HUMAN930-974450--
1.11ENST0000032189211ENSE00002166039chr17:65899905-65900034130BPTF_HUMAN974-1017440--
1.12ENST0000032189212ENSE00001750925chr17:65900818-65900956139BPTF_HUMAN1018-1064470--
1.13ENST0000032189213ENSE00001665602chr17:65905698-65905877180BPTF_HUMAN1064-1124610--
1.14ENST0000032189214ENSE00001606591chr17:65906993-659093032311BPTF_HUMAN1124-18947710--
1.15ENST0000032189215ENSE00001657056chr17:65914830-65914954125BPTF_HUMAN1894-1936430--
1.16ENST0000032189216ENSE00001625445chr17:65916131-65916259129BPTF_HUMAN1936-1979440--
1.17ENST0000032189217ENSE00001642854chr17:65918956-65919106151BPTF_HUMAN1979-2029510--
1.18ENST0000032189218ENSE00001783568chr17:65920663-6592070543BPTF_HUMAN2029-2043150--
1.19ENST0000032189219ENSE00001604847chr17:65924471-65924717247BPTF_HUMAN2044-2126830--
1.20ENST0000032189220ENSE00001680408chr17:65925452-65925603152BPTF_HUMAN2126-2176510--
1.21ENST0000032189221ENSE00001779718chr17:65928027-65928135109BPTF_HUMAN2177-2213370--
1.22ENST0000032189222ENSE00001770472chr17:65936555-65936772218BPTF_HUMAN2213-2285730--
1.23aENST0000032189223aENSE00001733774chr17:65940266-65940488223BPTF_HUMAN2286-2360750--
1.24cENST0000032189224cENSE00001223457chr17:65941525-65942441917BPTF_HUMAN2360-26653060--
1.25ENST0000032189225ENSE00001603899chr17:65943842-6594392483BPTF_HUMAN2666-2693280--
1.26ENST0000032189226ENSE00001707553chr17:65944197-65944422226BPTF_HUMAN2693-2768760--
1.27aENST0000032189227aENSE00001743235chr17:65955657-65955991335BPTF_HUMAN2769-28801122A:8-21
B:8-21
14
14
1.29ENST0000032189229ENSE00001707648chr17:65960328-65960520193BPTF_HUMAN2880-2944652A:21-85
B:21-85
65
65
1.30ENST0000032189230ENSE00001598996chr17:65962688-6596277285BPTF_HUMAN2945-2973292A:86-114
B:86-114
29
29
1.31ENST0000032189231ENSE00001755666chr17:65971888-65972074187BPTF_HUMAN2973-3035632A:114-173
B:114-170
60
57
1.32cENST0000032189232cENSE00001766345chr17:65978368-659804942127BPTF_HUMAN3035-3046120--

(-) Sequences/Alignments

Asymmetric/Biological 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:166
 aligned with BPTF_HUMAN | Q12830 from UniProtKB/Swiss-Prot  Length:3046

    Alignment length:166
                                  2876      2886      2896      2906      2916      2926      2936      2946      2956      2966      2976      2986      2996      3006      3016      3026      
          BPTF_HUMAN   2867 KLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 3032
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee......eee.hhhh.hhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ZF_PHD_2  PDB: A:8-59 UniProt: 2867-2918            -------------------------BROMODOMAIN_2  PDB: A:85-155 UniProt: 2944-3014                        ------------------ PROSITE (1)
                PROSITE (2) ---ZF_PHD_1  PDB: A:11-56 UniProt: 2870-2915     ---------------------------------BROMODOMAIN_1  PDB: A:90-147 UniProt: 2949-3006           -------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.27a    ----------------------------------------------------------------Exon 1.30  PDB: A:86-114     ----------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.29  PDB: A:21-85 UniProt: 2880-2944                       ----------------------------Exon 1.31  PDB: A:114-173 UniProt: 2973-3035 [INCOMPLETE]    Transcript 1 (2)
                2f6n A    8 KLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAmTVLTPLTEKDYEGLKRVLRSLQAHKmAWPFLEPVDPNDAPDYYGVIKEPmDLATmEERVQRRYYEKLTEFVADmTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK  173
                                    17        27        37        47        57     |  67        77        87 |      97       107     | 117|      127       137       147       157       167      
                                                                                  63-MSE                    89-MSE                 113-MSE|                137-MSE                                
                                                                                                                                        118-MSE                                                   

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with BPTF_HUMAN | Q12830 from UniProtKB/Swiss-Prot  Length:3046

    Alignment length:163
                                  2876      2886      2896      2906      2916      2926      2936      2946      2956      2966      2976      2986      2996      3006      3016      3026   
          BPTF_HUMAN   2867 KLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 3029
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee....eeee......hhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ZF_PHD_2  PDB: B:8-59 UniProt: 2867-2918            -------------------------BROMODOMAIN_2  PDB: B:85-155 UniProt: 2944-3014                        --------------- PROSITE (1)
                PROSITE (2) ---ZF_PHD_1  PDB: B:11-56 UniProt: 2870-2915     ---------------------------------BROMODOMAIN_1  PDB: B:90-147 UniProt: 2949-3006           ----------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.27a    ----------------------------------------------------------------Exon 1.30  PDB: B:86-114     -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.29  PDB: B:21-85 UniProt: 2880-2944                       ----------------------------Exon 1.31  PDB: B:114-170 UniProt: 2973-3035 [INCOMPLETE] Transcript 1 (2)
                2f6n B    8 KLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAmTVLTPLTEKDYEGLKRVLRSLQAHKmAWPFLEPVDPNDAPDYYGVIKEPmDLATmEERVQRRYYEKLTEFVADmTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK  170
                                    17        27        37        47        57     |  67        77        87 |      97       107     | 117|      127       137       147       157       167   
                                                                                  63-MSE                    89-MSE                 113-MSE|                137-MSE                             
                                                                                                                                        118-MSE                                                

   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 2F6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F6N)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BPTF_HUMAN | Q12830)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:1990090    cellular response to nerve growth factor stimulus    A process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nerve growth factor stimulus.
    GO: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:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0007492    endoderm development    The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009611    response to wounding    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 a stimulus indicating damage to the organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BPTF_HUMAN | Q128302f6j 2fsa 2fui 2fuu 2ri7 3qzs 3qzt 3qzv 3uv2

(-) Related Entries Specified in the PDB File

2f6j CRYSTAL STRUCTURE OF PHD FINGER-LINKER-BROMODOMAIN FRAGMENT OF HUMAN BPTF IN THE H3(1-15)K4ME3 BOUND STATE