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(-) Description

Title :  MOLECULAR BASIS OF HISTONE H3K4ME3 RECOGNITION BY ING4
 
Authors :  A. Palacios, I. G. Munoz, D. Pantoja-Uceda, M. J. Marcaida, D. Torres, J. M. Martin-Garcia, I. Luque, G. Montoya, F. J. Blanco
Date :  04 Feb 08  (Deposition) - 01 Apr 08  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Acetylation, Alternative Splicing, Anti-Oncogene, Cell Cycle, Coiled C Nucleus, Zinc, Zinc-Finger, Ing4, Phd Finger, Histone 3 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Palacios, I. G. Munoz, D. Pantoja-Uceda, M. J. Marcaida, D. Torres, J. M. Martin-Garcia, I. Luque, G. Montoya, F. J. Blanco
Molecular Basis Of Histone H3K4Me3 Recognition By Ing4
J. Biol. Chem. V. 283 15956 2008
PubMed-ID: 18381289  |  Reference-DOI: 10.1074/JBC.M710020200

(-) Compounds

Molecule 1 - INHIBITOR OF GROWTH PROTEIN 4
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 187-245
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymING 4, P29ING4
 
Molecule 2 - HISTONE H3
    ChainsB, D
    FragmentRESIDUES 2-11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
4NA1Ligand/IonSODIUM ION
5ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU-1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DTT-1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:244 , DTT A:1245 , HOH A:2058 , HOH A:2059 , HOH A:2061BINDING SITE FOR RESIDUE NA A 300
2AC2SOFTWARECYS A:199 , HIS A:202 , ILE A:219 , NA A:300 , HOH A:2007 , HOH A:2025 , HOH A:2048 , HOH A:2057 , HOH A:2060 , HOH A:2061BINDING SITE FOR RESIDUE DTT A1245
3AC3SOFTWAREHIS C:202 , ASN C:214 , GLN C:244 , HOH C:2031 , HOH C:2036 , HOH C:2039 , HOH C:2040 , HOH C:2041BINDING SITE FOR RESIDUE DTU C1246
4AC4SOFTWARECYS A:199 , CYS A:201 , HIS A:223 , CYS A:226BINDING SITE FOR RESIDUE ZN A1246
5AC5SOFTWARECYS C:199 , CYS C:201 , HIS C:223 , CYS C:226BINDING SITE FOR RESIDUE ZN C1247
6AC6SOFTWARECYS C:212 , CYS C:217 , CYS C:239 , CYS C:242BINDING SITE FOR RESIDUE ZN C1248
7AC7SOFTWARECYS A:212 , CYS A:217 , CYS A:239 , CYS A:242BINDING SITE FOR RESIDUE ZN A1247

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.ING4_HUMAN196-245
 
  2A:196-244
C:196-244
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.ING4_HUMAN199-242
 
  2A:199-242
C:199-242
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.ING4_HUMAN196-245
 
  1A:196-244
-
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.ING4_HUMAN199-242
 
  1A:199-242
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.ING4_HUMAN196-245
 
  1-
C:196-244
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.ING4_HUMAN199-242
 
  1-
C:199-242

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003968071cENSE00001945605chr12:6772306-677223176ING4_HUMAN1-13130--
1.7aENST000003968077aENSE00000866946chr12:6765964-676589372ING4_HUMAN13-37250--
1.9bENST000003968079bENSE00000715744chr12:6762562-6762396167ING4_HUMAN37-92560--
1.10bENST0000039680710bENSE00001789862chr12:6762216-6762102115ING4_HUMAN93-131390--
1.10dENST0000039680710dENSE00001526324chr12:6761936-6761828109ING4_HUMAN131-167370--
1.10iENST0000039680710iENSE00001721883chr12:6761584-6761437148ING4_HUMAN167-216502A:195-216
C:191-216
22
26
1.11bENST0000039680711bENSE00001640958chr12:6760551-676049062ING4_HUMAN217-237212A:217-237
C:217-237
21
21
1.11nENST0000039680711nENSE00001876036chr12:6760400-6759757644ING4_HUMAN237-249132A:237-244
C:237-244
8
8

(-) 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:50
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:50
                                   204       214       224       234       244
           ING4_HUMAN   195 EPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQ 244
               SCOP domains d2vnfa_ A: automated matches                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....ee....eee.........eee.hhhh..........hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ZF_PHD_2  PDB: A:196-244 UniProt: 196-245         PROSITE (1)
                PROSITE (2) ----ZF_PHD_1  PDB: A:199-242 UniProt: 199-242   -- PROSITE (2)
           Transcript 1 (1) Exon 1.10i            Exon 1.11b           ------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------1.11n    Transcript 1 (2)
                 2vnf A 195 EPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQ 244
                                   204       214       224       234       244

Chain B from PDB  Type:PROTEIN  Length:6
 aligned with Q5TEC6_HUMAN | Q5TEC6 from UniProtKB/TrEMBL  Length:136

    Alignment length:6
         Q5TEC6_HUMAN     2 ARTKQT   7
               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
                 2vnf B   1 ARTkQT   6
                               |  
                               4-M3L

Chain C from PDB  Type:PROTEIN  Length:54
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:54
                                   200       210       220       230       240    
           ING4_HUMAN   191 VDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQ 244
               SCOP domains d2vnfc_ C: automated matches                           SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
           Pfam domains (1) -------PHD-2vnfC01 C:198-244                           Pfam domains (1)
           Pfam domains (2) -------PHD-2vnfC02 C:198-244                           Pfam domains (2)
         Sec.struct. author ......ee....ee....eee.........eee.hhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----ZF_PHD_2  PDB: C:196-244 UniProt: 196-245         PROSITE (1)
                PROSITE (2) --------ZF_PHD_1  PDB: C:199-242 UniProt: 199-242   -- PROSITE (2)
           Transcript 1 (1) Exon 1.10i  PDB: C:191-216Exon 1.11b           ------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------1.11n    Transcript 1 (2)
                 2vnf C 191 VDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQ 244
                                   200       210       220       230       240    

Chain D from PDB  Type:PROTEIN  Length:10
 aligned with Q5TEC6_HUMAN | Q5TEC6 from UniProtKB/TrEMBL  Length:136

    Alignment length:10
                                    11
         Q5TEC6_HUMAN     2 ARTKQTARKS  11
               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
                 2vnf D   1 ARTkQTARKS  10
                               |    10
                               4-M3L  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: PHD (44)
1aPHD-2vnfC01C:198-244
1bPHD-2vnfC02C:198-244

(-) Gene Ontology  (28, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (ING4_HUMAN | Q9UNL4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006978    DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
    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: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:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0043983    histone H4-K12 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone.
    GO:0043984    histone H4-K16 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
    GO:0043981    histone H4-K5 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone.
    GO:0043982    histone H4-K8 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045926    negative regulation of growth    Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0006473    protein acetylation    The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
cellular component
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    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.

Chain B,D   (Q5TEC6_HUMAN | Q5TEC6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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
        ING4_HUMAN | Q9UNL42k1j 2m1r 2pnx 4afl
        Q5TEC6_HUMAN | Q5TEC62cnx 2co0 2v83 2v85 2v88 2v89 2x0l
UniProtKB/TrEMBL
        Q5TEC6_HUMAN | Q5TEC64h75

(-) Related Entries Specified in the PDB File

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