2QIC - JenaLib

Title :   CRYSTAL STRUCTURE OF THE ING1 PHD FINGER IN COMPLEX WITH A HISTONE H3K4ME3 PEPTIDE

Authors :   P. V. Pena, K. Champagne, R. Zhao, T. G. Kutateladze

Date :   03 Jul 07 (Deposition) - 13 May 08 (Release) - 22 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Phd, Ing1, Histone, H3K4Me3, Chromatin, Antitumor Protein, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. V. Pena, R. A. Hom, T. Hung, H. Lin, A. J. Kuo, R. P. Wong, O. M. Subach, K. S. Champagne, R. Zhao, V. V. Verkhusha, G. Li, O. Gozani, T. G. Kutateladze
Histone H3K4Me3 Binding Is Required For The Dna Repair And Apoptotic Activities Of Ing1 Tumor Suppressor.
J. Mol. Biol. V. 380 303 2008
PubMed-ID: 18533182 | Reference-DOI: 10.1016/J.JMB.2008.04.061
(for further references see the PDB file header)

Compounds

Molecule 1 - INHIBITOR OF GROWTH PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PHD DOMAIN (RESIDUES 345-404)
	Gene	:	ING1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - H3K4ME3 PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SYNTHETIC PEPTIDE H3K4ME3
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	M3L	-1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017421	C	358	S	ING1_HUMAN	Disease (HNSCC)	---	A	C	215	S
2	UniProt	VAR_017422	N	359	S	ING1_HUMAN	Disease (HNSCC)	---	A	N	216	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017421	C	358	S	ING1_HUMAN	Disease (HNSCC)	---	A	C	215	S
2	UniProt	VAR_017422	N	359	S	ING1_HUMAN	Disease (HNSCC)	---	A	N	216	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017421	C	358	S	ING1_HUMAN	Disease (HNSCC)	---	A	C	215	S
2	UniProt	VAR_017422	N	359	S	ING1_HUMAN	Disease (HNSCC)	---	A	N	216	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	ING1_HUMAN	353-402	1	A:210-259
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	ING1_HUMAN	356-399	1	A:213-256

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	ING1_HUMAN	353-402	1	A:210-259
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	ING1_HUMAN	356-399	1	A:213-256

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	ING1_HUMAN	353-402	1	A:210-259
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	ING1_HUMAN	356-399	1	A:213-256

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	ING1_HUMAN	353-402	0	-
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	ING1_HUMAN	356-399	0	-

Exons (0, 0)

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:51
 aligned with ING1_HUMAN | Q9UK53 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:51
                                   361       371       381       391       401 
           ING1_HUMAN   352 EPTYCLCNQVSYGEMIGCDNDECPIEWFHFSCVGLNHKPKGKWYCPKCRGE 402
               SCOP domains d2qica_ A: automated matches                        SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains ---PHD-2qicA01 A:212-259                            Pfam domains
         Sec.struct. author ..ee....ee...eeee.........eee.hhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------SS------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ZF_PHD_2  PDB: A:210-259 UniProt: 353-402          PROSITE (1)
                PROSITE (2) ----ZF_PHD_1  PDB: A:213-256 UniProt: 356-399   --- PROSITE (2)
                 Transcript --------------------------------------------------- Transcript
                 2qic A 209 EPTYCLCNQVSYGEMIGCDNDECPIEWFHFSCVGLNHKPKGKWYCPKCRGE 259
                                   218       228       238       248       258

Chain B from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .eeee... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2qic B   1 ARTkQTAR   8
                               |    
                               4-M3L

Legend:		→ Mismatch	(orange background)
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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (ING1_HUMAN | Q9UK53)

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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010941	regulation of cell death	Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
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.

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