3KV4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF PHF8 IN COMPLEX WITH HISTONE H3

Authors :   J. R. Horton, A. K. Upadhyay, H. H. Qi, X. Zhang, Y. Shi, X. Cheng

Date :   29 Nov 09 (Deposition) - 22 Dec 09 (Release) - 09 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A,B

Keywords :   Epigenetics, Histone Code, Covalent Histone Modifications, Jumonji Demethylase, Mental Retardation, Metal-Binding, Zinc, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Horton, A. K. Upadhyay, H. H. Qi, X. Zhang, Y. Shi, X. Cheng
Enzymatic And Structural Insights For Substrate Specificity Of A Family Of Jumonji Histone Lysine Demethylases.
Nat. Struct. Mol. Biol. V. 17 38 2010
PubMed-ID: 20023638 | Reference-DOI: 10.1038/NSMB.1753

Molecule 1 - PHD FINGER PROTEIN 8
	Chains	:	A
	EC Number	:	2.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PXC721
	Expression System Strain	:	BL21(DE3)CODONPLUS
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 37-483
	Gene	:	KIAA1111, PHF8, ZNF422
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HISTONE H3-LIKE
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 2-25
	Other Details	:	HISTONE H3 PEPTIDE
	Other Details - Source	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 20)

No.	Name	Count	Type	Full Name
1	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
2	FE2	1	Ligand/Ion	FE (II) ION
3	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
4	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
5	NI	1	Ligand/Ion	NICKEL (II) ION
6	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
7	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:8 , CYS A:10 , HIS A:31 , CYS A:34 , EDO A:452	BINDING SITE FOR RESIDUE ZN A 448
02	AC2	SOFTWARE	CYS A:23 , CYS A:26 , CYS A:50 , CYS A:53	BINDING SITE FOR RESIDUE ZN A 449
03	AC3	SOFTWARE	HIS A:247 , ASP A:249 , HIS A:319 , HOH A:553 , OGA A:5798	BINDING SITE FOR RESIDUE FE2 A 450
04	AC4	SOFTWARE	SER A:214 , TRP A:215 , VAL A:216 , PHE A:334 , LEU A:335	BINDING SITE FOR RESIDUE NI A 451
05	AC5	SOFTWARE	CYS A:10 , LEU A:12 , ARG A:18 , HIS A:31 , CYS A:34 , LEU A:104 , PHE A:115 , GLU A:118 , ASN A:119 , ZN A:448 , HOH A:472	BINDING SITE FOR RESIDUE EDO A 452
06	AC6	SOFTWARE	ARG A:92 , ASN A:202 , ILE A:265 , LYS A:302	BINDING SITE FOR RESIDUE EDO A 453
07	AC7	SOFTWARE	PHE A:96 , SER A:98 , ARG A:199 , HOH A:500 , HOH A:512 , HOH A:608	BINDING SITE FOR RESIDUE EDO A 454
08	AC8	SOFTWARE	ARG A:270 , HOH A:514	BINDING SITE FOR RESIDUE EDO A 455
09	AC9	SOFTWARE	ARG A:18 , SER A:33 , GLU A:118	BINDING SITE FOR RESIDUE EDO A 456
10	BC1	SOFTWARE	LYS A:212 , LEU A:213 , SER A:214 , TRP A:215 , EDO A:459	BINDING SITE FOR RESIDUE EDO A 457
11	BC2	SOFTWARE	ARG A:89 , ASP A:131 , GLY A:132 , GLY A:134	BINDING SITE FOR RESIDUE EDO A 458
12	BC3	SOFTWARE	SER A:337 , HIS A:374 , ILE A:378 , EDO A:457	BINDING SITE FOR RESIDUE EDO A 459
13	BC4	SOFTWARE	ASP A:44 , ILE A:45 , SER A:60 , ILE A:61 , MET A:62	BINDING SITE FOR RESIDUE EDO A 460
14	BC5	SOFTWARE	VAL A:35 , VAL A:37 , TYR A:48 , HIS A:49 , PRO A:51 , GLU A:54	BINDING SITE FOR RESIDUE EDO A 461
15	BC6	SOFTWARE	ASN A:52 , VAL A:55 , SER A:98 , ASP A:100 , GLU A:101	BINDING SITE FOR RESIDUE EDO A 462
16	BC7	SOFTWARE	THR A:355	BINDING SITE FOR RESIDUE EDO A 463
17	BC8	SOFTWARE	ASP A:161 , CYS A:168 , MET A:170 , LYS A:186	BINDING SITE FOR RESIDUE EDO A 464
18	BC9	SOFTWARE	ASN A:189 , THR A:244 , HIS A:247 , ASP A:249 , TYR A:257 , LYS A:264 , HIS A:319 , VAL A:321 , FE2 A:450 , HOH A:479 , HOH A:553 , MLY B:9	BINDING SITE FOR RESIDUE OGA A 5798

(no "SS Bond" information available for 3KV4)

(no "Cis Peptide Bond" information available for 3KV4)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_062250	F	315	S	PHF8_HUMAN	Disease (MRXSSD)	121918524	A	F	279	S

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

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_1	PS00322	Histone H3 signature 1.	H3C_HUMAN	15-21	1	B:14-14
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	PHF8_HUMAN	41-92	1	A:5-56
3	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	PHF8_HUMAN	44-89	1	A:8-53
4	JMJC	PS51184	JmjC domain profile.	PHF8_HUMAN	231-387	1	A:195-351

(no "Exon" information available for 3KV4)

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:432
 aligned with PHF8_HUMAN | Q9UPP1 from UniProtKB/Swiss-Prot  Length:1060

    Alignment length:445
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478     
           PHF8_HUMAN    39 SVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPSIMKKRRGSSKGHDTHKGKPVKTGSPTFVRELRSRTFDSSDEVILKPTGNQLTVEFLEENSFSVPILVLKKDGLGMTLPSPSFTVRDVEHYVGSDKEIDVIDVTRQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKCYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEIPETVRTVQLIKDLAREIRLVEDIFQQN 483
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----PHD-3kv4A02 A:7-56                                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3kv4A01 A:234-334                                                                               ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....ee......eee......eeehhhhh.hhhhhh.eee..hhhhhhhhh..ee..-------------......hhhhhhhhhh...ee.hhh.........hhhhhhhh.....eee...............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhhh......eeeeeee...hhhhhhh..hhhhhhhhhhhhhh.............eeeee...eeeeee.hhhhheeeeeeee.eeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eeee....eeeeee...eeeeeeee....hhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --ZF_PHD_2  PDB: A:5-56 UniProt: 41-92                ------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:195-351 UniProt: 231-387                                                                                                                        ------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----ZF_PHD_1  PDB: A:8-53 UniProt: 44-89          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kv4 A   3 SVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPSIMKK-------------KPVKTGSPTFVRELRSRTFDSSDEVILKPTGNQLTVEFLEENSFSVPILVLKKDGLGMTLPSPSFTVRDVEHYVGSDKEIDVIDVTRQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKCYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEIPETVRTVQLIKDLAREIRLVEDIFQQN 447
                                    12        22        32        42        52        62 |       -     |  82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442     
                                                                                        64            78

Chain B from PDB  Type:PROTEIN  Length:14
 aligned with H3C_HUMAN | Q6NXT2 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:14
                                    11    
            H3C_HUMAN     2 ARTKQTARKSTGGK  15
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------H PROSITE
                 Transcript -------------- Transcript
                 3kv4 B   1 ARTkQTARkSTGGK  14
                               |    10    
                               |    |     
                               4-M3L|     
                                    9-MLY

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 '\|'

(no "SCOP Domain" information available for 3KV4)

(no "CATH Domain" information available for 3KV4)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: JmjC (39)

Homo sapiens (Human) (31)

JmjC-3kv4A01

A:234-334

Clan: zf-FYVE-PHD (57)

Family: PHD (44)

Homo sapiens (Human) (33)

PHD-3kv4A02

A:7-56

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PHF8_HUMAN | Q9UPP1)

molecular function
	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:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0032452	histone demethylase activity	Catalysis of the removal of a methyl group from a histone.
	GO:0071558	histone demethylase activity (H3-K27 specific)	Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
	GO:0051864	histone demethylase activity (H3-K36 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
	GO:0032454	histone demethylase activity (H3-K9 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
	GO:0035575	histone demethylase activity (H4-K20 specific)	Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
	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:0000082	G1/S transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
	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: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:0071557	histone H3-K27 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
	GO:0070544	histone H3-K36 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
	GO:0033169	histone H3-K9 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
	GO:0035574	histone H4-K20 demethylation	The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone.
	GO:0061188	negative regulation of chromatin silencing at rDNA	Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0045943	positive regulation of transcription from RNA polymerase I promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I 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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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 (H3C_HUMAN | Q6NXT2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0031492	nucleosomal DNA binding	Interacting selectively and non-covalently with the DNA portion of a nucleosome.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
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:0005719	nuclear euchromatin	The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kv4)

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	3kv4
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	PHF8_HUMAN \| Q9UPP1
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	2.-.-.-
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	300263
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UniProtKB/Swiss-Prot
	H3C_HUMAN \| Q6NXT2	:	4z5t 5bwn 5bwo 5f6k 5i3l
	PHF8_HUMAN \| Q9UPP1	:	2wwu 3k3n 3k3o 4do0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 20)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (4, 4)

Exons (0, 0)

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Pfam Domains (2, 2)

Gene Ontology (38, 40)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File