4DIQ - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN NO66

Authors :   M. Vollmar, T. Krojer, S. Ng, E. Pilka, J. Bray, A. C. W. Pike, P. Filippak A. Roos, C. H. Arrowsmith, E. Edwards, C. Bountra, F. Von Delft, U. Opp Structural Genomics Consortium (Sgc)

Date :   31 Jan 12 (Deposition) - 07 Mar 12 (Release) - 07 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Histone Demethylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Vollmar, T. Krojer, Ng Stan, E. Pilka, C. Phillips, N. Burgess-Brown, J. Bray, A. C. W. Pike, P. Filippakopoulos, A. Roos, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von Delft, U. Oppermann
Crystal Structure Of Human No66
To Be Published
PubMed: search

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE NO66
	Chains	:	A, B
	EC Number	:	1.14.11.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 161-641
	Gene	:	NO66, C14ORF169
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEOLAR PROTEIN 66, HSNO66

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	NI	2	Ligand/Ion	NICKEL (II) ION
2	PD2	2	Ligand/Ion	PYRIDINE-2,4-DICARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	PD2	2	Ligand/Ion	PYRIDINE-2,4-DICARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	PD2	4	Ligand/Ion	PYRIDINE-2,4-DICARBOXYLIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:340 , ASP A:342 , HIS A:405 , PD2 A:701 , HOH A:835	BINDING SITE FOR RESIDUE NI A 700
2	AC2	SOFTWARE	TYR A:328 , PHE A:337 , HIS A:340 , ASP A:342 , LYS A:355 , HIS A:405 , HIS A:417 , THR A:419 , NI A:700 , HOH A:806 , HOH A:835	BINDING SITE FOR RESIDUE PD2 A 701
3	AC3	SOFTWARE	HIS B:340 , ASP B:342 , HIS B:405 , PD2 B:702 , HOH B:883	BINDING SITE FOR RESIDUE NI B 701
4	AC4	SOFTWARE	TYR B:328 , PHE B:337 , HIS B:340 , ASP B:342 , LYS B:355 , HIS B:405 , HIS B:417 , THR B:419 , NI B:701 , HOH B:856 , HOH B:883	BINDING SITE FOR RESIDUE PD2 B 702
5	AC5	SOFTWARE	HIS A:490 , ARG B:482 , ARG B:607 , ASP B:610	BINDING SITE FOR RESIDUE SO4 B 703

(no "SS Bond" information available for 4DIQ)

Asymmetric Unit

No.	Residues
1	Ala A:211	-	Pro A:212
2	Tyr A:602	-	Pro A:603
3	Ala B:211	-	Pro B:212
4	Tyr B:602	-	Pro B:603

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057819	F	218	S	RIOX1_HUMAN	Polymorphism	758109	A/B	F	218	S
2	UniProt	VAR_060191	Q	239	H	RIOX1_HUMAN	Polymorphism	34970526	A/B	Q	239	H
3	UniProt	VAR_062423	V	364	A	RIOX1_HUMAN	Polymorphism	3813563	A/B	A	364	A

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057819	F	218	S	RIOX1_HUMAN	Polymorphism	758109	A/B	F	218	S
2	UniProt	VAR_060191	Q	239	H	RIOX1_HUMAN	Polymorphism	34970526	A/B	Q	239	H
3	UniProt	VAR_062423	V	364	A	RIOX1_HUMAN	Polymorphism	3813563	A/B	A	364	A

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

Biological Unit 2 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057819	F	218	S	RIOX1_HUMAN	Polymorphism	758109	A/B	F	218	S
2	UniProt	VAR_060191	Q	239	H	RIOX1_HUMAN	Polymorphism	34970526	A/B	Q	239	H
3	UniProt	VAR_062423	V	364	A	RIOX1_HUMAN	Polymorphism	3813563	A/B	A	364	A

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	RIOX1_HUMAN	294-439	2	A:294-439 B:294-439

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	RIOX1_HUMAN	294-439	2	A:294-439 B:294-439

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	RIOX1_HUMAN	294-439	4	A:294-439 B:294-439

(no "Exon" information available for 4DIQ)

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:459
 aligned with RIOX1_HUMAN | Q9H6W3 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:461
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640 
          RIOX1_HUMAN   181 WDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLALN 641
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....eee............hhhhhhhhhhhh.......eeeeeee..eeee.......hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..............eeeeeeeee.eeeeee...hhhhh.........hhhhh....eeeee....eeee....eeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...ee..ee.--........eeee.....eeeeee..eeeeee..............eee.hhhhhhhhhhhhhh....ee.hhh...hhhhhhhhhhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------S--------------------H----------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------JMJC  PDB: A:294-439 UniProt: 294-439                                                                                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4diq A 181 WDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRAPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPV--GAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLALN 641
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530     | 540       550       560       570       580       590       600       610       620       630       640 
                                                                                                                                                                                                                                                                                                                                                                                             536  |                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                539

Chain B from PDB  Type:PROTEIN  Length:457
 aligned with RIOX1_HUMAN | Q9H6W3 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:459
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630         
          RIOX1_HUMAN   181 WDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLA 639
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....eee............hhhhhhhhhhhh.......eeeeeee..eeee.......hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..............eeeeeeeee.eeeeee...hhhhh.........hhhhh....eeeee....eeee....eeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...ee..ee..--.......eeee.....eeeeee..eeeeee..............eee.hhhhhhhhhhhhhh....ee.hhh...hhhhhhhhhhhhhhh..eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------S--------------------H----------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------JMJC  PDB: B:294-439 UniProt: 294-439                                                                                                             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4diq B 181 WDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRAPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVN--AQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLA 639
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530      |540       550       560       570       580       590       600       610       620       630         
                                                                                                                                                                                                                                                                                                                                                                                              537  |                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                 540

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 4DIQ)

(no "CATH Domain" information available for 4DIQ)

(no "Pfam Domain" information available for 4DIQ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIOX1_HUMAN | Q9H6W3)

molecular function
	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: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:0032453	histone demethylase activity (H3-K4 specific)	Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 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: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).
biological process
	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:0034720	histone H3-K4 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
	GO:0045668	negative regulation of osteoblast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
	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: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: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: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.

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	Cis Peptide Bonds
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		Ala B:211 - Pro B:212	[ RasMol ]
		Tyr A:602 - Pro A:603	[ RasMol ]
		Tyr B:602 - Pro B:603	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 5)

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