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Title :   60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE (NO66 S373C) IN COMPLEX WITH MN(II), N-OXALYLGLYCINE (NOG) AND 60S RIBOSOMAL PROTEIN L8 (RPL8 G214C) PEPTIDE FRAGMENT (COMPLEX-3)

Authors :   R. Chowdhury, C. J. Schofield

Date :   23 Oct 13 (Deposition) - 14 May 14 (Release) - 25 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Oxidoreductase, Non-Heme, Iron-Binding, Dsbh, 2-Oxoglutarate, Dioxygenase, Jmjc Domain, Ribosome Biogenesis, Nuclear Protein, Rpl8, Beta-Hydroxylation, Transcription And Epigenetic Regulation, Signaling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Chowdhury, R. Sekirnik, N. C. Brissett, T. Krojer, C. -H. Ho, S. S. Ng I. J. Clifton, W. Ge, N. J. Kershaw, G. C. Fox, J. R. C. Muniz, M. Vollmar, C. Phillips, E. S. Pilka, K. L. Kavanagh, F. Von Deflt, U. Oppermann, M. A. Mcdonough, A. J. Doherty, C. J. Schofield
Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes To Humans.
Nature V. 510 422 2014
PubMed-ID: 24814345 | Reference-DOI: 10.1038/NATURE13263
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL- HYDROXYLASE NO66
	Chains	:	A, B
	EC Number	:	1.14.11.-, 1.14.11.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PNIC-CTHF
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 183-641
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE, HISTONE LYSINE DEMETHYLASE NO66, MYC-ASSOCIATED PROTEIN WITH JMJC DOMAIN, NUCLEOLAR PROTEIN 66, HSNO66, RIBOSOMAL OXYGENASE NO66, ROX

Molecule 2 - 60S RIBOSOMAL PROTEIN L8
	Chains	:	C, D
	Fragment	:	RESIDUES 205-239
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	OGA	2	Ligand/Ion	N-OXALYLGLYCINE

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	OGA	4	Ligand/Ion	N-OXALYLGLYCINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:340 , ASP A:342 , HIS A:405 , OGA A:902 , HOH A:2122	BINDING SITE FOR RESIDUE MN A 901
2	AC2	SOFTWARE	TYR A:328 , PHE A:337 , HIS A:340 , ASP A:342 , LYS A:355 , HIS A:405 , ALA A:407 , HIS A:417 , THR A:419 , MN A:901 , HOH A:2122 , HOH A:2131 , HOH A:2132	BINDING SITE FOR RESIDUE OGA A 902
3	AC3	SOFTWARE	TRP A:223 , GLU A:224 , ARG A:225 , HOH A:2035 , ARG B:452	BINDING SITE FOR RESIDUE EDO A 903
4	AC4	SOFTWARE	MET A:459 , ASP A:460 , HIS A:466 , HOH A:2286 , ARG B:557	BINDING SITE FOR RESIDUE EDO A 904
5	AC5	SOFTWARE	HIS B:340 , ASP B:342 , HIS B:405 , OGA B:902 , HOH B:2123	BINDING SITE FOR RESIDUE MN B 901
6	AC6	SOFTWARE	TYR B:328 , PHE B:337 , HIS B:340 , ASP B:342 , LYS B:355 , HIS B:405 , ALA B:407 , HIS B:417 , THR B:419 , MN B:901 , HOH B:2123 , HOH B:2124 , HOH B:2129	BINDING SITE FOR RESIDUE OGA B 902
7	AC7	SOFTWARE	GLY A:320 , SER A:321 , ASN A:426 , ARG A:501 , HOH A:2113 , PHE B:458	BINDING SITE FOR RESIDUE EDO B 903
8	AC8	SOFTWARE	PHE A:458 , GLY B:320 , ASN B:426 , ARG B:501 , PHE B:505 , HOH B:2119	BINDING SITE FOR RESIDUE EDO B 904
9	AC9	SOFTWARE	ARG A:452 , GLU B:224 , ARG B:225	BINDING SITE FOR RESIDUE EDO B 905

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

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, 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, 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 4CCO)

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:458
 aligned with RIOX1_HUMAN | Q9H6W3 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:459
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631         
          RIOX1_HUMAN   182 DSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLAL 640
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhh.....eee............hhhhhhhhhhhh.......eeeeeee..eeee.......hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..............eeeeeeeee.eeeee....hhhhh.........hhhhh....eeeee....eeee.....eeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee.-..ee..........eeee.....eeeeee..eeeeee..............eeeehhhhhhhhhhhhhh....ee.hhh...hhhhhhhhhhhhhhhh.eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------S--------------------H----------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------JMJC  PDB: A:294-439 UniProt: 294-439                                                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cco A 182 MSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRAPTEELALTCSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWE-GEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLAL 640
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531 |     541       551       561       571       581       591       601       611       621       631         
                                                                                                                                                                                                                                                                                                                                                                                       531 |                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                         533

Chain B from PDB  Type:PROTEIN  Length:459
 aligned with RIOX1_HUMAN | Q9H6W3 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:459
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631         
          RIOX1_HUMAN   182 DSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLAL 640
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhh.....eee............hhhhhhhhhhhh.......eeeeeee..eeee.......hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeee..............eeeeeeeee.eeeeee...hhhhh.........hhhhh....eeeee....eeee....eeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..eee..eee..........eeee.....eeeeee..eeeeee..............eee.hhhhhhhhhhhhhhh...ee.hhh...hhhhhhhhhhhhhhhh.eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------S--------------------H----------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------JMJC  PDB: B:294-439 UniProt: 294-439                                                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cco B 182 MSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRAPTEELALTCSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLAL 640
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631

Chain C from PDB  Type:PROTEIN  Length:12
 aligned with RL8_HUMAN | P62917 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:12
                                   221  
            RL8_HUMAN   212 GGGNHQHIGKPS 223
               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
                 4cco C 212 GGCNHQHIGKPS 223
                                   221

Chain D from PDB  Type:PROTEIN  Length:12
 aligned with RL8_HUMAN | P62917 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:12
                                   221  
            RL8_HUMAN   212 GGGNHQHIGKPS 223
               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
                 4cco D 212 GGCNHQHIGKPS 223
                                   221

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 4CCO)

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

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

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.

Chain C,D (RL8_HUMAN | P62917)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
	GO:0002181	cytoplasmic translation	The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
	GO:0019083	viral transcription	The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0022625	cytosolic large ribosomal subunit	The large subunit of a ribosome located in the cytosol.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0015934	large ribosomal subunit	The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:211 - Pro A:212	[ RasMol ]
		Ala B:211 - Pro B:212	[ RasMol ]
		Tyr A:602 - Pro A:603	[ RasMol ]
		Tyr B:602 - Pro B:603	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4cco
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	RIOX1_HUMAN \| Q9H6W3
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	RL8_HUMAN \| P62917
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	1.14.11.-
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	1.14.11.27
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	RIOX1_HUMAN \| Q9H6W3
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2xdv	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF FLJ14393
4bu2	60S RIBOSOMAL PROTEIN L27A HISTIDINE HYDROXYLASE (MINA53 ) IN COMPLEX WITH NI(II) AND 2-OXOGLUTARATE (2OG)
4bxf	60S RIBOSOMAL PROTEIN L27A HISTIDINE HYDROXYLASE (MINA53 Y209C) IN COMPLEX WITH MN(II), 2-OXOGLUTARATE (2OG) AND 60S RIBOSOMAL PROTEIN L27A (RPL27A G37C) PEPTIDE FRAGMENT
4ccj	60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE (NO66) IN APO FORM
4cck	60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE (NO66) IN COMPLEX WITH MN(II) AND N-OXALYLGLYCINE (NOG)
4ccm	60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE (NO66) IN COMPLEX WITH MN(II), N-OXALYLGLYCINE (NOG) AND 60S RIBOSOMAL PROTEIN L8 (RPL8 G220C) PEPTIDE FRAGMENT ( COMPLEX-1)
4ccn	60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE (NO66 L299C/C300S) IN COMPLEX WITH MN(II), N-OXALYLGLYCINE (NOG) AND 60S RIBOSOMAL PROTEIN L8 (RPL8 G220C) PEPTIDE FRAGMENT (COMPLEX-2)
4diq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (37, 38)

Visualization

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Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File