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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSOMAL OXYGENASE NO66 IN COMPLEX WITH SUBSTRATE RPL8 PEPTIDE AND NI(II) AND COFACTOR N-OXALYGLYCINE
 
Authors :  C. Wang, Q. Zhang, J. Zang
Date :  10 Feb 15  (Deposition) - 07 Oct 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ribosomal Oxygenase, Quaternary Compound Structure, Jmjc-Domain, Oxidoreductase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wang, Q. Zhang, T. Hang, Y. Tao, X. Ma, M. Wu, X. Zhang, J. Zang
Structure Of The Jmjc Domain-Containing Protein No66 Complexed With Ribosomal Protein Rpl8.
Acta Crystallogr. , Sect. D V. 71 1955 2015
PubMed-ID: 26327385  |  Reference-DOI: 10.1107/S1399004715012948

(-) Compounds

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 Taxid: 562
    Fragment: UNP RESIDUES 176-641
    Gene: NO66, C14ORF169, MAPJD
    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 - RPL8 PEPTIDE
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3NI2Ligand/IonNICKEL (II) ION
4OGA2Ligand/IonN-OXALYLGLYCINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:340 , ASP A:342 , HIS A:405 , OGA A:702 , HOH A:836binding site for residue NI A 701
2AC2SOFTWARETYR 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 , NI A:701 , HOH A:836 , HOH A:919binding site for residue OGA A 702
3AC3SOFTWAREHIS B:340 , ASP B:342 , HIS B:405 , OGA B:702 , HOH B:1082binding site for residue NI B 701
4AC4SOFTWARETYR 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:839 , HOH B:886 , HOH B:985 , HOH B:1063 , HOH B:1082binding site for residue OGA B 702
5AC5SOFTWARETRP A:428 , PRO B:455 , PHE B:477 , LYS B:480 , HOH B:944 , HOH B:1032binding site for residue GOL B 703
6AC6SOFTWAREASP A:460 , HOH A:1020 , ARG B:199 , ASP B:553 , GLY B:554 , HOH B:849 , HOH B:900 , HOH B:1016 , HOH B:1020binding site for residue GOL B 704
7AC7SOFTWAREPHE A:458 , MET A:459 , GLY B:320 , SER B:321 , ASN B:426 , ARG B:501 , PHE B:505 , HOH B:879binding site for residue GOL B 705
8AC8SOFTWAREPHE B:605binding site for residue ACT B 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y3O)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y3O)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y3O)

(-) Sequences/Alignments

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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               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) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y3o A 181 WDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLA 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         


Chain B from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh.....eee............hhhhhhhhhhhh.......eeeeee....eee.......hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..............eeeeeeeee.eeeeee...hhhhh.........hhhhh....eeeee....eeee....eeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee....ee..........eeee.....eeeeee..eeeeee..............eee.hhhhhhhhhhhhhh....ee.hhh...hhhhhhhhhhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y3o B 181 WDSPLRRVLAELNRIPSSRRRAARLFEWLIAPMPPDHFYRRLWEREAVLVRRQDHTYYQGLFSTADLDSMLRNEEVQFGQHLDAARYINGRRETLNPPGRALPAAAWSLYQAGCSLRLLCPQAFSTTVWQFLAVLQEQFGSMAGSNVYLTPPNSQGFAPHYDDIEAFVLQLEGRKLWRVYRPRVPTEELALTSSPNFSQDDLGEPVLQTVLEPGDLLYFPRGFIHQAECQDGVHSLHLTLSTYQRNTWGDFLEAILPLAVQAAMEENVEFRRGLPRDFMDYMGAQHSDSKDPRRTAFMEKVRVLVARLGHFAPVDAVADQRAKDFIHDSLPPVLTDRERALSVYGLPIRWEAGEPVNVGAQLTTETEVHMLQDGIARLVGEGGHLFLYYTVENSRVYHLEEPKCLEIYPQQADAMELLLGSYPEFVRVGDLPCDSVEDQLSLATTLYDKGLLLTKMPLALN 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 


Chain C from PDB  Type:PROTEIN  Length: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
                 4y3o C 212 GGGNHQHIGKP 222
                                   221 


Chain D from PDB  Type:PROTEIN  Length: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
                 4y3o D 212 GGGNHQHIGKP 222
                                   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4Y3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y3O)

(-) Gene Ontology  (37, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RIOX1_HUMAN | Q9H6W3: 4ccj 4cck 4ccm 4ccn 4cco 4diq 4e4h 4y33 4y4r
        RL8_HUMAN | P62917: 4ccm 4ccn 4cco 4ug0 4v6x 5aj0 5t2c

(-) Related Entries Specified in the PDB File

4y33 4y4r