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(-) Description

Title :  CRYSTAL STRUCTURE OF OPTINEURIN UBAN IN COMPLEX WITH LINEAR UBIQUITIN
 
Authors :  R. Ishii, O. Nureki
Date :  12 Jun 16  (Deposition) - 07 Sep 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Ubiquitin, Coiled-Coil, Cellular, Signaling, Nfkb Pathway, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakazawa, D. Oikawa, R. Ishii, T. Ayaki, H. Takahashi, H. Takeda, R. Ishitani, K. Kamei, I. Takeyoshi, H. Kawakami, K. Iwai, I. Hatada, T. Sawasaki, H. Ito, O. Nureki, F. Tokunaga
Linear Ubiquitination Is Involved In The Pathogenesis Of Optineurin-Associated Amyotrophic Lateral Sclerosis
Nat Commun V. 7 12547 2016
PubMed-ID: 27552911  |  Reference-DOI: 10.1038/NCOMMS12547

(-) Compounds

Molecule 1 - TETRA UBIQUITIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UBC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - OPTINEURIN
    Chains: B, C, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 416-510
    Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: E3-14.7K-INTERACTING PROTEIN,FIP-2,HUNTINGTIN YEAST PARTNER L,HUNTINGTIN-INTERACTING PROTEIN 7,HIP-7,HUNTINGTIN-INTERACTING PROTEIN L,NEMO-RELATED PROTEIN,OPTIC NEUROPATHY-INDUCING PROTEIN, TRANSCRIPTION FACTOR IIIA-INTERACTING PROTEIN,TFIIIA-INTP

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5B83)

(-) Sites  (0, 0)

(no "Site" information available for 5B83)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B83)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys F:501 -Glu F:502

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B83)

(-) Exons   (0, 0)

(no "Exon" information available for 5B83)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee......hhhhhhhhhhh....hhh.eeeee..eee....hhhhh......eeeeee.....eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee.....eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee......eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b83 A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  


Chain B from PDB  Type:PROTEIN  Length:59
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 5b83 B 443 QMDEMKQTIAKQEEDLETMTILRAQMEVYCSDFHAERAAREKIHEEKEQLALQLAVLLK 501
                                   452       462       472       482       492         


Chain C from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5b83 C 445 DEMKQTIAKQEEDLETMTILRAQMEVYCSDFHAERAAREKIHEEKEQLALQLAVLLKENDA 505
                                   454       464       474       484       494       504 


Chain D from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.....eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee.....eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.....eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhhhheeee..ee................eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b83 D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain E from PDB  Type:PROTEIN  Length:50
                                                                                  
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 5b83 E 453 KQEEDLETMTILRAQMEVYCSDFHAERAAREKIHEEKEQLALQLAVLLKE 502
                                   462       472       482       492       502


Chain F from PDB  Type:PROTEIN  Length:59
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 5b83 F 447 MKQTIAKQEEDLETMTILRAQMEVYCSDFHAERAAREKIHEEKEQLALQLAVLLKENDA 505
                                   456       466       476       486       496
   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 5B83)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B83)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B83)

(-) Gene Ontology  (110, 117)

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  Cis Peptide Bonds
    Lys F:501 - Glu F:502   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        OPTN_HUMAN | Q96CV9: 2lo4 2lue 3vtv 3vtw 5aaz 5eoa 5eof
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4i6n 4ig7 4ium 4jqw 4k1r 4k7s 4k7u 4k7w 4ksk 4ksl 4lcd 4ldt 4mdk 4mm3 4msm 4msq 4nqk 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

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