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(-) Description

Title :  STRUCTURE OF PEDICULUS HUMANUS PARKIN BOUND TO PHOSPHO-UBIQUITIN
 
Authors :  T. Wauer, D. Komander
Date :  30 Jun 15  (Deposition) - 22 Jul 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ubiquitin, Parkin, Pink1, Phospho-Ubiquitin, Parkinson'S Disease, E3 Ligase, Rbr Domain, Mitophagy, Cell Signalling, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Wauer, M. Simicek, A. Schubert, D. Komander
Mechanism Of Phospho-Ubiquitin-Induced Parkin Activation.
Nature V. 524 370 2015
PubMed-ID: 26161729  |  Reference-DOI: 10.1038/NATURE14879

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE PARKIN
    ChainsA, C
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOKINK
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 141-461
    GenePHUM_PHUM233570
    Organism CommonBODY LOUSE
    Organism ScientificPEDICULUS HUMANUS SUBSP. CORPORIS
    Organism Taxid121224
    Other DetailsCOVALENTLY MODIFIED WITH PHOSPHO-UBIQUITIN AT CYS349
 
Molecule 2 - POLYUBIQUITIN-B
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUBB
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPHOSPHORYLATED AT SER65 GLY76 EXCHANGED WITH CHEMICAL PROBE, BROMOPROPYLAMINE. THE BROMIDE WAS LOST DURING THE COUPLING.

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
13CN2Mod. Amino Acid3-AMINOPROPANE
2SEP2Mod. Amino AcidPHOSPHOSERINE
3SO45Ligand/IonSULFATE ION
4ZN16Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
13CN1Mod. Amino Acid3-AMINOPROPANE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
13CN1Mod. Amino Acid3-AMINOPROPANE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:151 , CYS A:155 , CYS A:213 , HIS A:216binding site for residue ZN A 1001
02AC2SOFTWARECYS A:167 , CYS A:170 , CYS A:197 , CYS A:202binding site for residue ZN A 1002
03AC3SOFTWARECYS A:240 , CYS A:243 , CYS A:262 , CYS A:265binding site for residue ZN A 1003
04AC4SOFTWARECYS A:255 , HIS A:259 , CYS A:291 , CYS A:295binding site for residue ZN A 1004
05AC5SOFTWARECYS A:334 , CYS A:339 , CYS A:354 , CYS A:356binding site for residue ZN A 1005
06AC6SOFTWARECYS A:361 , CYS A:364 , HIS A:369 , CYS A:373binding site for residue ZN A 1006
07AC7SOFTWARECYS A:415 , CYS A:418 , CYS A:433 , CYS A:438binding site for residue ZN A 1007
08AC8SOFTWARECYS A:443 , CYS A:446 , CYS A:454 , HIS A:458binding site for residue ZN A 1008
09AC9SOFTWARESER A:183 , TRP A:184 , ARG A:258 , HOH A:1104binding site for residue SO4 A 1009
10AD1SOFTWARECYS C:151 , CYS C:155 , CYS C:213 , HIS C:216binding site for residue ZN C 1001
11AD2SOFTWARECYS C:167 , CYS C:170 , CYS C:197 , CYS C:202binding site for residue ZN C 1002
12AD3SOFTWARECYS C:240 , CYS C:243 , CYS C:262 , CYS C:265binding site for residue ZN C 1003
13AD4SOFTWARECYS C:255 , HIS C:259 , CYS C:291 , CYS C:295binding site for residue ZN C 1004
14AD5SOFTWARECYS C:334 , CYS C:339 , CYS C:354 , CYS C:356binding site for residue ZN C 1005
15AD6SOFTWARECYS C:361 , CYS C:364 , HIS C:369 , CYS C:373binding site for residue ZN C 1006
16AD7SOFTWARECYS C:415 , CYS C:418 , CYS C:433 , CYS C:438binding site for residue ZN C 1007
17AD8SOFTWARECYS C:443 , CYS C:446 , CYS C:454 , HIS C:458binding site for residue ZN C 1008
18AD9SOFTWARETRP C:184 , LYS C:232 , ARG C:258binding site for residue SO4 C 1009
19AE1SOFTWAREHIS A:441 , PRO A:449 , GLY C:195 , VAL C:196 , CYS C:197 , CYS C:202 , GLU C:203 , GLY C:204binding site for residue SO4 C 1010
20AE2SOFTWARETHR C:310 , ASP C:311binding site for residue SO4 C 1011
21AE3SOFTWAREARG D:42 , ARG D:72 , ARG D:74binding site for residue SO4 D 101
22AE4SOFTWAREASP C:346 , CYS C:349 , ARG C:351 , ARG D:74binding site for Di-peptide GLY D 75 and 3CN D 76

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:153 -Pro A:154
2Asp A:248 -Pro A:249
3Asn C:153 -Pro C:154
4Asp C:248 -Pro C:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CAW)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeeeeeeee.......eee.....hhhhhhh.....eee.........eeeeeee............ee...ee.................eee.......eeehhhhhhhhhhhhhh...eee...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eee......eee.....eee................hhhhhhhh......ee......ee.......eee........eee....ee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5caw A 143 NKAHFFIYCANPCKKINTGKLRVCCSECKHGAFTVDTDPQSWADVLDKNKITGVCNNVGCEGLYAKFYFKCASHPSQGENDTAVPLNLIKRNHKKIPCLACTDICDPVLVFSCDNRHVTCLECFKNYCGSRLKDRQFLSHPDFGYTLPCPAGCSNSFIEEVHHFRLLTDAQYEQYHRFATEEFILQAGGVLCPQPGCGQGILIDQNCNRVQCSCGYVFCGKCLEGFHLGECLNPLDPEKLEKARWDVLTKPCPKCRTSTERAGGCMHMICTRANCGFHWCWVCQGPWERDCMASHWFG 461
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372  ||   395     ||413       423       433       443       453        
                                                                                                                                                                                                                                                                  375|         401|                                                   
                                                                                                                                                                                                                                                                   389          410                                                   

Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee......hhhhh.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5caw B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKEsTLHLVLRLRGx  76
                                    10        20        30        40        50        60    |   70     |
                                                                                           65-SEP     76-3CN

Chain C from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeeeeeeee........ee.....hhhhhhh.....ee..........eeeeeee............ee...ee.................eee.......eeehhhhhhhhhhhhhh...eee...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eee......eee.....eee.........................hhhhhhh..............eee......eee......eee........eee....ee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5caw C 143 NKAHFFIYCANPCKKINTGKLRVCCSECKHGAFTVDTDPQSWADVLDKNKITGVCNNVGCEGLYAKFYFKCASHPSQGENDTAVPLNLIKRNHKKIPCLACTDICDPVLVFSCDNRHVTCLECFKNYCGSRLKDRQFLSHPDFGYTLPCPAGCSNSFIEEVHHFRLLTDAQYEQYHRFATEEFILQAGGVLCPQPGCGQGILIDQNCNRVQCSCGYVFCGKCLEGFHLGECLNPTDVPFLSQPLDPEKLEKARWDEASSTVIKVLTKPCPKCRTSTERAGGCMHMICTRANCGFHWCWVCQGPWERDCMASHWFG 461
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382 ||    396       406       416       426       436       446       456     
                                                                                                                                                                                                                                                                           384|                                                                        
                                                                                                                                                                                                                                                                            389                                                                        

Chain D from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5caw D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKEsTLHLVLRLRGx  76
                                    10        20        30        40        50        60    |   70     |
                                                                                           65-SEP     76-3CN

   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 5CAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (94, 97)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBB_HUMAN | P0CG471c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

(-) Related Entries Specified in the PDB File

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