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(-) Description

Title :  BRO1 V DOMAIN AND UBIQUITIN
 
Authors :  N. Pashkova, L. Gakhar, R. C. Piper
Date :  06 Mar 13  (Deposition) - 19 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A,B,U
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  U  (1x)
Keywords :  Membrane Trafficking, Escrt-I, Escrt-Iii, Ubiquitin, Endosome, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pashkova, L. Gakhar, S. C. Winistorfer, A. B. Sunshine, M. Rich, M. J. Dunham, L. Yu, R. C. Piper
The Yeast Alix Homolog Bro1 Functions As A Ubiquitin Receptor For Protein Sorting Into Multivesicular Endosomes.
Dev. Cell V. 25 520 2013
PubMed-ID: 23726974  |  Reference-DOI: 10.1016/J.DEVCEL.2013.04.007

(-) Compounds

Molecule 1 - BRO1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BRO1(AMINO ACIDS 370-708), NCAS0B02080, NCAS_0B02080
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: NAUMOVOZYMA CASTELLII
    Organism Taxid: 1064592
    Strain: ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630
 
Molecule 2 - UBIQUITIN
    Chains: U
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBA52, UBCEP2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABU
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   U

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MSE-1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4JIO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Pro A:367 -Phe A:368
2Lys A:597 -Ser A:598
3Glu A:601 -Leu A:602
4Asp A:649 -Lys A:650
5Thr A:651 -Pro A:652
6Asn B:425 -Asn B:426
7Asp B:428 -Ala B:429
8Glu B:451 -Phe B:452
9Pro B:477 -Ala B:478
10Asp B:599 -Ala B:600
11Gln B:648 -Asp B:649
12Asp B:649 -Lys B:650

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JIO)

(-) 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:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jio A 367 PFTEIYEKESIYSEEKAQLLRKEmESVETADLEYTSFVEFTNLPKLINDLAAAYTPQLEmmRDQIKSWAYAVQQNEFNDIERIINVISSKRKEILDILALPAEEKENILKLKASLVEASQSDEKLFRLIKPYVAEIKLLCNDSSLWRKFDDSKTELILSKLKAITQFAEDLRLLKEERARTmGELKDYVNNNDDITSLLLANKDKSDAELQSLFESELAKFEPLTTRIEATIFKQGSTINGVKIELDNIFGLTGIQDKTPEEQKAELERKLFFDKLEEATTKFTIFSSDIQKGLNFYNSLLKmSKDLQNS 702
                                   376       386   |   396       406       416    || 435|      445       455       465       476       486       496       506       516       526|      552       562       572 |     582       592       602       612       622       632       642       652       662       672       682       692  |    702
                                                 390-MSE                        421|   ||                                   474|                                               526|                            574-MSE                                                                                                                  695-MSE   
                                                                                 431   ||                                    476                                                543                                                                                                                                                               
                                                                                     435-MSE                                                                                                                                                                                                                                                      
                                                                                      436-MSE                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jio B 368 FTEIYEKESIYSEEKAQLLRKEmESVETADLEYTSFVEFTNLPKLINDLAAAYTTGGNNNDADPQLEmmRDQIKSWAYAVQQNEFNDIERIINVISSKRKEILDILATLPAEEKENILKLKASLVEASQSDEKLFRLIKPYVAEIKLLCNDSSLWRKFDEFQSDIDDSKTELILSKLKAITQFAEDLRLLKEERARTmGELKDYVNNNANKDKSDAELQSLFESELAKFEPLTTRIEATIFKQGSTINGVKIELDNIFGLTGIQDKTPEEQKAELERKLFFDKLEEATTKFTIFSSDIQKGLNFYNSLLKmSKDLQNSVE 704
                                   377       387  |    397       407       417       427       437       447       457       467       477       487       497       507       517       527  ||   546       556       566       576       594       604       614       624       634       644       654       664       674       684       694|      704
                                                390-MSE                                      435-MSE                                                                                        530|                               574-MSE   584|                                                                                                   695-MSE     
                                                                                              436-MSE                                                                                        540                                          593                                                                                                               


Chain U from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhh....hhh.eeeee..ee................eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4jio U   1 MQIFVKTLTGKTITLEVEPSDTIENVKMKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4JIO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (100, 102)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn B:425 - Asn B:426   [ RasMol ]  
    Asp A:649 - Lys A:650   [ RasMol ]  
    Asp B:428 - Ala B:429   [ RasMol ]  
    Asp B:599 - Ala B:600   [ RasMol ]  
    Asp B:649 - Lys B:650   [ RasMol ]  
    Gln B:648 - Asp B:649   [ RasMol ]  
    Glu A:601 - Leu A:602   [ RasMol ]  
    Glu B:451 - Phe B:452   [ RasMol ]  
    Lys A:597 - Ser A:598   [ RasMol ]  
    Pro A:367 - Phe A:368   [ RasMol ]  
    Pro B:477 - Ala B:478   [ RasMol ]  
    Thr A:651 - Pro A:652   [ RasMol ]  
 
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  RL40_HUMAN | P62987
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL40_HUMAN | P62987: 1c3t 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 2lj5 2mbh 2mjb 2mur 2n3u 2n3v 2n3w 2nbd 2nbe 2nr2 2o6v 2ojr 2pe9 2pea 2rsu 2w9n 2wdt 2xew 2xk5 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 3phd 4hjk 4p4h 4pig 4pih 4pij 4rf0 4rf1 4s1z 4ug0 4v6x 4xkl 5aj0 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5hpk 5hpl 5hps 5hpt 5j26 5j8p 5jbv 5jby 5t2c

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