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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF EBOLA (TAI FOREST) NUCLEOPROTEIN
 
Authors :  L. E. Baker, K. B. Handing, U. Derewenda, D. Utepbergenov, Z. S. Derewen
Date :  01 Oct 15  (Deposition) - 21 Oct 15  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Biol. Unit 9:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 10:  E (1x),F (1x),G (1x),H (1x)
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Baker, J. F. Ellena, K. B. Handing, U. Derewenda, D. Utepbergenov D. A. Engel, Z. S. Derewenda
Molecular Architecture Of The Nucleoprotein C-Terminal Domain From The Ebola And Marburg Viruses.
Acta Crystallogr D Struct V. 72 49 2016 Biol
PubMed-ID: 26894534  |  Reference-DOI: 10.1107/S2059798315021439
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NP
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PARALLEL1-MBPHIS
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 641-739)
    Gene: NP
    Organism Scientific: TAI FOREST EBOLAVIRUS
    Organism Taxid: 186541

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A       
Biological Unit 2 (1x):  B      
Biological Unit 3 (1x):   C     
Biological Unit 4 (1x):    D    
Biological Unit 5 (1x):     E   
Biological Unit 6 (1x):      F  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H
Biological Unit 9 (1x): A (1x)B (1x)C (1x)D (1x)    
Biological Unit 10 (1x):     E (1x)F (1x)G (1x)H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
12PE4Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
12PE-1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
12PE-1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
12PE-1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 8 (0, 0)
No.NameCountTypeFull Name
12PE-1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 9 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
Biological Unit 10 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:666 , TYR B:669 , HOH B:923 , HOH B:945 , ASP D:709 , PHE D:712 , GLN D:719binding site for residue 2PE B 801
2AC2SOFTWARELEU A:666 , TYR A:669 , ASP C:709 , GLN C:719 , HOH C:919binding site for residue 2PE C 801
3AC3SOFTWAREASP E:709 , GLN E:719 , HOH E:916 , HOH E:933 , HOH E:942 , LEU G:666 , TYR G:669 , HIS G:727binding site for residue 2PE E 801
4AC4SOFTWAREASP F:709 , GLN F:719 , HOH F:928 , LEU H:666 , TYR H:669 , HIS H:727binding site for residue 2PE F 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E2X)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:688 -Pro A:689
2Tyr B:688 -Pro B:689
3Tyr C:688 -Pro C:689
4Tyr D:688 -Pro D:689
5Tyr E:688 -Pro E:689
6Tyr F:688 -Pro F:689
7Tyr G:688 -Pro G:689
8Tyr H:688 -Pro H:689

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E2X)

(-) Exons   (0, 0)

(no "Exon" information available for 5E2X)

(-) 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:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.........hhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5e2x A 639 MAKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   648       658       668       678       688       698       708       718       728       738 


Chain B from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.........hhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5e2x B 639 MAKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   648       658       668       678       688       698       708       718       728       738 


Chain C from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.......hhhhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5e2x C 639 MAKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   648       658       668       678       688       698       708       718       728       738 


Chain D from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.......hhhhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5e2x D 639 MAKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   648       658       668       678       688       698       708       718       728       738 


Chain E from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.......hhhhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5e2x E 646 QSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   655       665       675       685       695       705       715       725       735    


Chain F from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.......hhhhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5e2x F 646 QSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   655       665       675       685       695       705       715       725       735    


Chain G from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.........hhhhhhhh.eeee..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5e2x G 639 MAKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   648       658       668       678       688       698       708       718       728       738 


Chain H from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhh.........hhhhhhhh.eee....eee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5e2x H 639 MAKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQFYWPVMNHRNKFMAILQHHK 739
                                   648       658       668       678       688       698       708       718       728       738
   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 5E2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E2X)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  5e2x
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 Related Entries

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(-) Related Entries Specified in the PDB File

4qaz THE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF EBOLA (ZAIRE) NUCLEOPROTEIN
4qb0 THE STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ZAIRE EBOLAVIRUS NUCLEOPROTEIN.
5dsd THE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF EBOLA (BUNDIBUGYO) NUCLEOPROTEIN