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(-) Description

Title :  CRYSTAL STRUCTURE OF EVP30 C-TERMINUS AND ENP PEPTIDE
 
Authors :  W. Xu, D. W. Leung, G. K. Amarasinghe
Date :  27 Mar 17  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,H  (1x)
Biol. Unit 4:  D,G  (1x)
Keywords :  Functional Class, Known Biologyical Activity, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Xu, P. Luthra, C. Wu, J. Batra, D. W. Leung, C. F. Basler, G. K. Amarasinghe
Ebola Virus Vp30 And Nucleoprotein Interactions Modulate Viral Rna Synthesis.
Nat Commun V. 8 15576 2017
PubMed-ID: 28593988  |  Reference-DOI: 10.1038/NCOMMS15576

(-) Compounds

Molecule 1 - MINOR NUCLEOPROTEIN VP30
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 139-267
    Gene: VP30
    Organism Common: ZEBOV
    Organism Scientific: EBOLA VIRUS
    Organism Taxid: 1570291
    Synonym: TRANSCRIPTION ACTIVATOR VP30
 
Molecule 2 - NP
    Chains: E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 601-611
    Organism Scientific: EBOLA VIRUS
    Organism Taxid: 1570291

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A    F  
Biological Unit 2 (1x):  B  E   
Biological Unit 3 (1x):   C    H
Biological Unit 4 (1x):    D  G 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL8Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:179 , LYS B:180 , PHE B:181 , SER B:182 , HIS B:215 , GOL B:302binding site for residue GOL B 301
02AC2SOFTWAREARG B:179 , GLU B:252 , GOL B:301 , HOH B:417binding site for residue GOL B 302
03AC3SOFTWARELYS B:141 , ILE B:142 , PRO B:250 , VAL B:258 , ARG B:262binding site for residue CL B 303
04AC4SOFTWAREARG B:168 , THR B:172 , GLY B:220 , GLU B:223 , VAL B:256binding site for residue PEG B 306
05AC5SOFTWAREARG C:179 , PHE C:181 , HIS C:215 , HOH C:411 , ARG D:179 , LYS D:180 , PEG D:307binding site for residue GOL C 301
06AC6SOFTWAREHOH C:408binding site for residue CL C 302
07AC7SOFTWAREGLU B:197 , SER C:182 , SER C:184 , GLU C:252 , SER C:253 , SER C:254 , GLY D:219 , TYR E:611binding site for residue PEG C 303
08AC8SOFTWAREGLU B:205 , LYS D:183 , GLN D:212 , HIS D:215 , SER D:216 , HOH D:407binding site for residue GOL D 301
09AC9SOFTWAREGLU B:209 , HOH B:414 , HOH B:416 , GLU D:209 , GLN D:212 , HOH D:404 , HOH D:421binding site for residue CA D 302
10AD1SOFTWARETHR D:161binding site for residue CL D 304
11AD2SOFTWAREARG B:213binding site for residue CL D 305
12AD3SOFTWARELEU D:199binding site for residue CL D 306
13AD4SOFTWAREARG C:179 , LYS C:180 , GOL C:301 , ARG D:179 , PHE D:181 , SER D:182 , HIS D:215 , GLU D:252binding site for residue PEG D 307
14AD5SOFTWAREHIS D:193 , SER D:234 , MET D:237 , PHE D:238 , HOH D:417 , HOH D:418 , PRO G:609 , TYR G:611binding site for residue PEG D 308
15AD6SOFTWAREHOH B:423 , LYS C:183 , ARG E:612binding site for residue PEG E 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VAO)

(-) 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:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vao A 140 PKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVP 266
                                   149       159       169       179       189       199       209       219       229       239       249       259       


Chain B from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vao B 139 GPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVPQ 267
                                   148       158       168       178       188       198       208       218       228       238       248       258         


Chain C from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vao C 139 GPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVPQ 267
                                   148       158       168       178       188       198       208       218       228       238       248       258         


Chain D from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vao D 139 GPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVPQ 267
                                   148       158       168       178       188       198       208       218       228       238       248       258         


Chain E 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
                 5vao E 602 PTVAPPAPVYR 612
                                   611 


Chain F 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
                 5vao F 602 PTVAPPAPVYR 612
                                   611 


Chain G 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
                 5vao G 602 PTVAPPAPVYR 612
                                   611 


Chain H 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
                 5vao H 602 PTVAPPAPVYR 612
                                   611
   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 5VAO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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        VP30_EBOZ5 | Q77DJ5: 2i8b 5vap

(-) Related Entries Specified in the PDB File

5vap