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(-) Description

Title :  COMPUTATIONALLY DESIGNED TWO-COMPONENT SELF-ASSEMBLING TETRAHEDRAL CAGE, T33-21, CRYSTALLIZED IN SPACE GROUP R32
 
Authors :  D. E. Mcnamara, N. P. King, J. B. Bale, W. Sheffler, D. Baker, T. O. Yeates
Date :  06 Dec 13  (Deposition) - 28 May 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (3x)
Keywords :  Two-Component, Self-Assembling, Tetrahedron, Designed Protein Cage, Computational Design, Computational Biology, Protein Engineering, Multimerization, Nanomaterial, Nanostructure, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. P. King, J. B. Bale, W. Sheffler, D. E. Mcnamara, S. Gonen, T. Gonen, T. O. Yeates, D. Baker
Accurate Design Of Co-Assembling Multi-Component Protein Nanomaterials
Nature 2014
PubMed: search  |  Reference-DOI: 10.1038/NATURE13297

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0671
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
 
Molecule 2 - UNCHARACTERIZED PROTEIN
    Chains: E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA1966
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (3x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 29)

Asymmetric Unit (2, 29)
No.NameCountTypeFull Name
1NH41Ligand/IonAMMONIUM ION
2SO428Ligand/IonSULFATE ION
Biological Unit 1 (2, 87)
No.NameCountTypeFull Name
1NH43Ligand/IonAMMONIUM ION
2SO484Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:134 , ASP H:73 , ILE H:74 , ARG H:77BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWARESER A:25 , THR A:131 , ARG A:134 , HOH A:304BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWARETRP A:86 , LYS A:89 , ARG A:93BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREGLU A:29 , ARG A:124 , LYS A:128 , HOH A:303 , HOH A:309BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWARETYR A:47BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWAREARG B:124 , LYS B:128 , HOH B:302 , HOH B:306 , HOH B:312 , GLU C:29 , ARG C:124 , LYS C:128 , HOH C:304 , HOH C:305 , ARG D:124 , LYS D:128 , HOH D:302BINDING SITE FOR RESIDUE SO4 B 201
07AC7SOFTWARETHR B:131 , ARG B:134 , HOH B:307 , SER C:25BINDING SITE FOR RESIDUE SO4 B 202
08AC8SOFTWAREHIS B:46 , LYS B:53 , HOH B:321BINDING SITE FOR RESIDUE SO4 B 203
09AC9SOFTWARETRP C:86 , ARG C:93BINDING SITE FOR RESIDUE SO4 C 201
10BC1SOFTWARETHR C:131 , ARG C:134 , SER D:25BINDING SITE FOR RESIDUE SO4 C 202
11BC2SOFTWAREHIS C:46 , LYS C:53BINDING SITE FOR RESIDUE SO4 C 203
12BC3SOFTWARESER B:25 , THR D:131 , ARG D:134 , HOH D:303BINDING SITE FOR RESIDUE SO4 D 201
13BC4SOFTWAREHIS D:46 , LYS D:53BINDING SITE FOR RESIDUE SO4 D 202
14BC5SOFTWARETYR B:47 , TYR C:47 , TYR D:47BINDING SITE FOR RESIDUE SO4 D 203
15BC6SOFTWAREARG C:134 , ASP E:73 , ILE E:74 , ARG E:77BINDING SITE FOR RESIDUE SO4 E 201
16BC7SOFTWARELEU E:69 , ARG E:72 , ARG E:111 , HOH E:318BINDING SITE FOR RESIDUE SO4 E 202
17BC8SOFTWAREARG E:107 , HOH E:309 , HOH E:311BINDING SITE FOR RESIDUE SO4 E 203
18BC9SOFTWAREPRO E:2 , HIS E:3 , LYS E:41 , TYR E:114BINDING SITE FOR RESIDUE SO4 E 204
19CC1SOFTWAREARG F:107 , HOH F:303 , HOH F:306 , ARG G:107 , ARG H:107 , HOH H:304 , HOH H:306BINDING SITE FOR RESIDUE SO4 F 201
20CC2SOFTWARELEU F:69 , ARG F:72 , ARG F:111 , HOH F:310BINDING SITE FOR RESIDUE SO4 F 202
21CC3SOFTWAREARG B:134 , ASP F:73 , ILE F:74 , ARG F:77BINDING SITE FOR RESIDUE SO4 F 203
22CC4SOFTWAREPRO F:2 , HIS F:3 , ASP F:39 , LYS F:41 , TYR F:114BINDING SITE FOR RESIDUE SO4 F 204
23CC5SOFTWAREARG D:134 , ASP G:73 , ILE G:74 , ARG G:77BINDING SITE FOR RESIDUE SO4 G 201
24CC6SOFTWAREPRO G:2 , HIS G:3 , ASP G:39 , LYS G:41 , TYR G:114 , LYS G:116 , SER H:103BINDING SITE FOR RESIDUE SO4 G 202
25CC7SOFTWARELEU G:69 , ARG G:72 , ARG G:111BINDING SITE FOR RESIDUE SO4 G 203
26CC8SOFTWAREGLY G:19 , HOH G:327 , ARG H:51 , HOH H:308BINDING SITE FOR RESIDUE SO4 H 201
27CC9SOFTWARELEU H:69 , ARG H:72 , ARG H:111 , HOH H:310BINDING SITE FOR RESIDUE SO4 H 202
28DC1SOFTWAREPRO H:2 , HIS H:3 , ASP H:39 , LYS H:41 , TYR H:114 , LYS H:116BINDING SITE FOR RESIDUE SO4 H 203
29DC2SOFTWAREMET G:109 , GLU G:110 , GLU H:105 , VAL H:106 , HOH H:304BINDING SITE FOR RESIDUE NH4 H 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NWP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NWP)

(-) 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:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp A  23 KDSPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYKIMGEIGSKGKIEGISEERIAWLLKLILRYMEMVNLSFVLPGGTLESAKLDVCRTIARRALRKVLTVTREFGIGAEAAAYLLALSDLLFLLARVIEIEKNKLK 168
                                    32        42        52        62        72        82        92       103       113       123       133       143       153       163     
                                                                                                       100|                                                                  
                                                                                                        102                                                                  


Chain B from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp B  23 KDSPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYKIMGEIGSKGKIEGISEERIAWLLKLILRYMEMVNLFVLPGGTLESAKLDVCRTIARRALRKVLTVTREFGIGAEAAAYLLALSDLLFLLARVIEIEKN 165
                                    32        42        52        62        72        82        92       104       114       124       134       144       154       164 
                                                                                                       100|                                                              
                                                                                                        103                                                              


Chain C from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp C  23 KDSPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYKIMGEIGSKGKIEGISEERIAWLLKLILRYMEMVNFVLPGGTLESAKLDVCRTIARRALRKVLTVTREFGIGAEAAAYLLALSDLLFLLARVIEIEKN 165
                                    32        42        52        62        72        82        92      |105       115       125       135       145       155       165
                                                                                                       99|                                                              
                                                                                                       103                                                              


Chain D from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp D  23 KDSPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYKIMGEIGSKGKIEGISEERIAWLLKLILRYMEMVNLKSFVLPGGTLESAKLDVCRTIARRALRKVLTVTREFGIGAEAAAYLLALSDLLFLLARVIEIEKNKLKEVR 171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162         


Chain E from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eee..hhhhhhhhhhhhhhh....hhhhheeeeeee.............eeeeeeeee...hhhhhhhhhhhhhhhhhhheeee.....eeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp E   2 PHLVIEATANLRLETSPGELLEQANKALFASGQFGEADIKSRFVTLEAYRQGTAAVERAYLHACLSILDGRDIATRTLLGASLCAVLAEAVAGGGEEGVQVSVEVREMERLSYAKRVV 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain F from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eee..hhhhhhhhhhhhhhh....hhhh.eeeeeee.............eeeeeeeee...hhhhhhhhhhhhhhhhhhheeee.....eeeeeeeee.....eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp F   2 PHLVIEATANLRLETSPGELLEQANKALFASGQFGEADIKSRFVTLEAYRQGTAAVERAYLHACLSILDGRDIATRTLLGASLCAVLAEAVAGGGEEGVQVSVEVREMERLSYAKRVV 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain G from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...ee..hhhhhhhhhhhhhhh....hhhhheeeeeee..eee........eeeeeeeee...hhhhhhhhhhhhhhhhhhheee.....eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp G   2 PHLVIEATANLRLETSPGELLEQANKALFASGQFGEADIKSRFVTLEAYRQGTAAVERAYLHACLSILDGRDIATRTLLGASLCAVLAEAVAGGGEEGVQVSVEVREMERLSYAKRVV 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain H from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...ee..hhhhhhhhhhhhhhh....hhhhheeeeeee............eeeeeeeee...hhhhhhhhhhhhhhhhhhheee......eeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwp H   2 PHLVIEATANLRLETSPGELLEQANKALFASGQFGEADIKSRFVTLEAYRQGTAVERAYLHACLSILDGRDIATRTLLGASLCAVLAEAVAGGGEEGVQVSVEVREMERLSYAKRVV 119
                                    11        21        31        41        51   ||   62        72        82        92       102       112       
                                                                                55|                                                              
                                                                                 57
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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 4NWP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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  Q9I2D8_PSEAE | Q9I2D8
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 Related Entries

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

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        O58404_PYRHO | O58404: 1wy1 4nwq
        Q9I2D8_PSEAE | Q9I2D8: 3e6q 4nwq

(-) Related Entries Specified in the PDB File

4nwn 4nwo 4nwq 4nwr