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(-) Description

Title :  CRYSTAL STRUCTURE OF CHAETOMIUM THERMOPHILUM NUP53 RRM (SPACE GROUP P3121)
 
Authors :  D. H. Lin, T. Stuwe, A. Hoelz
Date :  31 Dec 15  (Deposition) - 20 Apr 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Nucleocytoplasmic Transport, Protein Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Lin, T. Stuwe, S. Schilbach, E. J. Rundlet, T. Perriches, G. Mobbs Y. Fan, K. Thierbach, F. M. Huber, L. N. Collins, A. M. Davenport, Y. E. Jeon, A. Hoelz
Architecture Of The Symmetric Core Of The Nuclear Pore.
Science V. 352 F1015 2016
PubMed-ID: 27081075  |  Reference-DOI: 10.1126/SCIENCE.AAF1015

(-) Compounds

Molecule 1 - NUCLEOPORIN NUP53
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NUP53, CTHT_0012410
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: NUCLEAR PORE PROTEIN NUP53

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SIN6Ligand/IonSUCCINIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SIN2Ligand/IonSUCCINIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SIN2Ligand/IonSUCCINIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SIN1Ligand/IonSUCCINIC ACID
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:156 , ILE A:157 , ALA A:158 , GLY A:159 , LYS A:221 , HOH A:442 , GLN B:156 , ILE B:157 , ALA B:158 , GLY B:159 , LYS B:221 , HOH B:457 , GLU C:172 , GLU D:172binding site for residue SIN A 301
02AC2SOFTWARETYR A:148 , ALA A:149 , ASN A:152 , HIS A:153 , ARG A:167 , GLU A:168 , HOH A:403 , HOH A:426 , TYR D:224binding site for residue GOL A 302
03AC3SOFTWAREARG A:142 , HIS A:146 , GLN A:231 , HOH A:401 , HOH A:494 , VAL D:223 , TYR D:239 , HOH D:473binding site for residue SIN A 303
04AC4SOFTWARETYR B:148 , ALA B:149 , ASN B:152 , HIS B:153 , ARG B:167 , GLU B:168 , HOH B:487 , HOH B:494binding site for residue GOL B 301
05AC5SOFTWAREARG B:142 , HIS B:146 , GLN B:231 , HOH B:406 , HOH B:491 , HOH B:497 , HOH B:506 , ASP C:220 , VAL C:223 , TYR C:224 , TYR C:239binding site for residue SIN B 302
06AC6SOFTWARETHR B:134 , GLU B:135 , LYS B:198binding site for residue SIN B 303
07AC7SOFTWAREGLU A:172 , GLU B:172 , GLN C:156 , ILE C:157 , ALA C:158 , GLY C:159 , LYS C:221 , HOH C:429 , HOH C:447 , GLN D:156 , ILE D:157 , ALA D:158 , GLY D:159 , LYS D:221binding site for residue SIN C 301
08AC8SOFTWARETYR C:148 , ALA C:149 , ASN C:152 , HIS C:153 , ARG C:167 , GLU C:168 , HOH C:472binding site for residue GOL C 302
09AC9SOFTWAREALA D:149 , ASN D:152 , HIS D:153 , HOH D:401 , HOH D:462binding site for residue GOL D 301
10AD1SOFTWAREARG D:139 , TYR D:236 , ILE D:251binding site for residue GOL D 302
11AD2SOFTWAREVAL A:223 , TYR A:239 , HOH A:470 , ARG D:142 , HIS D:146 , GLN D:231 , HIS D:233 , HOH D:458binding site for residue SIN D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HB8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:226 -Pro A:227
2Ser B:226 -Pro B:227
3Ser C:226 -Pro C:227
4Ser D:226 -Pro D:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HB8)

(-) Exons   (0, 0)

(no "Exon" information available for 5HB8)

(-) 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:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhhhh.................hhhhhhhhhh......eeeeee.hhhhhhhhhhh..eee..eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5hb8 A 130 PHMPTEVILRGYRNAQHQYAAINHYEQIAGRICEDYPREPPVESRALTPEERAKVNRAMSGEHWVKVTFESAEAADKAVYSSPQLIQGHLVYAEYYKGVPPAQDEAIPD 253
                                   139       149       159       169    || 194       204       214       224       234       244         
                                                                      174|                                                               
                                                                       190                                                               


Chain B from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhhhh.................hhhhhhhhh.......eeeeee.hhhhhhhhhhh..eee..eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5hb8 B 130 PHMPTEVILRGYRNAQHQYAAINHYEQIAGRICEDYPREPPVESRALTPEERAKVNRAMSGEHWVKVTFESAEAADKAVYSSPQLIQGHLVYAEYYKGVPPAQDEAIPD 253
                                   139       149       159       169    || 194       204       214       224       234       244         
                                                                      174|                                                               
                                                                       190                                                               


Chain C from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhhhh..................hhhhhhhhhh......eeeeee.hhhhhhhhhhh..eee..eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5hb8 C 130 PHMPTEVILRGYRNAQHQYAAINHYEQIAGRICEDYPREPPVESRRALTPEERAKVNRAMSGEHWVKVTFESAEAADKAVYSSPQLIQGHLVYAEYYKGVPPAQDEAIPD 253
                                   139       149       159       169     ||193       203       213       223       233       243       253
                                                                       175|                                                               
                                                                        190                                                               


Chain D from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhh..................hhhhhhhhh.......eeeeee.hhhhhhhhhhh..eee..eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5hb8 D 131 HMPTEVILRGYRNAQHQYAAINHYEQIAGRICEDYPREPPVESRRALTPEERAKVNRAMSGEHWVKVTFESAEAADKAVYSSPQLIQGHLVYAEYYKGVPPAQDEAIPD 253
                                   140       150       160       170    || 194       204       214       224       234       244         
                                                                      175|                                                               
                                                                       190
   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 5HB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HB8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HB8)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  NUP53_CHATD | G0S156
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUP53_CHATD | G0S156: 5hax 5hb3 5hb7

(-) Related Entries Specified in the PDB File

5hax 5hay 5haz 5hb0 5hb1 5hb2 5hb3 5hb4 5hb5 5hb6 5hb7