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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PREFUSION GLYCOPROTEIN OF LCMV
 
Authors :  K. M. Hastie, E. O. Saphire
Date :  07 Mar 16  (Deposition) - 20 Apr 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Arenavirus, Lcmv, Glycoprotein, Pre-Fusion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Hastie, S. Igonet, B. M. Sullivan, P. Legrand, M. A. Zandonatti, J. E. Robinson, R. F. Garry, F. A. Rey, M. B. Oldstone, E. O. Saphire
Crystal Structure Of The Prefusion Surface Glycoprotein Of The Prototypic Arenavirus Lcmv.
Nat. Struct. Mol. Biol. V. 23 513 2016
PubMed-ID: 27111888  |  Reference-DOI: 10.1038/NSMB.3210

(-) Compounds

Molecule 1 - PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Taxid: 7227
    Gene: GP-C
    Organism Scientific: LYMPHOCYTIC CHORIOMENINGITIS MAMMARENAVIRUS
    Organism Taxid: 11623

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 45)

Asymmetric/Biological Unit (3, 45)
No.NameCountTypeFull Name
1BMA11Ligand/IonBETA-D-MANNOSE
2MAN5Ligand/IonALPHA-D-MANNOSE
3NAG29Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:82 , ASN A:85 , GLY A:104 , SER A:105 , TRP A:289binding site for Poly-Saccharide residues NAG A 518 through BMA A 520 bound to ASN A 85
02AC2SOFTWAREASN A:95 , SER A:97 , ARG A:233 , GLN A:334binding site for Poly-Saccharide residues NAG A 501 through MAN A 504 bound to ASN A 95
03AC3SOFTWAREASN A:114 , SER A:224 , GLN A:226binding site for Poly-Saccharide residues NAG A 505 through MAN A 508 bound to ASN A 114
04AC4SOFTWAREASN A:124 , THR B:271binding site for Mono-Saccharide NAG A 509 bound to ASN A 124
05AC5SOFTWARELEU A:118 , ASN A:121 , ASN A:171 , SER A:173 , TYR A:227binding site for Poly-Saccharide residues NAG A 510 through NAG A 511 bound to ASN A 171
06AC6SOFTWAREASN A:163 , ASN A:164 , ASN A:232 , THR A:234binding site for Poly-Saccharide residues NAG A 512 through BMA A 514 bound to ASN A 232
07AC7SOFTWARELYS A:202 , ARG A:240 , ALA A:242 , ASN A:371 , SER A:373 , VAL A:394 , GLY A:397 , TYR A:399binding site for Poly-Saccharide residues NAG A 515 through BMA A 517 bound to ASN A 371
08AC8SOFTWAREASN A:396binding site for Mono-Saccharide NAG A 521 bound to ASN A 396
09AC9SOFTWAREASN A:401 , GLU A:402binding site for Mono-Saccharide NAG A 522 bound to ASN A 401
10AD1SOFTWARESER B:82 , ASN B:85 , GLY B:104 , SER B:105 , TRP B:289binding site for Poly-Saccharide residues NAG B 501 through BMA B 503 bound to ASN B 85
11AD2SOFTWAREASN B:95 , SER B:97 , ARG B:233binding site for Poly-Saccharide residues NAG B 504 through MAN B 507 bound to ASN B 95
12AD3SOFTWAREASN B:114 , SER B:224 , GLN B:226binding site for Poly-Saccharide residues NAG B 508 through BMA B 510 bound to ASN B 114
13AD4SOFTWARETHR A:271 , GLU A:279 , ASN A:308 , ASN B:124binding site for Mono-Saccharide NAG B 511 bound to ASN B 124
14AD5SOFTWARELEU B:118 , ASN B:121 , ASN B:171 , SER B:173 , TYR B:227binding site for Poly-Saccharide residues NAG B 512 through BMA B 514 bound to ASN B 171
15AD6SOFTWAREASN B:163 , ASN B:164 , ASN B:232 , THR B:234binding site for Poly-Saccharide residues NAG B 515 through MAN B 518 bound to ASN B 232
16AD7SOFTWAREARG B:240 , ALA B:242 , ASN B:371 , SER B:373 , VAL B:394 , GLY B:397 , TYR B:399binding site for Poly-Saccharide residues NAG B 519 through MAN B 522 bound to ASN B 371
17AD8SOFTWAREASN B:401 , GLU B:402binding site for Mono-Saccharide NAG B 523 bound to ASN B 401

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:239
2A:123 -A:160
3A:184 -A:220
4A:285 -A:298
5A:307 -A:316
6A:370 -A:391
7B:92 -B:239
8B:123 -B:160
9B:184 -B:220
10B:285 -B:298
11B:307 -B:316
12B:370 -B:391

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5INE)

(-) Sequences/Alignments

Asymmetric/Biological 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:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...eeeeeee.hhhhhh....eeee....eeeeee..eeeeeeee...........hhhhhhh...hhhhhhhhhhhhhh.........eeee.....eeeee.......hhhhhhhhhhhhhhh.....................eeeeee...........hhhhhhhhhhhhhhh........hhhhhh.....eeee..........eee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........ee.............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ine A  63 NGPDIYKGVYQFKSVEFDMSHLNLTMPNACSANNSHHYISMGSSGLELTFTNDSILNHNFCNLTSAFNKKTFDHTLMSIVSSLHLSIRGNSNHKAVSCDFNNGITIQYNLSFSQCRTFRGRVLDMFRTAFGGKYMRSGWGWATTWCSQTSYQYLIIQNRTWENHCRYAGPFGMSRILFAQEKTKFLTTFTWTLSDSSGVENPGGYCLTKWMILAAELKCFGNTAVAKCNVNHDEEFCDMLRLIDYNKAALSKFKQDVESALHVFKTTVNSLISDQLLMRNHLRDLMGVPYCNYSKFWYLEHAKTGETSVPKCWLVTNGSYLNETHFSDQIEQEADNMITEMLRKDYIK 427
                                    72        82        92       102       112       122       132       142       152       162       172  ||   189       199       209 ||    224       234       244       254      |269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419        
                                                                                                                                          175|                         211|                                         261|                                                                                                                                                                
                                                                                                                                           183                          217                                          267                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eeeeeee.hhhhhh....eeee....eeeeee..eeeeeeee...........hhhhhhh...hhhhhhhhhhhhhh.........eeee.....eeeee.....hhhhhhhhhhhhhhh......................eeeeee...........hhhhhhhhhhhhhhh...............eee..........eeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........ee..ee..ee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ine B  63 NGPDIYKGVYQFKSVEFDMSHLNLTMPNACSANNSHHYISMGSSGLELTFTNDSILNHNFCNLTSAFNKKTFDHTLMSIVSSLHLSIRGNSNHKAVSCDFNNGITIQYNLSQCRTFRGRVLDMFRTAFGGKYMRSGWGWAGTTWCSQTSYQYLIIQNRTWENHCRYAGPFGMSRILFAQEKTKFLAGTFTWTLSDPGGYCLTKWMILAAELKCFGNTAVAKCNVNHDEEFCDMLRLIDYNKAALSKFKQDVESALHVFKTTVNSLISDQLLMRNHLRDLMGVPYCNYSKFWYLEHAKTGETSVPKCWLVTNGSYLNETHFSDQIEQEADNMITEMLRKD 424
                                    72        82        92       102       112       122       132       142       152       162       172||     191       201       211||     225       235       245       255   ||  269    || 285       295       305       315       325       335       345       355       365       375       385       395       405       415         
                                                                                                                                        173|                          212|                                       259|       274|                                                                                                                                               
                                                                                                                                         183                           217                                        264        281
   Legend:   → Mismatch (orange background)
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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 5INE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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