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(-) Description

Title :  A SUBTYPE N10 NEURAMINIDASE-LIKE PROTEIN OF A/LITTLE YELLOW-SHOULDERED BAT/GUATEMALA/060/2010
 
Authors :  X. Zhu, I. A. Wilson
Date :  31 Jul 12  (Deposition) - 26 Sep 12  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 :  Influenza Virus, Neuraminidase-Like, N10, Beta Propeller, Ectodomain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, H. Yang, Z. Guo, W. Yu, P. J. Carney, Y. Li, L. M. Chen, J. C. Paulson, R. O. Donis, S. Tong, J. Stevens, I. A. Wilson
Crystal Structures Of Two Subtype N10 Neuraminidase-Like Proteins From Bat Influenza A Viruses Reveal A Diverged Putative Active Site.
Proc. Natl. Acad. Sci. Usa V. 109 18903 2012
PubMed-ID: 23012478  |  Reference-DOI: 10.1073/PNAS.1212579109

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Gene: NA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 1129347
    Strain: A/LITTLE YELLOW-SHOULDERED BAT/GUATEMALA/060/2010(H17N10))

 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  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FUC4Ligand/IonALPHA-L-FUCOSE
3FUL4Ligand/IonBETA-L-FUCOSE
4NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3FUL1Ligand/IonBETA-L-FUCOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3FUL1Ligand/IonBETA-L-FUCOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3FUL1Ligand/IonBETA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (3, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3FUL1Ligand/IonBETA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:269 , THR A:271 , NAG A:502 , FUC A:503 , FUL A:504 , HOH A:644BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWARENAG A:501 , HOH A:644 , HOH A:697 , ASN B:401BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREILE A:314 , NAG A:501 , HOH A:643 , HOH A:774BINDING SITE FOR RESIDUE FUC A 503
04AC4SOFTWARENAG A:501 , HOH A:644 , HOH A:696 , HOH A:754 , GLU C:387 , THR C:390BINDING SITE FOR RESIDUE FUL A 504
05AC5SOFTWAREGLN A:258 , ASN A:259BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWAREASN A:248BINDING SITE FOR RESIDUE NAG A 506
07AC7SOFTWAREASN A:293 , ASP A:297 , ASP A:324 , GLY A:345 , GLY A:347 , HOH A:601BINDING SITE FOR RESIDUE CA A 507
08AC8SOFTWAREASN B:269 , THR B:271 , NAG B:502 , FUC B:503 , FUL B:504 , HOH B:656 , HOH B:711BINDING SITE FOR RESIDUE NAG B 501
09AC9SOFTWARENAG B:501 , FUL B:504 , HOH B:694 , ASN D:401BINDING SITE FOR RESIDUE NAG B 502
10BC1SOFTWAREILE B:314 , NAG B:501 , HOH B:740 , HOH B:762BINDING SITE FOR RESIDUE FUC B 503
11BC2SOFTWAREGLU A:387 , THR A:390 , HOH A:785 , NAG B:501 , NAG B:502 , HOH B:656 , HOH B:697BINDING SITE FOR RESIDUE FUL B 504
12BC3SOFTWAREGLN B:258 , ASN B:259 , GLN B:263 , HOH B:713BINDING SITE FOR RESIDUE NAG B 505
13BC4SOFTWAREASN B:248BINDING SITE FOR RESIDUE NAG B 506
14BC5SOFTWAREASN B:293 , ASP B:297 , ASP B:324 , GLY B:345 , GLY B:347 , HOH B:716BINDING SITE FOR RESIDUE CA B 507
15BC6SOFTWAREASN C:269 , NAG C:502 , FUC C:503 , FUL C:504 , HOH C:653 , HOH C:737 , GLN D:267 , LEU D:268BINDING SITE FOR RESIDUE NAG C 501
16BC7SOFTWARENAG C:501 , FUL C:504BINDING SITE FOR RESIDUE NAG C 502
17BC8SOFTWAREASN C:269 , ILE C:314 , NAG C:501 , HOH C:620BINDING SITE FOR RESIDUE FUC C 503
18BC9SOFTWARENAG C:501 , NAG C:502 , HOH C:658 , HOH C:664 , HOH C:700 , ARG D:219 , GLN D:249 , VAL D:251 , GLN D:267BINDING SITE FOR RESIDUE FUL C 504
19CC1SOFTWAREASN C:248BINDING SITE FOR RESIDUE NAG C 505
20CC2SOFTWAREASN C:293 , ASP C:297 , ASP C:324 , GLY C:345 , GLY C:347 , HOH C:601BINDING SITE FOR RESIDUE CA C 506
21CC3SOFTWAREARG C:219 , ASN D:269 , NAG D:502 , FUC D:503 , FUL D:504 , HOH D:718BINDING SITE FOR RESIDUE NAG D 501
22CC4SOFTWARENAG D:501 , FUL D:504 , HOH D:718BINDING SITE FOR RESIDUE NAG D 502
23CC5SOFTWAREILE D:314 , NAG D:501 , HOH D:674BINDING SITE FOR RESIDUE FUC D 503
24CC6SOFTWAREARG C:219 , ASN C:248 , GLN C:249 , NAG D:501 , NAG D:502 , HOH D:718BINDING SITE FOR RESIDUE FUL D 504
25CC7SOFTWAREASN D:248 , HOH D:711 , HOH D:734 , HOH D:754BINDING SITE FOR RESIDUE NAG D 505
26CC8SOFTWAREASN D:293 , ASP D:297 , ASP D:324 , GLY D:345 , GLY D:347 , HOH D:601BINDING SITE FOR RESIDUE CA D 506

(-) SS Bonds  (28, 28)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:183 -A:230
4A:232 -A:237
5A:280 -A:289
6A:318 -A:337
7A:421 -A:447
8B:92 -B:417
9B:124 -B:129
10B:183 -B:230
11B:232 -B:237
12B:280 -B:289
13B:318 -B:337
14B:421 -B:447
15C:92 -C:417
16C:124 -C:129
17C:183 -C:230
18C:232 -C:237
19C:280 -C:289
20C:318 -C:337
21C:421 -C:447
22D:92 -D:417
23D:124 -D:129
24D:183 -D:230
25D:232 -D:237
26D:280 -D:289
27D:318 -D:337
28D:421 -D:447

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:221 -Pro A:222
2Phe A:325 -Pro A:326
3Lys A:357 -Pro A:359
4Gly B:221 -Pro B:222
5Phe B:325 -Pro B:326
6Lys B:357 -Pro B:359
7Gly C:221 -Pro C:222
8Phe C:325 -Pro C:326
9Lys C:357 -Pro C:359
10Gly D:221 -Pro D:222
11Phe D:325 -Pro D:326
12Lys D:357 -Pro D:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GDJ)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4gdja_ A: automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...eeeeeeeeee....eeeeeeeeee....eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee..............eee..eeeeeeee..hhhhheeeeeeee..eeeeeee........eeeeeeee..eeeeeee.........eeeee....eeee........................................eeeee.......eeeeeeee...........eeeeeeeeeeeeeeeee.........eeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gdj A   91 MCEVKGWVPTHRDLILSRRAYVSCDLTSCFKFFIAYGLSAEESLYKTPIGSANTLSTSEMILPGRSSSACFDGLKWTVLVSNGRDRNSFIMIKYGEEITDTFSASRGGPLRLPNSECICVEGSCFVLVSDGPNVNQSVHRIYELQNGTVQRWKQLNTTGINFEYSTCYTINNLIKCTGTNLWNDAKRPLLRFTKDLNYQIVEPCNGAPTDFPRGGLTTPSCKMAQEKGEGGIQGFILDEKPAWTSKTKTELSQNGFVLEQIPDGIESEGTVSLSYELFSNKRTGRSGFFQPKGECQRVCFWLEIEIQELSTFCGINS  451
                                   100 ||    120       130       140||     164      |173       183       193       203       213       223       233       243       253       263       273       283       293       303   ||  314       324     ||336||     347       357|      368       378      |390       401       411  ||   422    || 444       
                                     102|                        140||           170A                                                                                                                                      307|                  330| 337|               357|                       385|||      399|         413A|        427|           
                                      113                         152|                                                                                                                                                      309                   333  339                359                        387||       401           416         440           
                                                                   156                                                                                                                                                                                                                                388|                                               
                                                                                                                                                                                                                                                                                                       390                                               


Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4gdjb_ B: automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeeee....eeeeeeeeee...eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee..............eee..eeeeeeee..hhhhheeeeeeee..eeeeeee........eeeeeeee..eeeeeee.........eeeee....eeee........................................eeeee.......eeeeeeee...........eeeeeeeeeeeeeeeee.........eeeeee...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gdj B   91 MCEVKGWVPTHRPGDLILSRRAYVSCDLTSCFKFFIAYGLSEESLYKTPIGSANTLSTSEMILPGRSSSACFDGLKWTVLVSNGRDRNSFIMIKYGEEITDTFSASRGGPLRLPNSECICVEGSCFVLVSDGPNVNQSVHRIYELQNGTVQRWKQLNTTGINFEYSTCYTINNLIKCTGTNLWNDAKRPLLRFTKDLNYQIVEPCNGAPTDFPRGGLTTPSCKMAQEKGEGGIQGFILDEKPAWTSKTKTELSQNGFVLEQIPDGIESEGTVSLSYELFSNKRTGRSGFFQPKGECQRVCFWLEIEIQELSTFCGINSPVQ  454
                                   100 ||    118       128       138|||    163       172       182       192       202       212       222       232       242       252       262       272       282       292       302    || 313       323      |335 ||    346       356||     367       377       388|      399|      410   ||  421     ||443       453 
                                     102|                         139||           170A                                                                                                                                      307|                  330| 337|               357|                       385|||      399|         413A|        427|              
                                      111                          152|                                                                                                                                                      309                   333  339                359                        387||       401           416         440              
                                                                    156                                                                                                                                                                                                                                388|                                                  
                                                                                                                                                                                                                                                                                                        390                                                  


Chain C from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gdjc_ C: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...eeeeeeeeee....eeeeeeeeee..eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee..............eee..eeeeeeee..hhhhheeeeeeee..eeeeeee........eeeeeeee..eeeeeee.........eeeee....eeee........................................eeeee.......eeeeeeee...........eeeeeeeeeeeeeeeee.........eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gdj C   91 MCEVKGWVPTHRDLILSRRAYVSCDLTSCFKFFIAYGLSESLYKTPIGSANTLSTSEMILPGRSSSACFDGLKWTVLVSNGRDRNSFIMIKYGEEITDTFSASRGGPLRLPNSECICVEGSCFVLVSDGPNVNQSVHRIYELQNGTVQRWKQLNTTGINFEYSTCYTINNLIKCTGTNLWNDAKRPLLRFTKDLNYQIVEPCNGAPTDFPRGGLTTPSCKMAQEKGEGGIQGFILDEKPAWTSKTKTELSQNGFVLEQIPDGIESEGTVSLSYELFSNKRTGRSGFFQPKGECQRVCFWLEIEQELSTFCGINS  451
                                   100 ||    120       130       156       166    |  175       185       195       205       215       225       235       245       255       265       275       285       295       305 ||    316       326   ||  339       349       360       370       380    |||392      |403       413||     424  ||   447    
                                     102|                       139|           170A                                                                                                                                      307|                  330| 337|               357|                       385|||      399|         413A|        427|          
                                      113                        156                                                                                                                                                      309                   333  339                359                        387||       401           416         441          
                                                                                                                                                                                                                                                                                                    388|                                              
                                                                                                                                                                                                                                                                                                     390                                              


Chain D from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gdjd_ D: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...eeeeeeeeee....eeeeeeeeee..eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee..............eee..eeeeeeee..hhhhheeeeeeee..eeeeeee........eeeeeeee..eeeeeee.........eeeee....eeee........................................eeeee.......eeeeeeee...........eeeeeeeeeeeeeeeee.........eeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gdj D   92 CEVKGWVPTHRDLILSRRAYVSCDLTSCFKFFIAYGLSESLYKTPIGSANTLSTSEMILPGRSSSACFDGLKWTVLVSNGRDRNSFIMIKYGEEITDTFSASRGGPLRLPNSECICVEGSCFVLVSDGPNVNQSVHRIYELQNGTVQRWKQLNTTGINFEYSTCYTINNLIKCTGTNLWNDAKRPLLRFTKDLNYQIVEPCNGAPTDFPRGGLTTPSCKMAQEKGEGGIQGFILDEKPAWTSKTKTELSQNGFVLEQIPDGIESEGTVSLSYELFSNKRTGRSGFFQPKGECQRVCFWLEIEIQELSTFCGINS  451
                                   101||     121       131       157       167   |   176       186       196       206       216       226       236       246       256       266       276       286       296       306||     317       327  ||   340       350      |361       371       381   ||||393     ||404      413A|      425 ||    447    
                                    102|                       139|           170A                                                                                                                                      307|                  330| 337|               357|                       385|||      399|         413A|        427|           
                                     113                        156                                                                                                                                                      309                   333  339                359                        387||       401           416         440           
                                                                                                                                                                                                                                                                                                   388|                                               
                                                                                                                                                                                                                                                                                                    390
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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  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Phe A:325 - Pro A:326   [ RasMol ]  
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  H6QM95_9INFA | H6QM95
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4GDJ)

(-) Related Entries Specified in the PDB File

4gdi A N10 SUBTYPE NEURAMINIDASE-LIKE PROTEIN OF A/LITTLE YELLOW -SHOULDERED BAT/GUATEMALA/164/2009