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(-) Description

Title :  THE STRUCTURE OF HEMAGGLUTININ FROM A AVIAN-ORIGIN H7N9 INFLUENZA VIRUS (A/SHANGHAI/1/2013) IN COMPLEX WITH AVIAN RECEPTOR ANALOG 3'SLNLN
 
Authors :  Y. Shi, W. Zhang, F. Wang, J. Qi, H. Song, Y. Wu, F. Gao, Y. Zhang, Z. Fan, W. D. Wang, Y. Shu, Y. Wang, J. Yan, G. F. Gao
Date :  07 Jul 13  (Deposition) - 06 Nov 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (3x)
Biol. Unit 3:  E,F  (3x)
Keywords :  Homotrimer, Virus Attachment, Membrane Fusion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shi, W. Zhang, F. Wang, J. Qi, Y. Wu, H. Song, F. Gao, Y. Bi, Y. Zhang, Z. Fan, C. Qin, H. Sun, J. Liu, J. Haywood, W. Liu, W. Gong, D. Wang, Y. Shu Y. Wang, J. Yan, G. F. Gao
Structures And Receptor Binding Of Hemagglutinins From Human-Infecting H7N9 Influenza Viruses
Science V. 342 243 2013
PubMed-ID: 24009358  |  Reference-DOI: 10.1126/SCIENCE.1242917

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A, C, E
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: HI5
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 1-316
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/SHANGHAI/1/2013
 
Molecule 2 - HEMAGGLUTININ
    Chains: B, D, F
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: HI5
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 322-491
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/SHANGHAI/1/2013

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (3x): AB    
Biological Unit 2 (3x):   CD  
Biological Unit 3 (3x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID
Biological Unit 3 (3, 9)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:88 , GLY A:124 , ALA A:125 , THR A:126 , SER A:127 , TRP A:142 , HIS A:174 , GLU A:181 , LEU A:185 , GLN A:213 , GLY A:216 , GLN A:217 , SER A:218 , ARG C:40 , ASP C:267BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 801 TO 803
2AC2SOFTWAREGLU B:393 , LYS B:396 , ASN B:400 , ASN B:403BINDING SITE FOR MONO-SACCHARIDE NAG B 601 BOUND TO ASN B 403
3AC3SOFTWARETYR C:88 , GLY C:124 , ALA C:125 , THR C:126 , SER C:127 , TRP C:142 , HIS C:174 , GLU C:181 , LEU C:185 , GLN C:217BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 801 TO 802
4AC4SOFTWAREGLU D:393 , LYS D:396 , ASN D:400 , ASN D:403BINDING SITE FOR MONO-SACCHARIDE NAG D 601 BOUND TO ASN D 403
5AC5SOFTWARETYR E:88 , GLY E:124 , ALA E:125 , THR E:126 , SER E:127 , TRP E:142 , HIS E:174 , GLU E:181 , LEU E:185 , GLN E:217BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 801 TO 802
6AC6SOFTWAREGLU F:393 , LYS F:396 , ASN F:400 , ASN F:403BINDING SITE FOR MONO-SACCHARIDE NAG F 601 BOUND TO ASN F 403

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:4 -B:458
2A:42 -A:268
3A:54 -A:66
4A:87 -A:129
5A:272 -A:296
6B:465 -B:469
7C:4 -D:458
8C:42 -C:268
9C:54 -C:66
10C:87 -C:129
11C:272 -C:296
12D:465 -D:469
13E:4 -F:458
14E:42 -E:268
15E:54 -E:66
16E:87 -E:129
17E:272 -E:296
18F:465 -F:469

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LKG)

(-) 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:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4lkga_ A: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee....eeeee..eee.ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..............hhhhhhhhhhh...eeeee.............eeeee...ee....eee............eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee....eeee....ee......eee..ee......ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkg A   1 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSSCRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKNPALIVWGIHHSGSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARTQVNGQSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDADCEGDCYYSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPE 316
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains d4lkgb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkg B 322 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFTEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNR 491
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491


Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4lkgc_ C: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee....eeeee..eee.ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..............hhhhhhhhhhh...eeeee.............eeeee...ee....eee............eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee....eeee....ee......eee..ee......ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkg C   1 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSSCRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKNPALIVWGIHHSGSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARTQVNGQSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDADCEGDCYYSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPE 316
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      


Chain D from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains d4lkgd_ D: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkg D 322 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFTEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNR 491
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491


Chain E from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4lkge_ E: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee....eeeee..eee.ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..............hhhhhhhhhhh...eeeee.............eeeee...ee....eee............eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeee....eeee....ee......eee..ee......ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkg E   1 DKICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSSCRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKNPALIVWGIHHSGSTAEQTKLYGSGNKLVTVGSSNYQQSFVPSPGARTQVNGQSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSGVQVDADCEGDCYYSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPE 316
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      


Chain F from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains d4lkgf_ F: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkg F 322 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFTEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLADSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQNR 491
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
   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  (2, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 20)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        V5IRU7_9INFA | V5IRU7: 4lcx 4lkh
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(-) Related Entries Specified in the PDB File

4lcx 4lkh 4lki 4lkj 4lkk