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(-) Description

Title :  STRUCTURE OF HEMAGGLUTININ WITH F95Y MUTATION OF INFLUENZA VIRUS B/LEE/40 COMPLEX WITH LSTC
 
Authors :  F. Ni, I. N. Mbawuike, E. Kondrashkina, Q. Wang
Date :  26 Nov 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ha, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ni, I. Nnadi Mbawuike, E. Kondrashkina, Q. Wang
The Roles Of Hemagglutinin Phe-95 In Receptor Binding And Pathogenicity Of Influenza B Virus.
Virology V. -451 71 2014
PubMed-ID: 24503069  |  Reference-DOI: 10.1016/J.VIROL.2013.11.038

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A, C, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: CV-1
    Expression System Plasmid: PRB21
    Expression System Taxid: 9606
    Expression System Vector Type: VACCINIA VIRUS
    Gene: HA
    Mutation: YES
    Organism Scientific: INFLUENZA B VIRUS
    Organism Taxid: 107412
    Strain: B/LEE/1940
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: CV-1
    Expression System Taxid: 9606
    Gene: HA
    Organism Scientific: INFLUENZA B VIRUS
    Organism Taxid: 107412
    Strain: B/LEE/1940

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 42)

Asymmetric/Biological Unit (4, 42)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3NAG35Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:12 , PRO A:13 , VAL A:15 , ASN A:25 , TYR A:336 , HOH A:563BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 25 RESIDUES 401 TO 402
02AC2SOFTWAREASN A:145 , THR A:147 , GLY A:149 , ASN A:150 , HOH A:574BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 145 RESIDUES 403 TO 404
03AC3SOFTWAREASN A:232BINDING SITE FOR MONO-SACCHARIDE NAG A 405 BOUND TO ASN A 232
04AC4SOFTWAREGLU A:291 , ASN A:303BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 303 RESIDUES 406 TO 407
05AC5SOFTWAREILE A:30 , ASN A:332 , TRP B:21 , GLN B:42 , ILE B:45BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 332 RESIDUES 408 TO 409
06AC6SOFTWARETYR A:95 , THR A:139 , SER A:140 , GLY A:141 , ASP A:195 , GLN A:199 , ARG A:202 , LEU A:203 , LYS A:240 , GLN A:241 , SER A:242 , HOH A:518BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 410 TO 412
07AC7SOFTWAREASN B:145BINDING SITE FOR MONO-SACCHARIDE NAG B 201 BOUND TO ASN B 145
08AC8SOFTWARESER C:12 , PRO C:13 , ASN C:25 , TYR C:336BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 25 RESIDUES 401 TO 402
09AC9SOFTWAREASN C:123 , ASN C:126 , GLU C:128 , THR C:129 , ASN C:145 , THR C:147 , GLY C:149 , ASN C:150 , HOH C:569BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 145 RESIDUES 403 TO 405
10BC1SOFTWAREASN C:232 , HOH C:550BINDING SITE FOR MONO-SACCHARIDE NAG C 406 BOUND TO ASN C 232
11BC2SOFTWAREGLU C:291 , ASN C:303BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 303 RESIDUES 407 TO 408
12BC3SOFTWAREILE C:30 , ASN C:332 , HOH C:522 , ILE D:45BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 332 RESIDUES 409 TO 410
13BC4SOFTWARETYR C:95 , THR C:139 , SER C:140 , GLY C:141 , TRP C:158 , ASP C:195 , ARG C:202 , LEU C:203 , LYS C:240 , GLN C:241 , SER C:242 , GLY C:243BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 411 TO 413
14BC5SOFTWAREASN D:145 , THR D:147 , HOH D:329BINDING SITE FOR MONO-SACCHARIDE NAG D 201 BOUND TO ASN D 145
15BC6SOFTWARESER E:12 , PRO E:13 , VAL E:15 , ASN E:25 , TYR E:336BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 25 RESIDUES 401 TO 402
16BC7SOFTWAREASN E:59 , ARG E:69 , GLU E:237BINDING SITE FOR MONO-SACCHARIDE NAG E 403 BOUND TO ASN E 59
17BC8SOFTWAREGLU A:182 , ASN E:145 , THR E:147 , GLY E:149 , ASN E:150BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 145 RESIDUES 404 TO 405
18BC9SOFTWAREPHE E:230 , ASN E:232 , HOH E:537 , HOH E:558 , HOH E:584BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 232 RESIDUES 406 TO 407
19CC1SOFTWAREGLU E:291 , ASN E:303 , HOH E:583BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 303 RESIDUES 408 TO 409
20CC2SOFTWAREILE E:30 , ASN E:332 , HOH E:552 , TRP F:21BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 332 RESIDUES 410 TO 411
21CC3SOFTWARETYR E:95 , THR E:139 , SER E:140 , GLY E:141 , TRP E:158 , ASP E:195 , GLN E:199 , ARG E:202 , LEU E:203 , LEU E:239 , LYS E:240 , GLN E:241 , SER E:242 , HOH E:564 , HOH E:594BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 412 TO 414
22CC4SOFTWAREASN F:145 , THR F:147BINDING SITE FOR MONO-SACCHARIDE NAG F 201 BOUND TO ASN F 145

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:4 -B:137
2A:54 -A:57
3A:60 -A:72
4A:94 -A:143
5A:180 -A:274
6A:294 -A:320
7B:144 -B:148
8C:4 -D:137
9C:54 -C:57
10C:60 -C:72
11C:94 -C:143
12C:180 -C:274
13C:294 -C:320
14D:144 -D:148
15E:4 -F:137
16E:54 -E:57
17E:60 -E:72
18E:94 -E:143
19E:180 -E:274
20E:294 -E:320
21F:144 -F:148

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:286 -Pro A:287
2Leu C:286 -Pro C:287
3Leu E:286 -Pro E:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NRK)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4nrka_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhhh............eeee.............hhhhhhhhhhhhhhh...eeee...............eeee.eeeee.....ee....eeeeee..........eeeee........eeeeeeeeee.hhhhhhhhhh.....eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeee...eeee.......ee.eee...eee.....ee......eee...ee.....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrk A   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTRSHFANLKGTQTRGKLCPNCFNCTDLDVALGRPKCMGNIPSAKVSILHEVKPVTSGCYPIMHDRTKIRQLPNLLRGYENIRLSTSNVINTETAPGGPYKVGTSGSCPNVTNGNGFFNTMAWVIPKDNNKIAINPVTVEVPYICSEGEDQITVWGFHSDDKTQMERLYGDSNPQKFTSSANGVTTHYVSQIGGFPNQTEDEGLKQSGRIVVDYMVQKPGKTGTIVYQRGILLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPA 340
                                    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       320       330       340


Chain B from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains d4nrkb_ B: Influenza hemagglutinin (stalk)                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh.............eeeeee....eeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nrk B   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMNELHDEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGDFSLPTFD 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain C from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4nrkc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhh.............eeee.............hhhhhhhhhhhhhhh...eeee...............eeee.eeeee.....ee....eeeeee.hhhh.....eeeee........eeeeeeeeee.hhhhhhhhhh.....eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeee...eeee.......ee.eee...eee.....ee......eee...ee.....eee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrk C   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTRSHFANLKGTQTRGKLCPNCFNCTDLDVALGRPKCMGNIPSAKVSILHEVKPVTSGCYPIMHDRTKIRQLPNLLRGYENIRLSTSNVINTETAPGGPYKVGTSGSCPNVTNGNGFFNTMAWVIPKDNNKIAINPVTVEVPYICSEGEDQITVWGFHSDDKTQMERLYGDSNPQKFTSSANGVTTHYVSQIGGFPNQTEDEGLKQSGRIVVDYMVQKPGKTGTIVYQRGILLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAK 341
                                    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       320       330       340 


Chain D from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains d4nrkd_ D: Influenza hemagglutinin (stalk)                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh.............eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nrk D   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMNELHDEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGDFSLPTFD 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain E from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4nrke_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhhh............eeee.............hhhhhhhhhhhhhhh...eeee...............eee..eeeee.....ee....eeeeee..........eeeee........eeeeeeeeee.hhhhhhhhhh.....eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeee...eeee.......ee.eee...eee.....ee......eee...ee.....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrk E   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTRSHFANLKGTQTRGKLCPNCFNCTDLDVALGRPKCMGNIPSAKVSILHEVKPVTSGCYPIMHDRTKIRQLPNLLRGYENIRLSTSNVINTETAPGGPYKVGTSGSCPNVTNGNGFFNTMAWVIPKDNNKIAINPVTVEVPYICSEGEDQITVWGFHSDDKTQMERLYGDSNPQKFTSSANGVTTHYVSQIGGFPNQTEDEGLKQSGRIVVDYMVQKPGKTGTIVYQRGILLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPA 340
                                    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       320       330       340


Chain F from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains d4nrkf_ F: Influenza hemagglutinin (stalk)                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh.............eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhh...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nrk F   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMNELHDEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGDFSLPTFD 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (2, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        HEMA_INBLE | P03460: 1tx1 2ffo 4nrj 4nrl

(-) Related Entries Specified in the PDB File

4nrj 4nrl