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(-) Description

Title :  STRUCTURE OF HEMAGGLUTININ WITH F95Y MUTATION OF INFLUENZA VIRUS B/LEE/40
 
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 :  2.72
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: PBR21
    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  (5, 48)

Asymmetric/Biological Unit (5, 48)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3GAL6Ligand/IonBETA-D-GALACTOSE
4NAG35Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA3Ligand/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:336BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 25 RESIDUES 406 TO 407
02AC2SOFTWAREASN A:145 , THR A:147 , GLY A:149 , ASN A:150 , HOH A:551BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 145 RESIDUES 408 TO 409
03AC3SOFTWAREASN A:232 , HOH A:544BINDING SITE FOR MONO-SACCHARIDE NAG A 410 BOUND TO ASN A 232
04AC4SOFTWAREGLU A:291 , ASN A:303BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 303 RESIDUES 411 TO 412
05AC5SOFTWAREILE A:30 , ASN A:332 , HOH A:548 , TRP B:21 , GLN B:42 , ILE B:45BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 332 RESIDUES 413 TO 414
06AC6SOFTWARETYR A:95 , GLY A:138 , THR A:139 , SER A:140 , GLY A:141 , ASP A:195 , THR A:198 , GLN A:199 , ARG A:202 , LEU A:203 , LYS A:240 , GLN A:241 , SER A:242 , HOH A:520BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 401 TO 405
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 406 TO 407
09AC9SOFTWAREASN C:123 , ASN C:126 , GLU C:128 , THR C:129 , ASN C:145 , GLY C:149 , ASN C:150 , HOH C:537 , HOH C:539 , HOH C:541BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 145 RESIDUES 408 TO 410
10BC1SOFTWAREASN C:232BINDING SITE FOR MONO-SACCHARIDE NAG C 411 BOUND TO ASN C 232
11BC2SOFTWAREGLU C:291 , ASN C:303 , HOH C:548BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 303 RESIDUES 412 TO 413
12BC3SOFTWAREILE C:30 , ASN C:332 , HOH C:504 , TRP D:21 , ILE D:45BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 332 RESIDUES 414 TO 415
13BC4SOFTWARETYR C:95 , GLY C:138 , THR C:139 , SER C:140 , GLY C:141 , TRP C:158 , ILE C:160 , ASP C:195 , THR C:198 , GLN C:199 , ARG C:202 , LEU C:239 , LYS C:240 , GLN C:241 , SER C:242BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 401 TO 405
14BC5SOFTWAREASN D:145 , THR D:147 , HOH D:315BINDING 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 406 TO 407
16BC7SOFTWAREASN E:59 , ARG E:69BINDING SITE FOR MONO-SACCHARIDE NAG E 408 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 409 TO 410
18BC9SOFTWAREPHE E:230 , ASN E:232 , HOH E:548BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 232 RESIDUES 411 TO 412
19CC1SOFTWAREGLU E:291 , ASN E:303BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 303 RESIDUES 413 TO 414
20CC2SOFTWAREILE E:30 , ASN E:332 , TRP F:21BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 332 RESIDUES 415 TO 416
21CC3SOFTWARETYR E:95 , GLY E:138 , THR E:139 , SER E:140 , GLY E:141 , TRP E:158 , ILE E:160 , ASP E:195 , ASP E:196 , GLN E:199 , ARG E:202 , LEU E:203 , LYS E:240 , GLN E:241 , SER E:242 , HOH E:553BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 401 TO 405
22CC4SOFTWAREASN F:145 , THR F:147 , HOH F:308BINDING 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 4NRL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NRL)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4nrla_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeee...eeeee..eee...........ee....ee..........hhhhhhhh............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
                 4nrl A   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 B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains d4nrlb_ B: 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
                 4nrl B   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMNELHDEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGDFSLPTFDSL 170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170


Chain C from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4nrlc_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeee...eeeee..eee.ee........ee....ee..........hhhhhhhh............eeee.............hhhhhhhhhhhhhhh...eeee...............eeee.eeeee.....ee....eeeeee.hhhh.....eeeee........eeeeeeeeee.hhhhhhhhh......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
                 4nrl 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:169
                                                                                                                                                                                                         
               SCOP domains d4nrld_ D: Influenza hemagglutinin (stalk)                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..............eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhh...hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrl D   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMNELHDEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGDFSLPTFDS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain E from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4nrle_ E: Hemagglutinin                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeee...eeeee..eee...........ee....ee..........hhhhhhhh............eeee.............hhhhhhhhhhhhhhh...eeee...............eee..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
                 4nrl E   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 F from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains d4nrlf_ 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
                 4nrl F   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMNELHDEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGDFSLPTFDS 169
                                    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 4NRL)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4nrj 4nrk