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Protein
Submitted name:

Hemagglutinin

Gene

HA

Organism
Influenza A virus (strain swl A/California/04/2009 H1N1)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.UniRule annotationSAAS annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei204 – 2041GalactoseCombined sources

GO - Biological processi

  1. clathrin-mediated endocytosis of virus by host cell Source: UniProtKB-KW
  2. fusion of virus membrane with host endosome membrane Source: UniProtKB-KW
  3. fusion of virus membrane with host plasma membrane Source: InterPro
  4. virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

HemagglutininUniRule annotationSAAS annotation

Keywords - Biological processi

Clathrin- and caveolin-independent endocytosis of virus by hostSAAS annotation, Clathrin-mediated endocytosis of virus by hostSAAS annotation, Fusion of virus membrane with host endosomal membraneSAAS annotation, Fusion of virus membrane with host membrane, Host-virus interaction, Viral attachment to host cellSAAS annotation, Viral penetration into host cytoplasm, Virus endocytosis by host, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Submitted name:
HemagglutininImported
Gene namesi
Name:HAImported
OrganismiInfluenza A virus (strain swl A/California/04/2009 H1N1)Imported
Taxonomic identifieri641501 [NCBI]
Taxonomic lineageiVirusesssRNA negative-strand virusesOrthomyxoviridaeInfluenzavirus A
Virus hostiAves [TaxID: 8782]
Homo sapiens (Human) [TaxID: 9606]
Sus scrofa (Pig) [TaxID: 9823]

Subcellular locationi

Virion membrane SAAS annotation; Single-pass type I membrane protein SAAS annotation. Host apical cell membrane SAAS annotation; Single-pass type I membrane protein SAAS annotation

GO - Cellular componenti

  1. host cell plasma membrane Source: UniProtKB-SubCell
  2. integral component of membrane Source: UniProtKB-KW
  3. viral envelope Source: UniProtKB-KW
  4. virion membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Host cell membraneSAAS annotation, Host membrane, Membrane, Viral envelope proteinUniRule annotationSAAS annotation, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1717 PotentialImportedAdd
BLAST
Chaini18 – 566549 PotentialImportedPRO_5000464216Add
BLAST
Chaini18 – 344327HA1ImportedPRO_5000464217Add
BLAST
Chaini345 – 566222HA2ImportedPRO_5000464218Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi21 ↔ 481Interchain (with C-481 in C3W5S1)Combined sources
Glycosylationi28 – 281N-linked (GlcNAc...)Combined sources
Glycosylationi40 – 401N-linked (GlcNAc...)Combined sources
Disulfide bondi59 ↔ 292Combined sources
Disulfide bondi72 ↔ 84Combined sources
Glycosylationi104 – 1041N-linked (GlcNAc...)Combined sources
Disulfide bondi107 ↔ 153Combined sources
Glycosylationi293 – 2931N-linked (GlcNAc...)Combined sources
Disulfide bondi296 ↔ 320Combined sources
Glycosylationi304 – 3041N-linked (GlcNAc...)Combined sources
Disulfide bondi488 ↔ 492Combined sources
Glycosylationi498 – 4981N-linked (GlcNAc...)Combined sources

Keywords - PTMi

Disulfide bondSAAS annotation

Interactioni

Subunit structurei

Homotrimer of disulfide-linked HA1-HA2.UniRule annotationSAAS annotation

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AL4X-ray2.87A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-520[»]
3LZGX-ray2.60A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBEX-ray2.15A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBJX-ray2.25A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBNX-ray2.51A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBQX-ray2.00A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UYWX-ray1.90A/B/C/D65-278[»]
3UYXX-ray1.80A/B65-278[»]
3ZTNX-ray3.00A18-344[»]
B345-520[»]
4JTVX-ray3.00A/C/E/G/I/K18-338[»]
B/D/F/H/J/L345-506[»]
4JTXX-ray3.00A/C/E/G/I/K18-339[»]
B/D/F/H/J/L345-510[»]
4JU0X-ray2.91A/C/E/G/I/K18-339[»]
B/D/F/H/J/L345-508[»]
4M4YX-ray2.20A/C/E18-344[»]
B/D/F345-518[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiC3W5S1.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni236 – 2394Galactose bindingCombined sources

Sequence similaritiesi

Belongs to the influenza viruses hemagglutinin family.UniRule annotation

Keywords - Domaini

SignalImported, Transmembrane, Transmembrane helixSAAS annotation

Family and domain databases

Gene3Di2.10.77.10. 1 hit.
3.90.20.10. 1 hit.
3.90.209.20. 1 hit.
InterProiIPR008980. Capsid_hemagglutn.
IPR013828. Hemagglutn_HA1_a/b_dom.
IPR013827. Hemagglutn_HA1_b-rbn_dom.
IPR000149. Hemagglutn_influenz_A.
IPR001364. Hemagglutn_influenz_A/B.
IPR013829. Hemagglutn_stalk.
[Graphical view]
PfamiPF00509. Hemagglutinin. 1 hit.
[Graphical view]
PRINTSiPR00330. HEMAGGLUTN1.
PR00329. HEMAGGLUTN12.
SUPFAMiSSF49818. SSF49818. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

C3W5S1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL
60 70 80 90 100
EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETP
110 120 130 140 150
SSDNGTCYPG DFIDYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT
160 170 180 190 200
AACPHAGAKS FYKNLIWLVK KGNSYPKLSK SYINDKGKEV LVLWGIHHPS
210 220 230 240 250
TSADQQSLYQ NADTYVFVGS SRYSKKFKPE IAIRPKVRDQ EGRMNYYWTL
260 270 280 290 300
VEPGDKITFE ATGNLVVPRY AFAMERNAGS GIIISDTPVH DCNTTCQTPK
310 320 330 340 350
GAINTSLPFQ NIHPITIGKC PKYVKSTKLR LATGLRNIPS IQSRGLFGAI
360 370 380 390 400
AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID EITNKVNSVI
410 420 430 440 450
EKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER
460 470 480 490 500
TLDYHDSNVK NLYEKVRSQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT
510 520 530 540 550
YDYPKYSEEA KLNREEIDGV KLESTRIYQI LAIYSTVASS LVLVVSLGAI
560
SFWMCSNGSL QCRICI
Length:566
Mass (Da):63,276
Last modified:June 15, 2009 - v1
Checksum:iFBCE01FBF1FCA445
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ966082 Viral cRNA. Translation: ACP41105.1.
GQ117044 Viral cRNA. Translation: ACQ76318.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ966082 Viral cRNA. Translation: ACP41105.1.
GQ117044 Viral cRNA. Translation: ACQ76318.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AL4X-ray2.87A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-520[»]
3LZGX-ray2.60A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBEX-ray2.15A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBJX-ray2.25A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBNX-ray2.51A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UBQX-ray2.00A/C/E/G/I/K18-344[»]
B/D/F/H/J/L345-518[»]
3UYWX-ray1.90A/B/C/D65-278[»]
3UYXX-ray1.80A/B65-278[»]
3ZTNX-ray3.00A18-344[»]
B345-520[»]
4JTVX-ray3.00A/C/E/G/I/K18-338[»]
B/D/F/H/J/L345-506[»]
4JTXX-ray3.00A/C/E/G/I/K18-339[»]
B/D/F/H/J/L345-510[»]
4JU0X-ray2.91A/C/E/G/I/K18-339[»]
B/D/F/H/J/L345-508[»]
4M4YX-ray2.20A/C/E18-344[»]
B/D/F345-518[»]
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiC3W5S1.

Family and domain databases

Gene3Di2.10.77.10. 1 hit.
3.90.20.10. 1 hit.
3.90.209.20. 1 hit.
InterProiIPR008980. Capsid_hemagglutn.
IPR013828. Hemagglutn_HA1_a/b_dom.
IPR013827. Hemagglutn_HA1_b-rbn_dom.
IPR000149. Hemagglutn_influenz_A.
IPR001364. Hemagglutn_influenz_A/B.
IPR013829. Hemagglutn_stalk.
[Graphical view]
PfamiPF00509. Hemagglutinin. 1 hit.
[Graphical view]
PRINTSiPR00330. HEMAGGLUTN1.
PR00329. HEMAGGLUTN12.
SUPFAMiSSF49818. SSF49818. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE.
    Strain: A/California/04/2009Imported.
  2. "Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans."
    Garten R.J., Davis C.T., Russell C.A., Shu B., Lindstrom S., Balish A., Sessions W.M., Xu X., Skepner E., Deyde V., Okomo-Adhiambo M., Gubareva L., Barnes J., Smith C.B., Emery S.L., Hillman M.J., Rivailler P., Smagala J.
    , de Graaf M., Burke D.F., Fouchier R.A., Pappas C., Alpuche-Aranda C.M., Lopez-Gatell H., Olivera H., Lopez I., Myers C.A., Faix D., Blair P.J., Yu C., Keene K.M., Dotson P.D.Jr., Boxrud D., Sambol A.R., Abid S.H., St George K., Bannerman T., Moore A.L., Stringer D.J., Blevins P., Demmler-Harrison G.J., Ginsberg M., Kriner P., Waterman S., Smole S., Guevara H.F., Belongia E.A., Clark P.A., Beatrice S.T., Donis R., Katz J., Finelli L., Bridges C.B., Shaw M., Jernigan D.B., Uyeki T.M., Smith D.J., Klimov A.I., Cox N.J.
    Science 325:197-201(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: A/California/04/2009Imported.
  3. "Human infection with novel swine H1N1 influenza."
    Shu B., Balish A., Garten R., Smith C., Emery S., Barnes J., Deyde V., Klimov A., Cox N.
    Submitted (APR-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: A/California/04/2009Imported.
  4. "Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus."
    Zhang W., Qi J., Shi Y., Li Q., Gao F., Sun Y., Lu X., Lu Q., Vavricka C.J., Liu D., Yan J., Gao G.F.
    Protein Cell 1:459-467(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.87 ANGSTROMS) OF 18-344 AND 345-520, ACTIVE SITE, GLYCOSYLATION AT ASN-40; ASN-104; ASN-293 AND ASN-304.
  5. "Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus."
    Xu R., Ekiert D.C., Krause J.C., Hai R., Crowe J.E., Wilson I.A.
    Science 328:357-360(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 18-344 AND 345-518, ACTIVE SITE, GLYCOSYLATION AT ASN-104 AND ASN-293.
  6. "Structural vaccinology: structure-based design of influenza A virus hemagglutinin subtype-specific subunit vaccines."
    Xuan C., Shi Y., Qi J., Zhang W., Xiao H., Gao G.F.
    Protein Cell 2:997-1005(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 65-278, ACTIVE SITE.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 18-344 AND 345-520, ACTIVE SITE, GLYCOSYLATION AT ASN-40 AND ASN-293.
  8. "Structural characterization of the hemagglutinin receptor specificity from the 2009 H1N1 influenza pandemic."
    Xu R., McBride R., Nycholat C.M., Paulson J.C., Wilson I.A.
    J. Virol. 86:982-990(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 18-344 AND 345-518 IN COMPLEX WITH GALACTOSE, ACTIVE SITE, GLYCOSYLATION AT ASN-28; ASN-40; ASN-104; ASN-293; ASN-304 AND ASN-498.
  9. "Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution."
    Zhang W., Shi Y., Qi J., Gao F., Li Q., Fan Z., Yan J., Gao G.F.
    J. Virol. 87:5949-5958(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.91 ANGSTROMS) OF 18-339 AND 345-508 IN COMPLEX WITH GALACTOSE, ACTIVE SITE, GLYCOSYLATION AT ASN-28; ASN-40; ASN-104 AND ASN-293.
  10. "Antibody recognition of the pandemic H1N1 Influenza virus hemagglutinin receptor binding site."
    Hong M., Lee P.S., Hoffman R.M., Zhu X., Krause J.C., Laursen N.S., Yoon S.I., Song L., Tussey L., Crowe J.E., Ward A.B., Wilson I.A.
    J. Virol. 87:12471-12480(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 18-344 AND 345-518, ACTIVE SITE, GLYCOSYLATION AT ASN-28; ASN-40; ASN-104 AND ASN-293.

Entry informationi

Entry nameiC3W5S1_I09A0
AccessioniPrimary (citable) accession number: C3W5S1
Entry historyi
Integrated into UniProtKB/TrEMBL: June 15, 2009
Last sequence update: June 15, 2009
Last modified: March 31, 2015
This is version 52 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.