[English] 日本語
Yorodumi
- PDB-9y3y: Crystal structure of hemagglutinin from H1N1 Influenza A virus A/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9y3y
TitleCrystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody
Components
  • (Antibody 49_C09 ...) x 2
  • (Hemagglutinin) x 2
KeywordsANTIVIRAL PROTEIN / Hemagglutinin / Head antibody / Influenza / Complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsWang, B. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93021C00015 United States
CitationJournal: Cell Host Microbe / Year: 2026
Title: Childhood immunological imprinting of cross-subtype antibodies targeting the hemagglutinin head domain of influenza viruses.
Authors: Shuk Hang Li / Bo Wang / Gyunghee Jo / Artem Mikelov / Reilly K Atkinson / Valerie Le Sage / Colleen Furey / Jordan T Ort / Naiqing Ye / Sydney Gang / Ruhi Shah / Jefferson J S Santos / ...Authors: Shuk Hang Li / Bo Wang / Gyunghee Jo / Artem Mikelov / Reilly K Atkinson / Valerie Le Sage / Colleen Furey / Jordan T Ort / Naiqing Ye / Sydney Gang / Ruhi Shah / Jefferson J S Santos / Katharina Röltgen / Shilpa A Joshi / Ji-Yeun Lee / Taylor A Pursell / Elizabeth M Drapeau / Julianna Han / Amy P Callear / Ronald G Collman / Arnold S Monto / Emily T Martin / Seema S Lakdawala / Andrew B Ward / Ian A Wilson / Scott D Boyd / Scott E Hensley /
Abstract: Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large ...Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large proportion of monoclonal antibodies (mAbs) isolated from individuals immunized with the 2021-22 seasonal influenza vaccine bound to an epitope on the HA head of both the H1N1 vaccine strain and H3N2 strains from the mid-1990s. The unmutated common ancestors of many of these mAbs reacted to both the 1990s H3s and the 2021-22 H1 vaccine strain. These cross-subtype antibodies were also found in polyclonal sera, but only among individuals born in the 1990s. Ferrets sequentially exposed to a 1990s H3N2 virus and contemporary influenza vaccine also produced H1/H3 cross-reactive antibodies. Recently, H1N1 viruses have acquired a substitution that abrogates the binding of these antibodies. Together, our study demonstrates how prior influenza virus exposures can influence the specificity of antibodies elicited by entirely different influenza virus subtypes.
History
DepositionSep 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.1May 13, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 20, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Hemagglutinin
D: Hemagglutinin
L: Antibody 49_C09 light chain
A: Hemagglutinin
B: Hemagglutinin
H: Antibody 49_C09 heavy chain
E: Antibody 49_C09 heavy chain
F: Antibody 49_C09 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,22814
Polymers206,9678
Non-polymers2,2616
Water00
1
C: Hemagglutinin
D: Hemagglutinin
L: Antibody 49_C09 light chain
H: Antibody 49_C09 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2916
Polymers103,4844
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hemagglutinin
B: Hemagglutinin
E: Antibody 49_C09 heavy chain
F: Antibody 49_C09 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9378
Polymers103,4844
Non-polymers1,4534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.919, 166.919, 347.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

-
Protein , 2 types, 4 molecules CADB

#1: Protein Hemagglutinin


Mass: 36243.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G8EHJ9
#2: Protein Hemagglutinin


Mass: 20206.320 Da / Num. of mol.: 2 / Fragment: HA2 subdomain (UNP residues 326-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I1ZFF9

-
Antibody , 2 types, 4 molecules LFHE

#3: Antibody Antibody 49_C09 light chain


Mass: 22939.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Antibody 49_C09 heavy chain


Mass: 24094.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 3 types, 6 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 6.76 Å3/Da / Density % sol: 81.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2M ammonium sulfate, 15% (v/v) ethylene glycol, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 43492 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 1 / Rpim(I) all: 0.15 / Net I/σ(I): 5.4
Reflection shellResolution: 3.8→3.87 Å / Num. unique obs: 1669 / CC1/2: 0.55

-
Processing

Software
NameVersionClassification
PHENIX1.21refinement
HKL-2000v722data scaling
HKL-2000v722data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→49.71 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 2005 4.61 %
Rwork0.2051 --
obs0.2067 43479 77.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14297 0 148 0 14445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614813
X-RAY DIFFRACTIONf_angle_d0.94320160
X-RAY DIFFRACTIONf_dihedral_angle_d12.9795516
X-RAY DIFFRACTIONf_chiral_restr0.0522271
X-RAY DIFFRACTIONf_plane_restr0.0072581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.890.3082540.24451094X-RAY DIFFRACTION29
3.89-40.2421610.2241294X-RAY DIFFRACTION35
4-4.110.2208770.2061580X-RAY DIFFRACTION42
4.11-4.250.2498960.21841929X-RAY DIFFRACTION51
4.25-4.40.25421130.21122376X-RAY DIFFRACTION62
4.4-4.570.22641370.19592908X-RAY DIFFRACTION77
4.57-4.780.24271590.19763302X-RAY DIFFRACTION87
4.78-5.030.24511800.20613709X-RAY DIFFRACTION97
5.03-5.350.24271840.20033806X-RAY DIFFRACTION100
5.35-5.760.25151870.19163818X-RAY DIFFRACTION100
5.76-6.340.25191800.21583837X-RAY DIFFRACTION100
6.34-7.250.24151890.21433898X-RAY DIFFRACTION100
7.26-9.130.21421870.20423900X-RAY DIFFRACTION100
9.13-49.710.23452010.19964082X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 75.6829 Å / Origin y: -4.9884 Å / Origin z: 63.4371 Å
111213212223313233
T0.2721 Å20.0061 Å20.0017 Å2-0.184 Å2-0.0452 Å2--0.1962 Å2
L0.0286 °20.0015 °2-0.0031 °2-0.0312 °20.0149 °2--0.0062 °2
S0.0065 Å °-0.0672 Å °0.0613 Å °0.0543 Å °0.0021 Å °-0.0148 Å °0.0091 Å °-0.01 Å °-0.0155 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more