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- PDB-9e55: Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza vir... -

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Basic information

Entry
Database: PDB / ID: 9.0E+55
TitleCrystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with cyclic peptide iHA-100
Components
  • Hemagglutinin HA1 subunit
  • Hemagglutinin HA2 subunit
  • IHA-100 peptide
KeywordsVIRAL PROTEIN / cyclic peptide complex
Function / homology
Function and homology information


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 / 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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsNguyen, T.K.Y. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: To Be Published
Title: Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with cyclic peptide iHA-100
Authors: Nguyen, T.K.Y. / Wilson, I.A.
History
DepositionOct 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 subunit
B: Hemagglutinin HA2 subunit
P: IHA-100 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9904
Polymers58,5663
Non-polymers4241
Water543
1
A: Hemagglutinin HA1 subunit
B: Hemagglutinin HA2 subunit
P: IHA-100 peptide
hetero molecules

A: Hemagglutinin HA1 subunit
B: Hemagglutinin HA2 subunit
P: IHA-100 peptide
hetero molecules

A: Hemagglutinin HA1 subunit
B: Hemagglutinin HA2 subunit
P: IHA-100 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,97012
Polymers175,6979
Non-polymers1,2733
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area34960 Å2
ΔGint-173 kcal/mol
Surface area63040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.729, 100.729, 328.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21B-201-

HOH

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Components

#1: Protein Hemagglutinin HA1 subunit


Mass: 36477.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2P1MB68
#2: Protein Hemagglutinin HA2 subunit


Mass: 20257.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2P1MB68
#3: Protein/peptide IHA-100 peptide


Mass: 1831.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: 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: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris 8.5, 0.2 M lithium sulfate, and 40 %(v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.89→43.24 Å / Num. obs: 14773 / % possible obs: 99.4 % / Redundancy: 7.6 % / CC1/2: 0.97 / Net I/σ(I): 7.2
Reflection shellResolution: 2.89→2.99 Å / Num. unique obs: 717 / CC1/2: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→43.24 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.312 714 5.12 %
Rwork0.2741 --
obs0.2762 13932 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 28 3 4144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034227
X-RAY DIFFRACTIONf_angle_d0.5995718
X-RAY DIFFRACTIONf_dihedral_angle_d8.577565
X-RAY DIFFRACTIONf_chiral_restr0.042608
X-RAY DIFFRACTIONf_plane_restr0.006747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.110.38551170.39442038X-RAY DIFFRACTION74
3.11-3.420.41281360.35072716X-RAY DIFFRACTION98
3.42-3.920.35011350.2812770X-RAY DIFFRACTION99
3.92-4.940.3131620.23582781X-RAY DIFFRACTION99
4.94-43.240.25831640.25122913X-RAY DIFFRACTION99

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