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- PDB-9pht: Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza vir... -

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Basic information

Entry
Database: PDB / ID: 9pht
TitleCrystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141085 (CP1)
Components
  • (Hemagglutinin) x 2
  • cyclic peptide CP141085
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin / glycoprotein / N-glycosylation
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
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsKadam, R.U. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Npj Viruses / Year: 2025
Title: V H H antibody loop guides design of a synthetic macrocyclic peptide that potently blocks influenza virus membrane fusion.
Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Garg, D. / Zhu, X. / Jongeneelen, M. / Schepens, W.B.G. / Stoops, B. / Vermond, J. / Goutier, W. / Tang, C. / Blokland, S. / Vogels, R. / ...Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Garg, D. / Zhu, X. / Jongeneelen, M. / Schepens, W.B.G. / Stoops, B. / Vermond, J. / Goutier, W. / Tang, C. / Blokland, S. / Vogels, R. / Friesen, R.H.E. / van Dongen, M.J.P. / Wilson, I.A.
History
DepositionJul 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
G: cyclic peptide CP141085
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7336
Polymers60,0693
Non-polymers6643
Water1,26170
1
A: Hemagglutinin
B: Hemagglutinin
G: cyclic peptide CP141085
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
G: cyclic peptide CP141085
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
G: cyclic peptide CP141085
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,19918
Polymers180,2089
Non-polymers1,9919
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area33810 Å2
ΔGint-155 kcal/mol
Surface area63500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.388, 116.388, 141.506
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-211-

HOH

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Components

#1: Protein Hemagglutinin


Mass: 37948.020 Da / Num. of mol.: 1 / Fragment: HA1 subdomain (UNP residues 17-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31
#2: Protein Hemagglutinin


Mass: 20200.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31
#3: Protein/peptide cyclic peptide CP141085


Mass: 1921.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 4.61 Å3/Da / Density % sol: 73.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: H5/Viet: 10 mg/ml, 0.2 M di-sodium tartrate, 20% (w/v) polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0331 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.76→47.48 Å / Num. obs: 29032 / % possible obs: 99 % / Redundancy: 9 % / Biso Wilson estimate: 53.53 Å2 / CC1/2: 0.98 / Net I/σ(I): 28.9
Reflection shellResolution: 2.76→2.81 Å / Num. unique obs: 1421 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→47.48 Å / SU ML: 0.377 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.0928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2908 1474 5.08 %
Rwork0.2612 27556 -
obs0.2627 29030 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.73 Å2
Refinement stepCycle: LAST / Resolution: 2.76→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 42 70 4232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314256
X-RAY DIFFRACTIONf_angle_d0.6295761
X-RAY DIFFRACTIONf_chiral_restr0.0505620
X-RAY DIFFRACTIONf_plane_restr0.0035752
X-RAY DIFFRACTIONf_dihedral_angle_d9.444579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.850.35561480.27932451X-RAY DIFFRACTION99.27
2.85-2.950.33051460.28862437X-RAY DIFFRACTION99.92
2.95-3.070.29521350.2592468X-RAY DIFFRACTION100
3.07-3.210.27691450.2422470X-RAY DIFFRACTION100
3.21-3.380.33311240.25022487X-RAY DIFFRACTION99.92
3.38-3.590.25851160.2482499X-RAY DIFFRACTION100
3.59-3.870.25011340.252490X-RAY DIFFRACTION99.92
3.87-4.250.29851040.24182538X-RAY DIFFRACTION99.96
4.26-4.870.27661280.23892529X-RAY DIFFRACTION99.92
4.87-6.130.24891360.242545X-RAY DIFFRACTION99.81
6.13-470.33521580.29652642X-RAY DIFFRACTION99.75

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