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- PDB-9phs: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -

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Basic information

Entry
Database: PDB / ID: 9phs
TitleCrystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141085 (CP1)
Components
  • Hemagglutinin
  • Hemagglutinin HA2 chain
  • cyclic peptide CP141085
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin / glycoprotein / N-glycosylation
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / extracellular region / plasma 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: 2.02 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

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin HA2 chain
C: Hemagglutinin
D: Hemagglutinin HA2 chain
E: Hemagglutinin
F: Hemagglutinin HA2 chain
G: cyclic peptide CP141085
H: cyclic peptide CP141085
K: cyclic peptide CP141085
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,97027
Polymers176,1309
Non-polymers3,84118
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37760 Å2
ΔGint-175 kcal/mol
Surface area62370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.799, 108.825, 118.240
Angle α, β, γ (deg.)90.000, 122.374, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin


Mass: 36650.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452
#2: Protein Hemagglutinin HA2 chain


Mass: 20138.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452

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Protein/peptide , 1 types, 3 molecules GHK

#3: Protein/peptide cyclic peptide CP141085


Mass: 1921.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 10 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
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

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Non-polymers , 3 types, 491 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: H1/PR8: 10 mg/ml, 0.2 M calcium acetate, 1 M HEPES, pH 7.4 , 40% (v/v) polyethylene glycol 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→47.98 Å / Num. obs: 131036 / % possible obs: 99 % / Redundancy: 3.1 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.95 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 6488 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→47.98 Å / SU ML: 0.2626 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 6584 5.04 %
Rwork0.2149 124084 -
obs0.2166 130668 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.91 Å2
Refinement stepCycle: LAST / Resolution: 2.02→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12100 0 245 483 12828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003312635
X-RAY DIFFRACTIONf_angle_d0.611117123
X-RAY DIFFRACTIONf_chiral_restr0.04891870
X-RAY DIFFRACTIONf_plane_restr0.00412216
X-RAY DIFFRACTIONf_dihedral_angle_d8.55841784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.050.40211910.35423735X-RAY DIFFRACTION89.9
2.05-2.070.38712040.39493963X-RAY DIFFRACTION93.75
2.07-2.10.43112230.36454052X-RAY DIFFRACTION97.92
2.1-2.120.38142320.31544083X-RAY DIFFRACTION99.01
2.12-2.150.35012060.3054168X-RAY DIFFRACTION98.96
2.15-2.180.32982080.28494140X-RAY DIFFRACTION98.95
2.18-2.210.32412210.27354114X-RAY DIFFRACTION99.54
2.21-2.240.3982100.33584130X-RAY DIFFRACTION98.73
2.24-2.280.41642140.37714153X-RAY DIFFRACTION98.2
2.28-2.320.30392380.26174127X-RAY DIFFRACTION99.73
2.32-2.360.3022130.24674123X-RAY DIFFRACTION99.82
2.36-2.40.27632110.23834182X-RAY DIFFRACTION99.43
2.4-2.440.28722190.2324158X-RAY DIFFRACTION99.73
2.44-2.490.2772170.22634179X-RAY DIFFRACTION99.59
2.49-2.550.28582290.23484168X-RAY DIFFRACTION99.66
2.55-2.610.28922190.22454157X-RAY DIFFRACTION99.45
2.61-2.670.26862430.2424105X-RAY DIFFRACTION98.91
2.67-2.750.27531950.23964197X-RAY DIFFRACTION99.57
2.75-2.830.27552210.23034180X-RAY DIFFRACTION99.82
2.83-2.920.27072230.22994125X-RAY DIFFRACTION99.82
2.92-3.020.2842210.2284218X-RAY DIFFRACTION99.84
3.02-3.140.25412510.22194125X-RAY DIFFRACTION99.73
3.14-3.290.2522310.21494204X-RAY DIFFRACTION99.48
3.29-3.460.24612050.21314127X-RAY DIFFRACTION98.97
3.46-3.680.25172010.20114185X-RAY DIFFRACTION98.81
3.68-3.960.20732440.18494144X-RAY DIFFRACTION99.39
3.96-4.360.1812300.16914196X-RAY DIFFRACTION99.37
4.36-4.990.19592370.16534155X-RAY DIFFRACTION98.96
4.99-6.280.24272230.19074192X-RAY DIFFRACTION99.33
6.28-47.980.18992040.19044299X-RAY DIFFRACTION99.23

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