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

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Basic information

Entry
Database: PDB / ID: 9phd
TitleCrystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141076 (CP8)
Components
  • Hemagglutinin
  • Hemagglutinin HA2 chain
  • cyclic peptide CP141076
KeywordsVIRAL PROTEIN / Influenza Virus / Hemagglutinin / Fusion inhibitors / Cyclic peptide
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
DI(HYDROXYETHYL)ETHER / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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
C: Hemagglutinin
D: Hemagglutinin HA2 chain
G: cyclic peptide CP141076
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,37311
Polymers58,4043
Non-polymers1,9708
Water10,575587
1
C: Hemagglutinin
D: Hemagglutinin HA2 chain
G: cyclic peptide CP141076
hetero molecules

C: Hemagglutinin
D: Hemagglutinin HA2 chain
G: cyclic peptide CP141076
hetero molecules

C: Hemagglutinin
D: Hemagglutinin HA2 chain
G: cyclic peptide CP141076
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,12033
Polymers175,2119
Non-polymers5,90924
Water1629
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 area36980 Å2
ΔGint-205 kcal/mol
Surface area64310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.092, 102.092, 335.149
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
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
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11C-704-

HOH

21D-327-

HOH

31D-340-

HOH

41D-362-

HOH

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Components

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Protein , 2 types, 2 molecules CD

#1: Protein Hemagglutinin


Mass: 36650.293 Da / Num. of mol.: 1
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.: 1
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, 1 molecules G

#3: Protein/peptide cyclic peptide CP141076


Mass: 1614.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(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.: 2 / 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 , 4 types, 592 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: H1/PR8: 10 mg/ml, 0.2 M lithium sulfate, 20% (w/v) polyethylene glycol 1000, 0.1 M phosphate-citrate, pH 4.2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 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: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.59→42.19 Å / Num. obs: 89949 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.42 Å2 / CC1/2: 0.98 / Net I/σ(I): 27.6
Reflection shellResolution: 1.59→1.62 Å / Num. unique obs: 4486 / CC1/2: 0.91

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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: 1.59→42.1 Å / SU ML: 0.143 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.9142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 4551 5.06 %
Rwork0.1916 85387 -
obs0.1926 89938 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.59 Å2
Refinement stepCycle: LAST / Resolution: 1.59→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 126 587 4659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644292
X-RAY DIFFRACTIONf_angle_d0.84635836
X-RAY DIFFRACTIONf_chiral_restr0.0544646
X-RAY DIFFRACTIONf_plane_restr0.0056749
X-RAY DIFFRACTIONf_dihedral_angle_d18.52671647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.28511420.24322849X-RAY DIFFRACTION99.67
1.61-1.630.25241610.23452820X-RAY DIFFRACTION99.77
1.63-1.650.23511680.22892801X-RAY DIFFRACTION99.87
1.65-1.670.26091450.21762872X-RAY DIFFRACTION99.83
1.67-1.690.23221690.2152789X-RAY DIFFRACTION99.8
1.69-1.710.24341460.21682857X-RAY DIFFRACTION99.9
1.71-1.740.24471560.21832813X-RAY DIFFRACTION99.76
1.74-1.760.22811490.21072836X-RAY DIFFRACTION99.7
1.76-1.790.25211590.21142858X-RAY DIFFRACTION99.83
1.79-1.820.24241470.21222772X-RAY DIFFRACTION97.95
1.82-1.850.24931540.21482823X-RAY DIFFRACTION99.6
1.85-1.890.23371580.2112853X-RAY DIFFRACTION99.97
1.89-1.920.27121400.20932832X-RAY DIFFRACTION99.97
1.92-1.960.21041540.212868X-RAY DIFFRACTION99.93
1.96-20.2461260.2032892X-RAY DIFFRACTION99.97
2-2.050.22781570.20332811X-RAY DIFFRACTION99.8
2.05-2.10.22011610.19692819X-RAY DIFFRACTION99.33
2.1-2.160.22541410.19732825X-RAY DIFFRACTION98.37
2.16-2.220.20891560.18752821X-RAY DIFFRACTION97.73
2.22-2.290.21271450.19152826X-RAY DIFFRACTION99.97
2.29-2.380.18671470.192898X-RAY DIFFRACTION100
2.38-2.470.21491520.19132856X-RAY DIFFRACTION99.97
2.47-2.580.24751560.19232844X-RAY DIFFRACTION99.67
2.58-2.720.22081650.19082836X-RAY DIFFRACTION98.65
2.72-2.890.24091420.2012794X-RAY DIFFRACTION96.2
2.89-3.110.23161400.19042889X-RAY DIFFRACTION99.84
3.11-3.430.17761520.18372908X-RAY DIFFRACTION99.67
3.43-3.920.19631450.16952904X-RAY DIFFRACTION99.32
3.92-4.940.16771690.15112818X-RAY DIFFRACTION96.08
4.94-42.10.20261490.20473003X-RAY DIFFRACTION97.16

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