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

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Basic information

Entry
Database: PDB / ID: 9phq
TitleCrystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141088 (CP14)
Components
  • Hemagglutinin
  • Hemagglutinin HA2 chain
  • cyclic peptide CP141088
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin / glycoprotein
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: 2.87 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
G: cyclic peptide CP141088
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1557
Polymers58,0673
Non-polymers1,0884
Water30617
1
A: Hemagglutinin
B: Hemagglutinin HA2 chain
G: cyclic peptide CP141088
hetero molecules

A: Hemagglutinin
B: Hemagglutinin HA2 chain
G: cyclic peptide CP141088
hetero molecules

A: Hemagglutinin
B: Hemagglutinin HA2 chain
G: cyclic peptide CP141088
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,46521
Polymers174,2019
Non-polymers3,26412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area31620 Å2
ΔGint-159 kcal/mol
Surface area64110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.195, 159.195, 159.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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 / Non-polymers , 2 types, 18 molecules G

#3: Protein/peptide cyclic peptide CP141088


Mass: 1278.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#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: 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

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: H1/PR8: 10 mg/ml, 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / 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: 2.87→37.52 Å / Num. obs: 15428 / % possible obs: 99 % / Redundancy: 17.7 % / Biso Wilson estimate: 70.69 Å2 / CC1/2: 0.97 / Net I/σ(I): 36.8
Reflection shellResolution: 2.87→2.92 Å / Num. unique obs: 702 / CC1/2: 0.79

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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: 2.87→37.52 Å / SU ML: 0.3388 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3129
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2616 714 4.63 %
Rwork0.2029 14705 -
obs0.2057 15419 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.98 Å2
Refinement stepCycle: LAST / Resolution: 2.87→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3931 0 70 17 4018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264091
X-RAY DIFFRACTIONf_angle_d0.57535542
X-RAY DIFFRACTIONf_chiral_restr0.0596604
X-RAY DIFFRACTIONf_plane_restr0.0032719
X-RAY DIFFRACTIONf_dihedral_angle_d5.6503567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.090.34471340.25492836X-RAY DIFFRACTION97.79
3.09-3.40.33541430.2382934X-RAY DIFFRACTION100
3.4-3.890.29581450.20142943X-RAY DIFFRACTION100
3.9-4.90.23391480.18182953X-RAY DIFFRACTION99.97
4.91-37.520.22931440.19843039X-RAY DIFFRACTION99.91

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