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- PDB-8sd2: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -

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Basic information

Entry
Database: PDB / ID: 8sd2
TitleCrystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with small molecule fusion inhibitor compound 4
Components(Hemagglutinin ...) x 2
KeywordsANTIVIRAL PROTEIN / influenza virus / fusion inhibitor
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
: / NITRATE ION / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsKadam, R.U. / Zhu, X.Y. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150885 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Ultrapotent influenza hemagglutinin fusion inhibitors developed through SuFEx-enabled high-throughput medicinal chemistry.
Authors: Kitamura, S. / Lin, T.H. / Lee, C.D. / Takamura, A. / Kadam, R.U. / Zhang, D. / Zhu, X. / Dada, L. / Nagai, E. / Yu, W. / Yao, Y. / Sharpless, K.B. / Wilson, I.A. / Wolan, D.W.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2767
Polymers56,8462
Non-polymers1,4305
Water73941
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,82721
Polymers170,5376
Non-polymers4,28915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area30960 Å2
ΔGint-141 kcal/mol
Surface area62580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.638, 166.638, 166.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 36707.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: 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 (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452

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Sugars , 2 types, 3 molecules

#3: 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
#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.: 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 , 3 types, 43 molecules

#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-FIE / (S~6~S)-N-{3-chloro-4-[(2S)-2-phenylmorpholine-4-carbonyl]phenyl}-5,7-dihydro-6H-pyrrolo[3,4-b]pyridine-6-sulfonimidoyl fluoride


Mass: 500.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22ClFN4O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 1 M lithium chloride, 0.1 M MES, pH 6, 20% wt/vol PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.81→44.58 Å / Num. obs: 18876 / % possible obs: 100 % / Redundancy: 35.2 % / Biso Wilson estimate: 70 Å2 / CC1/2: 0.981 / Rpim(I) all: 0.02 / Rsym value: 0.12 / Net I/σ(I): 39
Reflection shellResolution: 2.81→2.87 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 958 / CC1/2: 0.57 / Rpim(I) all: 0.45 / Rsym value: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→44.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.841 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R: 0.841 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26126 997 5.3 %RANDOM
Rwork0.21671 ---
obs0.21946 17813 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.81→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 94 41 3918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133976
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153538
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.6775417
X-RAY DIFFRACTIONr_angle_other_deg1.3181.6078128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66823.5200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8731518
X-RAY DIFFRACTIONr_chiral_restr0.0550.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.0228.6671970
X-RAY DIFFRACTIONr_mcbond_other7.0068.6661969
X-RAY DIFFRACTIONr_mcangle_it10.30613.0062459
X-RAY DIFFRACTIONr_mcangle_other10.30613.0092460
X-RAY DIFFRACTIONr_scbond_it7.1528.8712005
X-RAY DIFFRACTIONr_scbond_other7.1468.872003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.50213.1862956
X-RAY DIFFRACTIONr_long_range_B_refined14.621161.76315555
X-RAY DIFFRACTIONr_long_range_B_other14.623161.79615547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.813→2.886 Å
RfactorNum. reflection% reflection
Rfree0.445 67 -
Rwork0.445 1310 -
obs--100 %

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