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- PDB-9dip: Crystal structure of H5 hemagglutinin from the influenza virus A/... -

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Basic information

Entry
Database: PDB / ID: 9dip
TitleCrystal structure of H5 hemagglutinin from the influenza virus A/Texas/37/2024 (H5N1) with LSTa
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / H1N1 / Antibody / Hemagglutinin
Function / homology
Function and homology information


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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLin, T.H. / Zhu, Y. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93021C00015 United States
CitationJournal: Science / Year: 2024
Title: A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors.
Authors: Lin, T.H. / Zhu, X. / Wang, S. / Zhang, D. / McBride, R. / Yu, W. / Babarinde, S. / Paulson, J.C. / Wilson, I.A.
History
DepositionSep 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 22, 2025Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,07712
Polymers170,3756
Non-polymers3,7016
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36270 Å2
ΔGint-138 kcal/mol
Surface area61040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.539, 74.760, 131.101
Angle α, β, γ (deg.)90.00, 96.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACIBDJ

#1: Protein Hemagglutinin HA1


Mass: 36534.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6B7HPT9
#2: Protein Hemagglutinin HA2


Mass: 20257.311 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6B7HQ27

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Sugars , 4 types, 6 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a3-b1_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1a_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-2-4/a4-b1_b3-c1_c3-d1_d3-e2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#5: 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
#6: 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 / 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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Non-polymers , 1 types, 141 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.32→31.38 Å / Num. obs: 85509 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.98 / Rpim(I) all: 0.06 / Rrim(I) all: 0.15 / Net I/σ(I): 15.7
Reflection shellResolution: 2.32→2.36 Å / Num. unique obs: 8523 / CC1/2: 0.34 / Rpim(I) all: 0.78 / Rrim(I) all: 2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→31.18 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 4311 5.04 %
Rwork0.2163 --
obs0.2185 85509 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11874 0 249 141 12264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212396
X-RAY DIFFRACTIONf_angle_d0.53316789
X-RAY DIFFRACTIONf_dihedral_angle_d16.84505
X-RAY DIFFRACTIONf_chiral_restr0.0431836
X-RAY DIFFRACTIONf_plane_restr0.0052173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.340.36541300.3292481X-RAY DIFFRACTION90
2.34-2.370.33231340.30462669X-RAY DIFFRACTION99
2.37-2.40.36811580.29132761X-RAY DIFFRACTION100
2.4-2.430.30361500.29482693X-RAY DIFFRACTION99
2.43-2.460.38261250.29572725X-RAY DIFFRACTION100
2.46-2.50.32411510.29612751X-RAY DIFFRACTION100
2.5-2.530.35621470.29832675X-RAY DIFFRACTION99
2.53-2.570.40131460.30222724X-RAY DIFFRACTION99
2.57-2.610.31931370.28672735X-RAY DIFFRACTION99
2.61-2.650.31031330.27142744X-RAY DIFFRACTION99
2.65-2.70.31641260.26552696X-RAY DIFFRACTION99
2.7-2.750.3331440.24992685X-RAY DIFFRACTION97
2.75-2.80.31941560.24872667X-RAY DIFFRACTION98
2.8-2.860.28931510.24832632X-RAY DIFFRACTION97
2.86-2.920.331220.25272610X-RAY DIFFRACTION95
2.92-2.990.32891500.25442743X-RAY DIFFRACTION99
2.99-3.060.2991430.27392701X-RAY DIFFRACTION100
3.06-3.140.33861460.25522743X-RAY DIFFRACTION99
3.14-3.240.32771520.24842724X-RAY DIFFRACTION99
3.24-3.340.28491400.24572716X-RAY DIFFRACTION99
3.34-3.460.26851600.23272711X-RAY DIFFRACTION100
3.46-3.60.30611560.23552722X-RAY DIFFRACTION99
3.6-3.760.27571410.21632757X-RAY DIFFRACTION99
3.76-3.960.24881420.20142718X-RAY DIFFRACTION98
3.96-4.210.23691210.18912625X-RAY DIFFRACTION95
4.21-4.530.22271530.18092735X-RAY DIFFRACTION98
4.53-4.980.18581490.1652760X-RAY DIFFRACTION100
4.98-5.70.20891610.17812763X-RAY DIFFRACTION100
5.7-7.170.22031440.19572768X-RAY DIFFRACTION99
7.17-31.180.19411430.18422764X-RAY DIFFRACTION96

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