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- PDB-9diq: Crystal structure of Apo-H5 hemagglutinin from the influenza viru... -

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Basic information

Entry
Database: PDB / ID: 9diq
TitleCrystal structure of Apo-H5 hemagglutinin from the influenza virus A/Texas/37/2024 (H5N1)
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 / 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: 2.69 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
I: Hemagglutinin HA1
J: Hemagglutinin HA2
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,58018
Polymers340,75012
Non-polymers2,8306
Water73941
1
I: Hemagglutinin HA1
J: Hemagglutinin HA2
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,9739
Polymers170,3756
Non-polymers1,5973
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31980 Å2
ΔGint-142 kcal/mol
Surface area61060 Å2
MethodPISA
2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,6079
Polymers170,3756
Non-polymers1,2323
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31350 Å2
ΔGint-143 kcal/mol
Surface area61420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.367, 72.061, 206.859
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 12 molecules IACEGKJBDFHL

#1: Protein
Hemagglutinin HA1


Mass: 36534.414 Da / Num. of mol.: 6
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.: 6
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 , 3 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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.: 2
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.: 1 / 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, 41 molecules

#6: 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes 16% 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: 2.69→33.74 Å / Num. obs: 103266 / % possible obs: 96.1 % / Redundancy: 3.9 % / CC1/2: 0.93 / Rpim(I) all: 0.11 / Rrim(I) all: 0.22 / Net I/σ(I): 8.5
Reflection shellResolution: 2.69→2.75 Å / Num. unique obs: 9020 / CC1/2: 0.39 / Rpim(I) all: 0.84 / Rrim(I) all: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→33.74 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 5237 5.08 %
Rwork0.2096 --
obs0.2125 103169 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23522 0 187 41 23750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324251
X-RAY DIFFRACTIONf_angle_d0.57132838
X-RAY DIFFRACTIONf_dihedral_angle_d4.9483271
X-RAY DIFFRACTIONf_chiral_restr0.0443529
X-RAY DIFFRACTIONf_plane_restr0.0044290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.3621090.30631986X-RAY DIFFRACTION59
2.72-2.750.36881570.31843305X-RAY DIFFRACTION97
2.75-2.790.34971720.31093247X-RAY DIFFRACTION97
2.79-2.820.38251670.30423255X-RAY DIFFRACTION97
2.82-2.860.35271980.29513251X-RAY DIFFRACTION97
2.86-2.90.34511700.27983236X-RAY DIFFRACTION96
2.9-2.940.30021790.28133262X-RAY DIFFRACTION99
2.94-2.980.35781830.29123399X-RAY DIFFRACTION100
2.98-3.030.33211700.28373385X-RAY DIFFRACTION100
3.03-3.080.38171590.27593339X-RAY DIFFRACTION100
3.08-3.130.29551790.24883406X-RAY DIFFRACTION100
3.13-3.190.33321850.25873323X-RAY DIFFRACTION100
3.19-3.250.31931810.24593337X-RAY DIFFRACTION99
3.25-3.320.28931780.24513358X-RAY DIFFRACTION99
3.32-3.390.31861530.23963394X-RAY DIFFRACTION100
3.39-3.470.31161730.2323355X-RAY DIFFRACTION99
3.47-3.560.27461780.22513324X-RAY DIFFRACTION98
3.56-3.650.24531760.21593331X-RAY DIFFRACTION98
3.65-3.760.31521670.21223332X-RAY DIFFRACTION98
3.76-3.880.24562060.20533233X-RAY DIFFRACTION97
3.88-4.020.25991860.20183279X-RAY DIFFRACTION96
4.02-4.180.25811620.19773145X-RAY DIFFRACTION94
4.18-4.370.2721550.18593241X-RAY DIFFRACTION94
4.37-4.60.23552310.17693146X-RAY DIFFRACTION94
4.6-4.890.22261750.16783247X-RAY DIFFRACTION95
4.89-5.260.22141620.17173331X-RAY DIFFRACTION97
5.26-5.790.23211730.17593339X-RAY DIFFRACTION98
5.79-6.620.22911790.18813421X-RAY DIFFRACTION99
6.62-8.320.2321880.19243271X-RAY DIFFRACTION95
8.32-33.740.23771860.18353454X-RAY DIFFRACTION97

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