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- PDB-3uyw: Crystal structures of globular head of 2009 pandemic H1N1 hemaggl... -

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Basic information

Entry
Database: PDB / ID: 3uyw
TitleCrystal structures of globular head of 2009 pandemic H1N1 hemagglutinin
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Influenza virus / subunit vaccine / hemagglutinin (HA)
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / metal ion binding / membrane
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-AMINOETHANESULFONIC ACID / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsXuan, C.L. / Shi, Y. / Qi, J.X. / Xiao, H.X. / Gao, G.F.
CitationJournal: Protein Cell / Year: 2011
Title: Structural vaccinology: structure-based design of influenza A virus hemagglutinin subtype-specific subunit vaccines
Authors: Xuan, C.L. / Shi, Y. / Qi, J.X. / Zhang, W. / Xiao, H.X. / Gao, G.F.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7996
Polymers96,5484
Non-polymers2502
Water14,790821
1
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2622
Polymers24,1371
Non-polymers1251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)24,1371
Polymers24,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2622
Polymers24,1371
Non-polymers1251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)24,1371
Polymers24,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 65.916, 79.485
Angle α, β, γ (deg.)94.46, 89.97, 94.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hemagglutinin


Mass: 24137.064 Da / Num. of mol.: 4 / Fragment: UNP residues 65-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1
#2: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 6000, 5% MPD, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 59386 / Num. obs: 59386 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AL4

3al4


Resolution: 1.903→35.134 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8704 / SU ML: 0.24 / σ(F): 0.08 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 2943 5.06 %Random
Rwork0.1842 ---
all0.1849 58137 --
obs0.1849 58137 95.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.099 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 187.55 Å2 / Biso mean: 27.8911 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1-6.0046 Å21.7181 Å2-0.9276 Å2
2---5.0213 Å22.175 Å2
3----0.9833 Å2
Refinement stepCycle: LAST / Resolution: 1.903→35.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6811 0 14 821 7646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167052
X-RAY DIFFRACTIONf_angle_d1.3029567
X-RAY DIFFRACTIONf_dihedral_angle_d18.3952516
X-RAY DIFFRACTIONf_chiral_restr0.126990
X-RAY DIFFRACTIONf_plane_restr0.0071230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9032-1.93440.21841210.2007233382
1.9344-1.96780.22321330.2021243091
1.9678-2.00360.2381330.2078255891
2.0036-2.04210.27281240.2069255792
2.0421-2.08380.22731430.1914251593
2.0838-2.12910.23251450.1933262794
2.1291-2.17860.19971380.192257894
2.1786-2.23310.211410.191261595
2.2331-2.29340.21741460.2265995
2.2934-2.36090.18511200.201267096
2.3609-2.43710.22351410.202266996
2.4371-2.52420.24041390.2021268697
2.5242-2.62520.21331450.2027265697
2.6252-2.74460.23351330.2102273597
2.7446-2.88930.22471460.1982262397
2.8893-3.07020.19181490.1933272198
3.0702-3.30710.17811440.1758273798
3.3071-3.63960.17511580.1588268398
3.6396-4.16550.15691330.1483274598
4.1655-5.24530.151630.142269398
5.2453-35.13960.18341480.1867270498
Refinement TLS params.Method: refined / Origin x: 8.5222 Å / Origin y: -17.6252 Å / Origin z: 32.2131 Å
111213212223313233
T0.0605 Å20.0034 Å20.0076 Å2-0.0953 Å2-0.0026 Å2--0.0959 Å2
L0.0146 °20.0146 °20.031 °2-0.139 °2-0.068 °2--0.2313 °2
S-0.0155 Å °0.0025 Å °0.0129 Å °-0.0035 Å °-0.0005 Å °-0.0174 Å °-0.0033 Å °-0.0102 Å °0.0129 Å °
Refinement TLS groupSelection details: all

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