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

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Basic information

Entry
Database: PDB / ID: 3uyx
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
NITRATE ION / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2824
Polymers48,1582
Non-polymers1242
Water7,909439
1
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2033
Polymers24,0791
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)24,0791
Polymers24,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.661, 75.052, 60.134
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 24079.027 Da / Num. of mol.: 2 / Fragment: UNP residues 65-278 / Mutation: D228G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: HA / Plasmid: PET21a / Production host: Escherichia coli (E. coli) / References: UniProt: C3W5S1
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG 3350, 0.2M ammonium nitrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 37337 / Num. obs: 37337 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.25 Å2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.381 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.74 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8785 / SU ML: 0.22 / σ(F): 0 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1808 5.01 %Random
Rwork0.165 ---
all0.1668 36068 --
obs0.1668 36068 96.16 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.164 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 159.04 Å2 / Biso mean: 24.2371 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.7542 Å20 Å2-3.8624 Å2
2---1.2168 Å20 Å2
3----2.5374 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 8 439 3819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053526
X-RAY DIFFRACTIONf_angle_d0.9644783
X-RAY DIFFRACTIONf_dihedral_angle_d12.4541279
X-RAY DIFFRACTIONf_chiral_restr0.066495
X-RAY DIFFRACTIONf_plane_restr0.004617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7963-1.84490.31981260.2663232985
1.8449-1.89910.25021360.2106244191
1.8991-1.96040.20831330.1694257393
1.9604-2.03030.20031060.1617264896
2.0303-2.11160.19771420.1539259396
2.1116-2.20750.21021470.157265997
2.2075-2.32370.19461430.1582265597
2.3237-2.46910.22731460.1711268598
2.4691-2.65930.21021330.1659270199
2.6593-2.92610.21861540.1696272599
2.9261-3.34780.20241330.164274199
3.3478-4.21110.15891530.15092747100
4.2111-19.74170.19361560.1616276399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06070.0181-0.01860.08990.07030.0486-0.0041-0.08910.04810.10.0367-0.16780.04160.07980.00070.13350.0054-0.00070.1359-0.00610.17536.9095-15.274629.3123
20.2812-0.04930.03380.30040.10420.4187-0.0090.0107-0.00110.03410.0111-0.01390.0050.0222-0.00010.1016-0.00840.00520.09760.00550.1017-3.04690.782827.8543
30.10.12980.050.19150.17490.5999-0.02950.0676-0.4683-0.08280.1803-0.00180.2103-0.0190.05050.2233-0.0157-0.02630.1647-0.00360.266-15.7593-12.0929-5.2535
40.32970.15070.15870.4862-0.04120.6354-0.030.02110.048-0.02580.01280.0317-0.035-0.011400.12560.0027-0.0040.1262-0.00290.1214-10.82465.2111-1.2295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 54:88)
2X-RAY DIFFRACTION2chain 'A' and (resseq 89:269)
3X-RAY DIFFRACTION3chain 'B' and (resseq 53:98)
4X-RAY DIFFRACTION4chain 'B' and (resseq 99:265)

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