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- PDB-3mlh: Crystal structure of the 2009 H1N1 influenza virus hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 3mlh
TitleCrystal structure of the 2009 H1N1 influenza virus hemagglutinin receptor-binding domain
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / receptor-binding domain / lectin / antigen
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsDuBois, R.M. / Aguilar-Yanez, J.M. / Mendoza-Ochoa, G.I. / Schultz-Cherry, S. / Alvarez, M.M. / White, S.W. / Russell, C.J.
CitationJournal: J.Virol. / Year: 2011
Title: The Receptor-Binding Domain of Influenza Virus Hemagglutinin Produced in Escherichia coli Folds into Its Native, Immunogenic Structure.
Authors: Dubois, R.M. / Aguilar-Yanez, J.M. / Mendoza-Ochoa, G.I. / Oropeza-Almazan, Y. / Schultz-Cherry, S. / Alvarez, M.M. / White, S.W. / Russell, C.J.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3818
Polymers52,8292
Non-polymers5536
Water3,477193
1
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7835
Polymers26,4141
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5993
Polymers26,4141
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.857, 74.065, 75.180
Angle α, β, γ (deg.)90.000, 94.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin /


Mass: 26414.424 Da / Num. of mol.: 2 / Fragment: receptor-binding domain (UNP residues 63-286)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Mexico/4603/2009(H1N1) / Gene: HA / Plasmid: pJexpress404 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 strain / References: UniProt: C4RSQ3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 2000MME, Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 25593 / Num. obs: 25588 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 12.73 / Redundancy: 5 % / Biso Wilson estimate: 19.628 Å2 / Rmerge(I) obs: 0.127 / Χ2: 1.147 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.83 / Num. unique all: 2518 / Χ2: 1.123 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.07 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.72 Å
Translation2.5 Å39.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RUY

1ruy


Resolution: 2.09→39.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.233 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1306 5.1 %RANDOM
Rwork0.177 ---
all0.178 25564 --
obs0.178 25564 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.65 Å2 / Biso mean: 19.628 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.02 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.09→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 36 193 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223514
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9474758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81223.797158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4071517
X-RAY DIFFRACTIONr_chiral_restr0.070.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212679
X-RAY DIFFRACTIONr_mcbond_it0.4581.52119
X-RAY DIFFRACTIONr_mcangle_it0.90823415
X-RAY DIFFRACTIONr_scbond_it1.34131395
X-RAY DIFFRACTIONr_scangle_it2.34.51342
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 73 -
Rwork0.183 1487 -
all-1560 -
obs-1487 84.19 %
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)
10.52240.4320.14350.68170.18620.63120.0041-0.007-0.0189-0.00460.0043-0.04280.04330.0018-0.00830.00790.0055-0.00470.0099-0.0120.018814.2183-10.55917.8688
20.7840.04530.36560.39280.16710.5082-0.0258-0.03270.03040.03050.02180.0121-0.0111-0.00930.0040.00810.0050.00650.00960.00240.013311.787915.511926.3445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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