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Basic information

Entry
Database: PDB / ID: 3ubj
TitleInfluenza hemagglutinin from the 2009 pandemic in complex with ligand LSTa
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral envelope protein / hemagglutinin / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Influenza a virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2012
Title: Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic.
Authors: Xu, R. / McBride, R. / Nycholat, C.M. / Paulson, J.C. / Wilson, I.A.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,69531
Polymers340,88212
Non-polymers5,81319
Water14,106783
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,42512
Polymers170,4416
Non-polymers1,9846
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32960 Å2
ΔGint-158 kcal/mol
Surface area56860 Å2
MethodPISA
2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,27019
Polymers170,4416
Non-polymers3,83013
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35170 Å2
ΔGint-130 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.851, 116.090, 118.397
Angle α, β, γ (deg.)61.05, 77.00, 80.39
Int Tables number1
Space group name H-MP1

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Components

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Hemagglutinin ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin HA1


Mass: 36535.281 Da / Num. of mol.: 6 / Fragment: Ectodomain HA1, residues 18-344 / Mutation: G205C, R220C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: SW1 A/CALIFORNIA/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1
#2: Protein
Hemagglutinin HA2


Mass: 20278.383 Da / Num. of mol.: 6 / Fragment: Ectodomain HA2, residues 345-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza a virus / Strain: SW1 A/CALIFORNIA/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1

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Sugars , 3 types, 19 molecules

#3: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}}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.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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, 783 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 27% PEG-MME 2000, 0.1M Tris pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2010
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionRedundancy: 2.1 % / Av σ(I) over netI: 9.32 / Number: 274313 / Rmerge(I) obs: 0.082 / Χ2: 1.02 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 131425 / % possible obs: 91
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.855099.510.0370.9992.2
3.854.8598.910.0411.0452.2
3.363.8598.810.0651.0572.2
3.053.3698.610.1111.092.2
2.833.0598.210.1741.0322.2
2.672.8396.810.2330.992.1
2.532.679210.2971.0312
2.422.5384.210.3460.9821.9
2.332.4275.610.3910.9471.8
2.252.3367.510.4340.9631.7
ReflectionResolution: 2.25→50 Å / Num. obs: 131425 / % possible obs: 91 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.331.70.434167.5
2.33-2.421.80.391175.6
2.42-2.531.90.346184.2
2.53-2.6720.297192
2.67-2.832.10.233196.8
2.83-3.052.20.174198.2
3.05-3.362.20.111198.6
3.36-3.852.20.065198.8
3.85-4.852.20.041198.9
4.85-502.20.037199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.32 Å
Translation2.5 Å49.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LZG

3lzg


Resolution: 2.25→49.316 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.97 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 6522 4.99 %
Rwork0.2015 --
obs0.204 130790 91.04 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.644 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6283 Å23.2031 Å27.3836 Å2
2--2.4958 Å213.4355 Å2
3---2.2024 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23264 0 376 783 24423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324253
X-RAY DIFFRACTIONf_angle_d0.78332828
X-RAY DIFFRACTIONf_dihedral_angle_d14.7288913
X-RAY DIFFRACTIONf_chiral_restr0.0523598
X-RAY DIFFRACTIONf_plane_restr0.0034196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.3091440.27982969X-RAY DIFFRACTION65
2.2756-2.30230.38961760.27413077X-RAY DIFFRACTION68
2.3023-2.33040.35061640.26953155X-RAY DIFFRACTION70
2.3304-2.35990.34251860.27713283X-RAY DIFFRACTION73
2.3599-2.3910.36861570.27733541X-RAY DIFFRACTION76
2.391-2.42370.35091870.26273552X-RAY DIFFRACTION79
2.4237-2.45840.31821940.25933704X-RAY DIFFRACTION81
2.4584-2.4950.32681900.26843839X-RAY DIFFRACTION84
2.495-2.5340.3262370.26263942X-RAY DIFFRACTION87
2.534-2.57560.33182090.26714116X-RAY DIFFRACTION89
2.5756-2.620.32071940.26224157X-RAY DIFFRACTION92
2.62-2.66760.34752260.25444341X-RAY DIFFRACTION94
2.6676-2.71890.34792370.24494344X-RAY DIFFRACTION96
2.7189-2.77440.28582350.23024430X-RAY DIFFRACTION97
2.7744-2.83470.29232290.21894421X-RAY DIFFRACTION97
2.8347-2.90070.25962490.23434474X-RAY DIFFRACTION98
2.9007-2.97320.28342140.23014448X-RAY DIFFRACTION98
2.9732-3.05360.31052550.22044475X-RAY DIFFRACTION98
3.0536-3.14340.26552360.20744454X-RAY DIFFRACTION98
3.1434-3.24490.24322440.21154482X-RAY DIFFRACTION99
3.2449-3.36080.25472360.20264498X-RAY DIFFRACTION99
3.3608-3.49530.23882490.20274508X-RAY DIFFRACTION99
3.4953-3.65440.24912470.1824422X-RAY DIFFRACTION99
3.6544-3.8470.21252380.16754538X-RAY DIFFRACTION99
3.847-4.08790.18792530.15944453X-RAY DIFFRACTION99
4.0879-4.40330.20162210.15974555X-RAY DIFFRACTION99
4.4033-4.84610.18842420.14944485X-RAY DIFFRACTION99
4.8461-5.54650.2142260.174556X-RAY DIFFRACTION99
5.5465-6.98490.2442120.19044538X-RAY DIFFRACTION99
6.9849-49.3280.20552350.18134511X-RAY DIFFRACTION99

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