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- PDB-3qqe: Crystal structure of HA2 R106H mutant of H2 hemagglutinin, re-neu... -

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Basic information

Entry
Database: PDB / ID: 3qqe
TitleCrystal structure of HA2 R106H mutant of H2 hemagglutinin, re-neutralized form
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / viral envelope protein / hemagglutinin / viral fusion protein
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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; 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
DI(HYDROXYETHYL)ETHER / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2011
Title: Structural Characterization of an Early Fusion Intermediate of Influenza Virus Hemagglutinin.
Authors: Xu, R. / Wilson, I.A.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)57,6597
Polymers56,6242
Non-polymers1,0355
Water7,674426
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,97821
Polymers169,8736
Non-polymers3,10515
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area31720 Å2
ΔGint-126 kcal/mol
Surface area62620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.339, 70.339, 237.093
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-365-

HOH

21B-434-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 36504.227 Da / Num. of mol.: 1 / Fragment: HA1 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C7S226
#2: Protein Hemagglutinin /


Mass: 20120.248 Da / Num. of mol.: 1 / Fragment: HA2 chain ectodomain / Mutation: R106H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C7S226

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Sugars , 2 types, 3 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.: 1
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 3 types, 428 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 24% PEG 3000, 0.1M Tris, pH 9.0, vapor diffusion, sitting drop, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 21, 2009
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 18.35 / Number: 290928 / Rmerge(I) obs: 0.084 / Χ2: 1.06 / D res high: 2.1 Å / D res low: 40 Å / Num. obs: 37509 / % possible obs: 97.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.524099.710.051.06611
3.594.5210010.0691.06510.4
3.143.5910010.0910.9889.8
2.853.1410010.1360.9969.4
2.652.8510010.1981.0868.8
2.492.6510010.2591.0067.8
2.372.4910010.3211.0836.6
2.262.3799.310.4111.285.4
2.182.269510.4721.0934.2
2.12.1881.810.5141.2423.1
ReflectionResolution: 2.1→40 Å / Num. obs: 37509 / % possible obs: 97.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.084 / Χ2: 1.064 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.183.10.51431411.24281.8
2.18-2.264.20.47236741.09395
2.26-2.375.40.41137551.2899.3
2.37-2.496.60.32138581.083100
2.49-2.657.80.25938231.006100
2.65-2.858.80.19838151.086100
2.85-3.149.40.13638430.996100
3.14-3.599.80.09138470.988100
3.59-4.5210.40.06938601.065100
4.52-40110.0538931.06699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.15 Å
Translation2.5 Å33.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2434 / WRfactor Rwork: 0.1984 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8242 / SU B: 9.885 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2027 / SU Rfree: 0.1781 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1874 5 %RANDOM
Rwork0.189 ---
obs0.1913 37441 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.22 Å2 / Biso mean: 42.617 Å2 / Biso min: 17.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.38 Å20 Å2
2--0.77 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 67 426 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214084
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9615525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59625.178197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.515697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1241517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023086
X-RAY DIFFRACTIONr_nbd_refined0.1810.21712
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2362
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.223
X-RAY DIFFRACTIONr_mcbond_it0.7731.52532
X-RAY DIFFRACTIONr_mcangle_it1.30123945
X-RAY DIFFRACTIONr_scbond_it1.92231787
X-RAY DIFFRACTIONr_scangle_it3.134.51580
LS refinement shellResolution: 2.1→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 109 -
Rwork0.281 2112 -
all-2221 -
obs--79.01 %
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)
10.39730.0791-0.02510.1974-0.18581.8641-0.0564-0.05850.0594-0.0090.0053-0.00320.0449-0.08840.0511-0.09530.0075-0.0235-0.0909-0.01970.003715.9128-14.0726-35.7974
20.1407-0.2742-0.82780.56021.2779.2359-0.05370.01180.00340.0661-0.04260.0439-0.3664-0.44670.0963-0.05710.0054-0.00080.0425-0.0092-0.100323.9719-15.927816.5619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 326
2X-RAY DIFFRACTION2B1 - 172

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