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- PDB-3whe: A new conserved neutralizing epitope at the globular head of hema... -

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Basic information

Entry
Database: PDB / ID: 3whe
TitleA new conserved neutralizing epitope at the globular head of hemagglutinin in H3N2 influenza viruses
Components
  • (immunoglobulin ...Antibody) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsFujii, Y. / Sumida, T. / Shirouzu, M. / Yokoyama, S.
CitationJournal: J.Virol. / Year: 2014
Title: Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses.
Authors: Iba, Y. / Fujii, Y. / Ohshima, N. / Sumida, T. / Kubota-Koketsu, R. / Ikeda, M. / Wakiyama, M. / Shirouzu, M. / Okada, J. / Okuno, Y. / Kurosawa, Y. / Yokoyama, S.
History
DepositionAug 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn
Item: _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Mar 4, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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 / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
M: immunoglobulin heavy chain
O: immunoglobulin heavy chain
Q: immunoglobulin heavy chain
S: immunoglobulin heavy chain
U: immunoglobulin heavy chain
W: immunoglobulin heavy chain
Y: immunoglobulin heavy chain
1: immunoglobulin heavy chain
3: immunoglobulin heavy chain
5: immunoglobulin heavy chain
7: immunoglobulin heavy chain
9: immunoglobulin heavy chain
N: immunoglobulin light chain
P: immunoglobulin light chain
R: immunoglobulin light chain
T: immunoglobulin light chain
V: immunoglobulin light chain
X: immunoglobulin light chain
Z: immunoglobulin light chain
2: immunoglobulin light chain
4: immunoglobulin light chain
6: immunoglobulin light chain
8: immunoglobulin light chain
0: immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,268,21096
Polymers1,228,16636
Non-polymers40,04460
Water0
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
M: immunoglobulin heavy chain
O: immunoglobulin heavy chain
Q: immunoglobulin heavy chain
N: immunoglobulin light chain
P: immunoglobulin light chain
R: immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,05324
Polymers307,0419
Non-polymers10,01115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
S: immunoglobulin heavy chain
U: immunoglobulin heavy chain
W: immunoglobulin heavy chain
T: immunoglobulin light chain
V: immunoglobulin light chain
X: immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,05324
Polymers307,0419
Non-polymers10,01115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
Y: immunoglobulin heavy chain
1: immunoglobulin heavy chain
3: immunoglobulin heavy chain
Z: immunoglobulin light chain
2: immunoglobulin light chain
4: immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,05324
Polymers307,0419
Non-polymers10,01115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
5: immunoglobulin heavy chain
7: immunoglobulin heavy chain
9: immunoglobulin heavy chain
6: immunoglobulin light chain
8: immunoglobulin light chain
0: immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,05324
Polymers307,0419
Non-polymers10,01115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)391.037, 241.173, 223.214
Angle α, β, γ (deg.)90.000, 123.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Hemagglutinin /


Mass: 55221.602 Da / Num. of mol.: 12 / Fragment: UNP RESIDUES 25-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Aichi/2-1/1968 (H3N2) / Gene: 126567434, HA / Plasmid: pBAC-3 / Cell line (production host): SF+ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: T2HNI1

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Antibody , 2 types, 24 molecules MOQSUWY13579NPRTVXZ24680

#2: Antibody
immunoglobulin heavy chain /


Mass: 24187.277 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: protein selected by phage display / Plasmid: pCMVscript / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1
#3: Antibody
immunoglobulin light chain /


Mass: 22938.275 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: protein selected by phage display / Plasmid: pCMVscript / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1

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Sugars , 4 types, 60 molecules

#4: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG8000, KCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 22, 2011
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 142111 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.905 % / Rmerge(I) obs: 0.236 / Net I/σ(I): 6.35
Reflection shell

Rmerge(I) obs: 2.1 / Diffraction-ID: 1

Resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
4-4.250.2710.669131923989235282.43398.1
4.25-4.50.5411.267309218999186541.27698.2
4.5-50.7291.9910608027505270230.8398.2
5-5.50.8422.827115918425181240.57398.4
5.5-60.8773.354939312817126010.47998.3
6-70.9545.816138215944156790.27498.3
7-80.98610.1834473897488300.15198.4
8-100.99722.7333998892387630.06298.2
10-200.99936.6731022825580920.03498
20-300.99948.96296912318170.02566.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNS1.3refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA0

1ha0


Resolution: 4→30 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 17247948 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3084 7106 4.9 %RANDOM
Rwork0.235 ---
obs0.236 142111 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 146.958 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 381.87 Å2 / Biso mean: 205.8505 Å2 / Biso min: 87.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.8 Å0.8 Å
Luzzati d res low-5 Å
Luzzati sigma a1.25 Å1.42 Å
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms85488 0 2664 0 88152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.023
X-RAY DIFFRACTIONc_mcbond_it7.44315
X-RAY DIFFRACTIONc_scbond_it11.61620
X-RAY DIFFRACTIONc_mcangle_it11.53620
X-RAY DIFFRACTIONc_scangle_it16.93825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)Rfactor Rfree error
4-4.140.39726860.3959129641365094.4
4.14-4.310.38367080.3969135121422098.3
4.31-4.50.40357090.3901134931420298.4
4.5-4.740.3697090.38134991420898.4
4.74-5.040.37697110.373135021421398.5
5.04-5.420.35737160.3534135371425398.6
5.42-5.960.34987130.3512135681428198.6
5.96-6.820.30527150.2975135801429598.6
6.82-8.560.27897180.2545136401435898.7
8.56-300.230972150.2237137101443198.50.012
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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