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- PDB-5vjk: Crystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S... -

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Basic information

Entry
Database: PDB / ID: 5vjk
TitleCrystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S) from the influenza virus A/Shanghai/2/2013 (H7N9)
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin / mutant / receptor specificity
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 / metal ion binding
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Three mutations switch H7N9 influenza to human-type receptor specificity.
Authors: de Vries, R.P. / Peng, W. / Grant, O.C. / Thompson, A.J. / Zhu, X. / Bouwman, K.M. / de la Pena, A.T.T. / van Breemen, M.J. / Ambepitiya Wickramasinghe, I.N. / de Haan, C.A.M. / Yu, W. / ...Authors: de Vries, R.P. / Peng, W. / Grant, O.C. / Thompson, A.J. / Zhu, X. / Bouwman, K.M. / de la Pena, A.T.T. / van Breemen, M.J. / Ambepitiya Wickramasinghe, I.N. / de Haan, C.A.M. / Yu, W. / McBride, R. / Sanders, R.W. / Woods, R.J. / Verheije, M.H. / Wilson, I.A. / Paulson, J.C.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Data collection
Revision 1.2Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_struct_special_symmetry / 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 / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4765
Polymers56,4472
Non-polymers1,0293
Water1,27971
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,42815
Polymers169,3416
Non-polymers3,0879
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area35090 Å2
ΔGint-127 kcal/mol
Surface area56500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.440, 115.440, 294.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-305-

HOH

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Components

#1: Protein Hemagglutinin HA1


Mass: 35365.891 Da / Num. of mol.: 1 / Mutation: V186K, K193T, G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2


Mass: 21081.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21
#3: 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.: 1
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
#4: 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.: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M tri-potassium citrate, 5% (v/v) ethylene glycol and 22% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.593→50 Å / Num. obs: 23692 / % possible obs: 99.3 % / Redundancy: 4 % / CC1/2: 0.998 / Rpim(I) all: 0.05 / Rsym value: 0.09 / Net I/σ(I): 16.4
Reflection shellResolution: 2.593→2.64 Å / Redundancy: 2.8 % / Num. unique obs: 1102 / CC1/2: 0.548 / Rpim(I) all: 0.44 / Rsym value: 0.66 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5J

4n5j


Resolution: 2.593→49.772 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1210 5.11 %
Rwork0.203 --
obs0.2054 23688 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.593→49.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 67 71 3904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123914
X-RAY DIFFRACTIONf_angle_d1.6665297
X-RAY DIFFRACTIONf_dihedral_angle_d5.9322327
X-RAY DIFFRACTIONf_chiral_restr0.097583
X-RAY DIFFRACTIONf_plane_restr0.01694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5927-2.69660.38351250.33792346X-RAY DIFFRACTION94
2.6966-2.81930.33411330.27562464X-RAY DIFFRACTION99
2.8193-2.96790.28641220.24962500X-RAY DIFFRACTION100
2.9679-3.15380.32911470.23872460X-RAY DIFFRACTION100
3.1538-3.39730.27221470.23732497X-RAY DIFFRACTION100
3.3973-3.7390.24081470.20092482X-RAY DIFFRACTION100
3.739-4.27980.22021340.17712520X-RAY DIFFRACTION100
4.2798-5.39110.22831250.16772551X-RAY DIFFRACTION100
5.3911-49.78160.2311300.19862658X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -52.8954 Å / Origin y: 17.8726 Å / Origin z: 7.9076 Å
111213212223313233
T0.2926 Å20.0358 Å20.0132 Å2-0.2026 Å20.0612 Å2--0.5334 Å2
L1.3591 °20.2549 °20.0932 °2-1.2627 °20.3318 °2--0.9061 °2
S-0.0428 Å °-0.1301 Å °-0.1333 Å °0.1508 Å °0.1333 Å °-0.1115 Å °0.0678 Å °0.107 Å °-0.0395 Å °
Refinement TLS groupSelection details: all

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