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- PDB-5v2a: Crystal structure of Fab H7.167 in complex with influenza virus h... -

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Basic information

Entry
Database: PDB / ID: 5v2a
TitleCrystal structure of Fab H7.167 in complex with influenza virus hemagglutinin from A/Shanghai/02/2013 (H7N9)
Components
  • (Hemagglutinin) x 2
  • Heavy chain of H7.167 antibody
  • Light chain (kappa) of H7.167 antibody
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / receptor-binding site / human antibody / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.656 Å
AuthorsZhang, H. / Zhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: J. Clin. Invest. / Year: 2016
Title: H7N9 influenza virus neutralizing antibodies that possess few somatic mutations.
Authors: Thornburg, N.J. / Zhang, H. / Bangaru, S. / Sapparapu, G. / Kose, N. / Lampley, R.M. / Bombardi, R.G. / Yu, Y. / Graham, S. / Branchizio, A. / Yoder, S.M. / Rock, M.T. / Creech, C.B. / ...Authors: Thornburg, N.J. / Zhang, H. / Bangaru, S. / Sapparapu, G. / Kose, N. / Lampley, R.M. / Bombardi, R.G. / Yu, Y. / Graham, S. / Branchizio, A. / Yoder, S.M. / Rock, M.T. / Creech, C.B. / Edwards, K.M. / Lee, D. / Li, S. / Wilson, I.A. / Garcia-Sastre, A. / Albrecht, R.A. / Crowe, J.E.
History
DepositionMar 3, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionApr 5, 2017ID: 5F45
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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 / _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
B: Hemagglutinin
L: Light chain (kappa) of H7.167 antibody
H: Heavy chain of H7.167 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9297
Polymers103,9004
Non-polymers1,0293
Water00
1
A: Hemagglutinin
B: Hemagglutinin
L: Light chain (kappa) of H7.167 antibody
H: Heavy chain of H7.167 antibody
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
L: Light chain (kappa) of H7.167 antibody
H: Heavy chain of H7.167 antibody
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
L: Light chain (kappa) of H7.167 antibody
H: Heavy chain of H7.167 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,78721
Polymers311,70012
Non-polymers3,0879
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area49600 Å2
ΔGint-176 kcal/mol
Surface area118940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.276, 207.276, 207.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 34993.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HA1
Source: (gene. exp.) Influenza A virus (A/chicken/Henan/109/2013(H7N9))
Strain: A/chicken/Henan/109/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0R5TXT5
#2: Protein Hemagglutinin


Mass: 21081.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HA2
Source: (gene. exp.) Influenza A virus (A/pigeon/Wuxi/0405007G/2013(H7N9))
Strain: A/pigeon/Wuxi/0405007G/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A097PHH8

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Antibody , 2 types, 2 molecules LH

#3: Antibody Light chain (kappa) of H7.167 antibody


Mass: 24215.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Heavy chain of H7.167 antibody


Mass: 23609.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#5: 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
#6: 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.: 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% (w/v) PEG 8000, 0.1 M HEPES, 8% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.65→50 Å / Num. obs: 8097 / % possible obs: 100 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.019 / Χ2: 0.947 / Net I/σ(I): 46.7
Reflection shellResolution: 4.65→4.73 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 2.15 / Num. unique all: 373 / Num. unique obs: 393 / CC1/2: 0.87 / Rpim(I) all: 0.283 / Χ2: 0.513 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5J

4n5j


Resolution: 4.656→46.348 Å / SU ML: 0.81 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 47.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3335 409 5.05 %
Rwork0.2575 --
obs0.261 8095 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.656→46.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7131 0 67 0 7198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167359
X-RAY DIFFRACTIONf_angle_d2.1829967
X-RAY DIFFRACTIONf_dihedral_angle_d14.4452671
X-RAY DIFFRACTIONf_chiral_restr0.211105
X-RAY DIFFRACTIONf_plane_restr0.0111294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6558-5.32870.37351280.3182541X-RAY DIFFRACTION100
5.3287-6.71030.40251280.35452531X-RAY DIFFRACTION100
6.7103-46.35060.30861530.21922614X-RAY DIFFRACTION100

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