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- PDB-5gjt: Crystal structure of H1 hemagglutinin from A/Washington/05/2011 i... -

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Basic information

Entry
Database: PDB / ID: 5gjt
TitleCrystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1
Components
  • (Hemagglutinin) x 2
  • heavy chain of human neutralizing antibody 3E1
  • light chain of human neutralizing antibody 3E1
KeywordsIMMUNE SYSTEM / epitope / Fab / complementarity determining region / paratope
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
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, W. / Zhang, T. / Ding, J.
CitationJournal: Nat Commun / Year: 2016
Title: Human antibody 3E1 targets the HA stem region of H1N1 and H5N6 influenza A viruses
Authors: Wang, W. / Sun, X. / Li, Y. / Su, J. / Ling, Z. / Zhang, T. / Wang, F. / Zhang, H. / Chen, H. / Ding, J. / Sun, B.
History
DepositionJul 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
L: light chain of human neutralizing antibody 3E1
H: heavy chain of human neutralizing antibody 3E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9475
Polymers104,5234
Non-polymers4241
Water0
1
A: Hemagglutinin
B: Hemagglutinin
L: light chain of human neutralizing antibody 3E1
H: heavy chain of human neutralizing antibody 3E1
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
L: light chain of human neutralizing antibody 3E1
H: heavy chain of human neutralizing antibody 3E1
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
L: light chain of human neutralizing antibody 3E1
H: heavy chain of human neutralizing antibody 3E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,84215
Polymers313,56912
Non-polymers1,2733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area47540 Å2
ΔGint-249 kcal/mol
Surface area110240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.806, 130.806, 366.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin /


Mass: 36507.160 Da / Num. of mol.: 1 / Fragment: UNP residues 1344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Washington/05/2011(H1N1) / Gene: HA / Plasmid: pFast-HTB / Production host: Baculovirus expression vector pFastBac1-HM / Strain (production host): Sf9 / References: UniProt: N0C8E5
#2: Protein Hemagglutinin /


Mass: 20869.203 Da / Num. of mol.: 1 / Fragment: hemagglutinin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Washington/05/2011(H1N1) / Gene: HA / Plasmid: pFast-HTB / Production host: Baculovirus expression vector pFastBac1-HM / Strain (production host): Sf9 / References: UniProt: N0C8E5
#3: Antibody light chain of human neutralizing antibody 3E1


Mass: 23483.084 Da / Num. of mol.: 1 / Fragment: light chain of neutralizing antibody 3E1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AbVec-hIgKappa2 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
#4: Antibody heavy chain of human neutralizing antibody 3E1


Mass: 23663.646 Da / Num. of mol.: 1 / Fragment: heavy chain of neutralizing antibody 3E1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AbVec-hIgG1 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
#5: 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

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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: 2.89 Å3/Da / Density % sol: 57.44 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Na HEPES, 20% PEG400 and 0.1M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jan 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 22417 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Blu-Icedata collection
HKL-3000data scaling
PHENIXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJS

5gjs


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1143 5.1 %RANDOM
Rwork0.216 ---
obs0.218 21207 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å20 Å2
2--0.85 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7069 0 28 0 7097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9489882
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4675899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45324.727311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.924151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5561526
X-RAY DIFFRACTIONr_chiral_restr0.0670.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215459
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7787.0093623
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4710.5094513
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3097.0283652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 83 -
Rwork0.293 1548 -
obs--99.51 %

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