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- PDB-5y2l: Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in... -

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Basic information

Entry
Database: PDB / ID: 5y2l
TitleCrystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the 1968 H3N2 pandemic (H3-AC/68) hemagglutinin
Components
  • (Hemagglutinin) x 2
  • (a group 2 HA binding antibody AF4H1K1 Fab ...) x 2
KeywordsANTIMICROBIAL PROTEIN / neutralizing antibody / influenza virus / HA / H3-clade
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane
Similarity search - Function
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 / Immunoglobulins ...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 / 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 / Resolution: 2.902 Å
AuthorsXiao, H. / Qi, J. / Gao, F.G.
CitationJournal: To Be Published
Title: An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins
Authors: Xiao, H. / Qi, J. / Gao, F.G.
History
DepositionJul 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
I: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
J: a group 2 HA binding antibody AF4H1K1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0468
Polymers105,7554
Non-polymers1,2914
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-53 kcal/mol
Surface area41900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.482, 157.482, 355.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 36222.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Aichi/2/1968 H3N2)
Strain: A/Aichi/2/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437
#2: Protein Hemagglutinin /


Mass: 20311.480 Da / Num. of mol.: 1 / Fragment: UNP residues 346-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Aichi/2/1968 H3N2)
Strain: A/Aichi/2/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437

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Antibody , 2 types, 2 molecules IJ

#3: Antibody a group 2 HA binding antibody AF4H1K1 Fab heavy chain


Mass: 24977.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody a group 2 HA binding antibody AF4H1K1 Fab light chain


Mass: 24243.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#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.: 2
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
#6: 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.19 mM CYMAL7, 0.1M HEPES pH 7.5, 40% ployethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 37831 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 23
Reflection shellResolution: 2.9→3 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3739 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.902→47.331 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.53
RfactorNum. reflection% reflection
Rfree0.2436 1881 4.99 %
Rwork0.2119 --
obs0.2136 37724 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.902→47.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7105 0 84 0 7189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087363
X-RAY DIFFRACTIONf_angle_d1.1649997
X-RAY DIFFRACTIONf_dihedral_angle_d15.8692655
X-RAY DIFFRACTIONf_chiral_restr0.0441123
X-RAY DIFFRACTIONf_plane_restr0.0061292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9019-2.98030.43441590.35412706X-RAY DIFFRACTION99
2.9803-3.0680.38881290.31722705X-RAY DIFFRACTION99
3.068-3.1670.30871390.30452729X-RAY DIFFRACTION99
3.167-3.28020.39741340.28872745X-RAY DIFFRACTION100
3.2802-3.41150.32891460.28342717X-RAY DIFFRACTION100
3.4115-3.56670.30011520.25222746X-RAY DIFFRACTION100
3.5667-3.75470.2611510.24212735X-RAY DIFFRACTION100
3.7547-3.98980.2831310.21532743X-RAY DIFFRACTION100
3.9898-4.29770.22231490.17812755X-RAY DIFFRACTION100
4.2977-4.72980.19371550.16242759X-RAY DIFFRACTION100
4.7298-5.41340.17981480.16522783X-RAY DIFFRACTION100
5.4134-6.8170.22791430.19692824X-RAY DIFFRACTION100
6.817-47.33690.20221450.19432896X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 45.6564 Å / Origin y: -47.1799 Å / Origin z: -27.6507 Å
111213212223313233
T0.5971 Å2-0.0375 Å20.0156 Å2-0.5277 Å20.0171 Å2--0.5838 Å2
L0.3265 °2-0.0452 °2-0.0763 °2-0.0094 °2-0.0249 °2--0.294 °2
S-0.0131 Å °-0.0733 Å °-0.0342 Å °0.0177 Å °0.0365 Å °0.041 Å °0.0111 Å °0.0416 Å °-0 Å °
Refinement TLS groupSelection details: all

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