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- PDB-5y2m: Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in... -

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Basic information

Entry
Database: PDB / ID: 5y2m
TitleCrystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin
Components
  • (Hemagglutinin) x 2
  • a group 2 HA binding antibody AF4H1K1 Fab heavy chain
  • a group 2 HA binding antibody AF4H1K1 Fab light chain
KeywordsIMMUNE SYSTEM / 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 / 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 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 / MOLECULAR REPLACEMENT / Resolution: 3.8 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 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 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
D: Hemagglutinin
B: Hemagglutinin
E: Hemagglutinin
C: Hemagglutinin
F: Hemagglutinin
I: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
J: a group 2 HA binding antibody AF4H1K1 Fab light chain
K: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
L: a group 2 HA binding antibody AF4H1K1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,69616
Polymers267,36810
Non-polymers1,3276
Water00
1
A: Hemagglutinin
D: Hemagglutinin
B: Hemagglutinin
E: Hemagglutinin
C: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,25412
Polymers168,9276
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33460 Å2
ΔGint-128 kcal/mol
Surface area56330 Å2
MethodPISA
2
I: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
J: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19930 Å2
MethodPISA
3
K: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
L: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-24 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.175, 140.940, 138.100
Angle α, β, γ (deg.)90.00, 95.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 35966.461 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09
#2: Protein Hemagglutinin


Mass: 20342.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09
#3: Antibody a group 2 HA binding antibody AF4H1K1 Fab heavy chain


Mass: 24977.014 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: 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.: 6
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: 4.14 Å3/Da / Density % sol: 70.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris pH6.5, 10% polyethylene glycol 10,000

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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 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 43204 / % possible obs: 99.8 % / Redundancy: 4 % / Net I/σ(I): 0.255
Reflection shellResolution: 3.8→3.94 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4301 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XL1

5xl1


Resolution: 3.8→49.212 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2774 2164 5.02 %
Rwork0.2355 --
obs0.2377 43072 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→49.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18231 0 84 0 18315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418741
X-RAY DIFFRACTIONf_angle_d0.75825412
X-RAY DIFFRACTIONf_dihedral_angle_d14.2826798
X-RAY DIFFRACTIONf_chiral_restr0.0342804
X-RAY DIFFRACTIONf_plane_restr0.0043336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7901-3.87820.33551280.31192605X-RAY DIFFRACTION95
3.8782-3.97520.40191360.35112733X-RAY DIFFRACTION99
3.9752-4.08260.31221550.27582718X-RAY DIFFRACTION100
4.0826-4.20270.30121390.26072726X-RAY DIFFRACTION100
4.2027-4.33820.27251280.23712757X-RAY DIFFRACTION100
4.3382-4.49320.28231770.2382690X-RAY DIFFRACTION100
4.4932-4.6730.25421600.22382708X-RAY DIFFRACTION100
4.673-4.88550.27841370.21742760X-RAY DIFFRACTION100
4.8855-5.14280.25111530.222736X-RAY DIFFRACTION100
5.1428-5.46460.2451470.21812744X-RAY DIFFRACTION100
5.4646-5.88590.28211390.23092744X-RAY DIFFRACTION100
5.8859-6.4770.28871470.22782757X-RAY DIFFRACTION100
6.477-7.41150.27181310.22062772X-RAY DIFFRACTION100
7.4115-9.32730.24641390.20272767X-RAY DIFFRACTION100
9.3273-49.21590.25261480.20932691X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 15.7004 Å / Origin y: -23.8604 Å / Origin z: 13.7179 Å
111213212223313233
T0.3511 Å2-0.0206 Å20.01 Å2-0.3446 Å20.0075 Å2--0.3127 Å2
L0.1988 °20.026 °20.0204 °2-0.3763 °2-0.0145 °2---0.0195 °2
S0.0521 Å °0.0168 Å °0.0467 Å °0.1247 Å °-0.0992 Å °0.0071 Å °0.0619 Å °0.0625 Å °-0.0014 Å °
Refinement TLS groupSelection details: all

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