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- PDB-6a4k: Human antibody 32D6 Fab in complex with H1N1 influenza A virus HA1 -

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Basic information

Entry
Database: PDB / ID: 6a4k
TitleHuman antibody 32D6 Fab in complex with H1N1 influenza A virus HA1
Components
  • (immunoglobulin Fab ...) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody Fab / influenza hemagglutinin / complex structure / specific binding / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 (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 ...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
ACETATE ION / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsLee, C.C. / Ko, T.P. / Lin, L.L. / Wang, A.H.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Sci Rep / Year: 2019
Title: An Effective Neutralizing Antibody Against Influenza Virus H1N1 from Human B Cells.
Authors: Lee, C.C. / Yang, C.Y. / Lin, L.L. / Ko, T.P. / Chang, A.H. / Chang, S.S. / Wang, A.H.
History
DepositionJun 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
H: immunoglobulin Fab heavy chain
L: immunoglobulin Fab light chain
B: Hemagglutinin
I: immunoglobulin Fab heavy chain
M: immunoglobulin Fab light chain
C: Hemagglutinin
J: immunoglobulin Fab heavy chain
N: immunoglobulin Fab light chain
D: Hemagglutinin
K: immunoglobulin Fab heavy chain
O: immunoglobulin Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,09323
Polymers299,89012
Non-polymers1,20311
Water3,513195
1
A: Hemagglutinin
H: immunoglobulin Fab heavy chain
L: immunoglobulin Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2345
Polymers74,9723
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin
I: immunoglobulin Fab heavy chain
M: immunoglobulin Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2936
Polymers74,9723
Non-polymers3203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hemagglutinin
J: immunoglobulin Fab heavy chain
N: immunoglobulin Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2345
Polymers74,9723
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hemagglutinin
K: immunoglobulin Fab heavy chain
O: immunoglobulin Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3337
Polymers74,9723
Non-polymers3604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.743, 181.743, 248.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11O-301-

CA

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Components

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Antibody , 2 types, 8 molecules HIJKLMNO

#2: Antibody
immunoglobulin Fab heavy chain


Mass: 25556.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody
immunoglobulin Fab light chain


Mass: 23007.432 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Hemagglutinin


Mass: 26408.572 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/7/2009(H1N1))
Production host: Homo sapiens (human) / References: UniProt: C3W5X2*PLUS
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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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Non-polymers , 3 types, 202 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE EUROPEAN NUCLEOTIDE ARCHIVE ACCESSION NUMBER IS ACP41953.1 FOR THE HA CHAINS.

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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: 3.94 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14%(w/v) PEG 8000, 160mM Calcium acetate, 20%(v/v) glycerol, 80mM Sodium Cacodylate, Hydrochloric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2017
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. obs: 79824 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.7
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7965 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBN, 3N9G

3gbn

3n9g


Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 17.413 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23287 3824 5 %RANDOM
Rwork0.17511 ---
obs0.17792 72829 94.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.545 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20354 0 69 195 20618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920982
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218640
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9528580
X-RAY DIFFRACTIONr_angle_other_deg0.972343550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03652661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96524.074810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.646153285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0431580
X-RAY DIFFRACTIONr_chiral_restr0.0820.23171
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02123323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024217
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_it4.9088.60310682
X-RAY DIFFRACTIONr_mcbond_other4.9058.60310679
X-RAY DIFFRACTIONr_mcangle_it8.07912.88513329
X-RAY DIFFRACTIONr_mcangle_other8.07812.88613330
X-RAY DIFFRACTIONr_scbond_it4.4728.38110300
X-RAY DIFFRACTIONr_scbond_other4.4728.38110301
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.54712.5715252
X-RAY DIFFRACTIONr_long_range_B_refined11.42293.93922284
X-RAY DIFFRACTIONr_long_range_B_other11.42493.95522278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 238 -
Rwork0.275 3626 -
obs--66.28 %

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