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- PDB-5gjs: Crystal structure of H1 hemagglutinin from A/California/04/2009 i... -

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Basic information

Entry
Database: PDB / ID: 5gjs
TitleCrystal structure of H1 hemagglutinin from A/California/04/2009 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 / 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: 2.9 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 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 / diffrn_radiation_wavelength / 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 / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _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.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

Downloads & links

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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)105,1606
Polymers104,5144
Non-polymers6462
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)315,47918
Polymers313,54212
Non-polymers1,9376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area47310 Å2
ΔGint-261 kcal/mol
Surface area110860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.162, 130.162, 365.853
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 36525.242 Da / Num. of mol.: 1 / Fragment: UNP residues 18-344 / Mutation: G212C, R227C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: HA / Plasmid: pFast-HTB / Production host: Baculovirus expression vector pFastBac1-HM / Strain (production host): Sf9 / References: UniProt: C3W5S1
#2: Protein Hemagglutinin /


Mass: 20842.113 Da / Num. of mol.: 1 / Fragment: neutralizing antibody 3E1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: HA / Plasmid: pFast-HTB / Production host: Baculovirus expression vector pFastBac1-HM / Strain (production host): Sf9 / References: UniProt: C3W5S1

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Antibody , 2 types, 2 molecules LH

#3: Antibody light chain of human neutralizing antibody 3E1


Mass: 23483.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AbVec-hIgKappa2 / Production host: Cloning vector AbVec-hIgKappa (others)
#4: Antibody heavy chain of human neutralizing antibody 3E1


Mass: 23663.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AbVec-hIgG1 / Production host: Cloning vector AbVec-hIgG1 (others)

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Sugars , 2 types, 2 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.: 1 / Source method: obtained synthetically
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-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES and 16% PEG 550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25201 / % possible obs: 93.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
REFMAC5.8.0135refinement
Cootmodel building
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZJ, 3NFS

3lzj

3nfs


Resolution: 2.9→47.98 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.814 / SU B: 48.675 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Details: U VALUES : WITH TLS ADDED,
RfactorNum. reflection% reflectionSelection details
Rfree0.3035 1238 5 %RANDOM
Rwork0.2509 ---
obs0.2536 23695 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.37 Å2 / Biso mean: 51.878 Å2 / Biso min: 20.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 2.9→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 42 0 7070
Biso mean--73.75 --
Num. residues----905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197245
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.959841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2924.723307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.583151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6021525
X-RAY DIFFRACTIONr_chiral_restr0.0830.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215424
X-RAY DIFFRACTIONr_mcbond_it3.1474.5763606
X-RAY DIFFRACTIONr_mcangle_it4.9916.8464483
X-RAY DIFFRACTIONr_scbond_it4.164.8023639
LS refinement shellResolution: 2.901→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 98 -
Rwork0.281 1859 -
all-1957 -
obs--99.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0029-0.00750.00210.0251-0.02340.2174-0.00550.00160.0029-0.0047-0.0066-0.02060.01420.01020.0120.04130.00080.02550.0569-0.01470.049515.547662.8515-76.6803
20.0082-0.01240.01580.0546-0.00670.2543-0.0157-0.00520.00060.03050.06790.0052-0.01750.0037-0.05210.07550.021-0.01490.09420.01010.020310.546368.2211-24.1083
30.1086-0.0671-0.0410.30.06210.0217-0.00610.0028-0.0240.00920.0048-0.0063-0.00390.00190.00130.04480.013-0.02870.0453-0.01930.044531.068428.909-38.907
40.1915-0.1829-0.14650.20330.14170.139-0.0287-0.012200.03840.0083-0.043-0.00510.01380.02040.03420.0025-0.04870.03930.00080.093540.279237.8688-24.9507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 333
2X-RAY DIFFRACTION2B4 - 171
3X-RAY DIFFRACTION3L1 - 212
4X-RAY DIFFRACTION4H1 - 221

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