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- PDB-5w6g: Human antibody 6649 in complex with influenza hemagglutinin H1 So... -

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Basic information

Entry
Database: PDB / ID: 5w6g
TitleHuman antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
Components
  • (6649 antibody ...) x 2
  • (Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / FAB / Influenza H1N1 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / viral budding from plasma membrane / antigen binding / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / immune response / apical plasma membrane / fusion of virus membrane with host plasma membrane ...immunoglobulin complex / immunoglobulin mediated immune response / viral budding from plasma membrane / antigen binding / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / immune response / 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 / extracellular space / plasma 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsRaymond, D.D. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody.
Authors: Raymond, D.D. / Bajic, G. / Ferdman, J. / Suphaphiphat, P. / Settembre, E.C. / Moody, M.A. / Schmidt, A.G. / Harrison, S.C.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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.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 / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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 HA1
B: Hemagglutinin HA2
H: 6649 antibody heavy chain
L: 6649 antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,35917
Polymers105,2894
Non-polymers2,07013
Water19811
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: 6649 antibody heavy chain
L: 6649 antibody light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: 6649 antibody heavy chain
L: 6649 antibody light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: 6649 antibody heavy chain
L: 6649 antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,07851
Polymers315,86812
Non-polymers6,20939
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area54800 Å2
ΔGint-422 kcal/mol
Surface area117530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.310, 177.310, 177.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1


Mass: 37239.723 Da / Num. of mol.: 1 / Fragment: UNP residues 18-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0
#2: Protein Hemagglutinin HA2


Mass: 20356.586 Da / Num. of mol.: 1 / Fragment: UNP residues 344-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0

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Antibody , 2 types, 2 molecules HL

#3: Antibody 6649 antibody heavy chain


Mass: 24791.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B2B6
#4: Antibody 6649 antibody light chain


Mass: 22901.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4

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Sugars , 2 types, 5 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: 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-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, 19 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 4.53 Å3/Da / Density % sol: 72.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: 1.9 M ammonium sulfate, 0.1 M of HEPES, pH 7

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.999976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2016
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999976 Å / Relative weight: 1
ReflectionResolution: 2.79→49.18 Å / Num. obs: 46038 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 14.323 % / Biso Wilson estimate: 90.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.229 / Rrim(I) all: 0.237 / Χ2: 0.985 / Net I/σ(I): 12.04 / Num. measured all: 659405 / Scaling rejects: 654
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.79-2.9611.4083.8680.7271670.3644.04796.1
2.96-3.1715.0092.1951.5471630.6952.272100
3.17-3.4215.141.063.2363950.8811.09699.9
3.42-3.7415.1260.5036.5358700.9650.52199.9
3.74-4.1815.0320.24812.2754460.990.25699.8
4.18-4.8214.8290.12421.1947870.9970.12899.8
4.82-5.8914.7210.09825.5740940.9980.101100
5.89-8.2814.1410.06932.4832300.9990.072100
8.28-49.1813.6490.03753.818860.9990.03899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5UGY & 3H42

5ugy

3h42


Resolution: 2.79→49.18 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.404 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.381 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.282
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2291 4.98 %RANDOM
Rwork0.218 ---
obs0.22 46038 99.3 %-
Displacement parametersBiso max: 192.77 Å2 / Biso mean: 85.96 Å2 / Biso min: 38.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.79→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 0 126 11 7347
Biso mean--118.94 59.89 -
Num. residues----933
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2520SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes179HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1088HARMONIC5
X-RAY DIFFRACTIONt_it7525HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion988SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8115SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7525HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10250HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion21.07
LS refinement shellResolution: 2.79→2.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 148 4.8 %
Rwork0.252 2933 -
all0.254 3081 -
obs--91.42 %

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