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- PDB-6fyt: Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 6fyt
TitleStructure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38
Components
  • (Hemagglutinin) x 2
  • Single domain antibody SD38
KeywordsVIRAL PROTEIN / Influenza / single domain antibody / hemagglutinin
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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLaursen, N.S. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of HealthR56 AI117675 United States
National Institutes of HealthR56 AI127371 United States
CitationJournal: Science / Year: 2018
Title: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.
Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson /
Abstract: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.
History
DepositionMar 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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: Single domain antibody SD38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,68211
Polymers70,1493
Non-polymers3,5328
Water00
1
A: Hemagglutinin
B: Hemagglutinin
I: Single domain antibody SD38
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
I: Single domain antibody SD38
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
I: Single domain antibody SD38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,04533
Polymers210,4489
Non-polymers10,59724
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
Unit cell
Length a, b, c (Å)107.540, 107.540, 198.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 36764.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#2: Protein Hemagglutinin


Mass: 19956.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1

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Antibody , 1 types, 1 molecules I

#3: Antibody Single domain antibody SD38


Mass: 13429.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): expi293F / Production host: Homo sapiens (human)

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Sugars , 4 types, 8 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: 4.7 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 0.2 M calcium acetate, 10 % PEG800 and o.1 M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 31685 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 65 Å2 / CC1/2: 1 / Rpim(I) all: 0.06 / Rsym value: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3141 / CC1/2: 0.69 / Rpim(I) all: 0.53 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.268 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2007 6.34 %
Rwork0.1999 --
obs0.2021 31667 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4863 0 233 0 5096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035232
X-RAY DIFFRACTIONf_angle_d0.5937122
X-RAY DIFFRACTIONf_dihedral_angle_d13.1243094
X-RAY DIFFRACTIONf_chiral_restr0.042808
X-RAY DIFFRACTIONf_plane_restr0.004902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.87010.36481350.33222092X-RAY DIFFRACTION97
2.8701-2.94770.33331440.29652102X-RAY DIFFRACTION100
2.9477-3.03440.29871440.2712106X-RAY DIFFRACTION100
3.0344-3.13230.32791450.26062146X-RAY DIFFRACTION100
3.1323-3.24430.31611420.2672124X-RAY DIFFRACTION99
3.2443-3.37410.26031420.24882122X-RAY DIFFRACTION99
3.3741-3.52760.29591430.23342083X-RAY DIFFRACTION99
3.5276-3.71360.27631430.22592097X-RAY DIFFRACTION98
3.7136-3.94610.27571440.21762105X-RAY DIFFRACTION99
3.9461-4.25060.2181430.17282122X-RAY DIFFRACTION100
4.2506-4.6780.17071470.14462141X-RAY DIFFRACTION100
4.678-5.35410.16741440.14842132X-RAY DIFFRACTION100
5.3541-6.74250.21031480.18262130X-RAY DIFFRACTION100
6.7425-47.27510.19891430.17712158X-RAY DIFFRACTION99
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)
11.587-0.15030.27061.3003-0.99023.2831-0.08510.20.1123-0.276-0.0607-0.18430.44040.4172-0.03010.534-0.00480.09740.45870.04620.530617.823965.9509-43.6794
20.1127-0.2146-1.1244-0.5633-0.22444.59090.19180.0310.0377-0.23620.1435-0.2535-1.57850.8576-0.10760.7375-0.14020.05870.57130.0140.550520.996877.3393-1.7629
31.3358-0.3905-0.09942.211-0.72456.70790.130.2588-0.1516-0.40220.1571-0.3021-0.99540.5412-0.32990.6121-0.1037-0.00950.5076-0.13530.564818.815474.179313.3472
41.5844-0.94340.28682.1754-0.23273.5424-0.1947-0.07670.23140.23350.115-0.1193-0.39840.29030.0630.3783-0.0417-0.05390.3456-0.02820.524613.926479.289529.8416
52.5138-1.335-0.72082.2359-0.35363.64740.05010.0621-0.25040.0110.01250.3765-0.14310.1504-0.04010.313-0.0441-0.07630.3113-0.04920.49458.79774.69126.285
66.25422.2655-0.35343.62960.89863.0668-0.21310.37640.3827-0.37650.16-0.6899-1.77890.55830.14421.0078-0.1018-0.02720.56280.0380.629221.714977.9551-3.5208
71.5767-0.2661.28370.4665-1.59337.2136-0.5006-0.6329-0.00540.1599-0.04170.2518-1.0841-0.55950.43230.48940.171-0.06580.69340.01420.508715.606469.5283-19.7559
82.18930.46920.12763.5905-0.84811.3565-0.05140.20760.1162-0.37180.0214-0.1103-0.33290.2114-0.04480.4086-0.0275-0.01980.46950.0670.431212.282674.264-44.5901
90.18690.0418-1.06930.9231-1.82145.4572-0.08070.0891-0.0164-0.10890.0193-0.060.1461-0.00660.11090.3496-0.05090.00630.45810.06310.49137.108764.7836-27.4506
102.75280.60841.00152.13370.19973.4938-0.30140.70770.0566-1.17970.66810.1854-0.9901-0.5856-0.3581.0637-0.05520.01681.00920.17140.57078.821676.6362-70.5152
112.28351.03450.34583.78540.15611.9139-0.21480.16530.0129-0.34580.2122-0.1962-0.21310.15280.04220.6495-0.0439-0.03810.60210.12650.555520.4034100.0579-49.1988
122.13430.5028-1.1824.1687-0.31952.488-0.0862-0.2753-0.05190.24020.0392-0.0288-0.43840.44270.04370.668-0.1053-0.07340.63240.08820.504416.3352101.2204-40.3977
132.63530.4672-0.49133.19830.36610.9636-0.1681-0.42330.27420.19290.1919-0.0697-0.7750.55060.15860.7874-0.1297-0.08580.56350.01780.54419.8597110.1497-42.9724
140.63471.25480.86664.21160.61140.69020.0107-0.0101-0.0450.5455-0.1051-0.5124-0.01080.15080.08090.5931-0.1205-0.06360.57450.12430.612719.690989.5214-40.7267
155.1451-0.1859-0.16860.0906-0.6835.15640.35270.04030.1011-0.10060.2865-1.095-0.7932-0.1357-0.48430.784-0.1448-0.16740.52210.08770.645329.4775112.9752-42.954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 266 )
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 284 )
7X-RAY DIFFRACTION7chain 'A' and (resid 285 through 324 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 62 )
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 137 )
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 173 )
11X-RAY DIFFRACTION11chain 'I' and (resid 1 through 32 )
12X-RAY DIFFRACTION12chain 'I' and (resid 33 through 76 )
13X-RAY DIFFRACTION13chain 'I' and (resid 77 through 87 )
14X-RAY DIFFRACTION14chain 'I' and (resid 88 through 106 )
15X-RAY DIFFRACTION15chain 'I' and (resid 107 through 113 )

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