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- PDB-4fqm: Structure of B/Brisbane/60/2008 Influenza Hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 4fqm
TitleStructure of B/Brisbane/60/2008 Influenza Hemagglutinin
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN / Influenza B Virus / Hemagglutinin
Function / homology
Function and homology information


host cell surface receptor binding / symbiont entry into host cell / 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
Haemagglutinin, influenzavirus 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, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Haemagglutinin, influenzavirus 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, 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 B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsDreyfus, C. / Laursen, N.S. / Wilson, I.A.
CitationJournal: Science / Year: 2012
Title: Highly conserved protective epitopes on influenza B viruses.
Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt ...Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt / Mohammed Lamrani / Hans J W M Korse / Eric Geelen / Özcan Sahin / Martijn Sieuwerts / Just P J Brakenhoff / Ronald Vogels / Olive T W Li / Leo L M Poon / Malik Peiris / Wouter Koudstaal / Andrew B Ward / Ian A Wilson / Jaap Goudsmit / Robert H E Friesen /
Abstract: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. ...Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,44558
Polymers341,78212
Non-polymers18,66246
Water0
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,50430
Polymers170,8916
Non-polymers9,61324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42030 Å2
ΔGint-53 kcal/mol
Surface area64020 Å2
MethodPISA
2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,94128
Polymers170,8916
Non-polymers9,04922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41400 Å2
ΔGint-60 kcal/mol
Surface area63750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.690, 242.540, 135.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:341 )
211chain 'C' and (resseq 1:341 )
311chain 'E' and (resseq 1:341 )
411chain 'G' and (resseq 1:341 )
511chain 'I' and (resseq 1:341 )
611chain 'K' and (resseq 1:341 )
112chain 'B' and (resseq 348:511 )
212chain 'D' and (resseq 348:511 )
312chain 'F' and (resseq 348:511 )
412chain 'H' and (resseq 348:511 )
512chain 'J' and (resseq 348:511 )
612chain 'L' and (resseq 348:511 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
Hemagglutinin HA1 / hemagglutinin receptor binding subunit HA1


Mass: 37699.113 Da / Num. of mol.: 6 / Fragment: UNP residues 16-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Brisbane/60/2008 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0LT38
#2: Protein
Hemagglutinin HA2 / hemagglutinin membrane fusion subunit HA2


Mass: 19264.588 Da / Num. of mol.: 6 / Fragment: UNP residues 363-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Brisbane/60/2008 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0LT38
#3: 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.: 16
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
#4: 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.: 13
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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17
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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% PEG3350, 160 mM sodium fluoride, 20 mM Tris, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97975 Å / Relative weight: 1
ReflectionResolution: 3.45→135.066 Å / Num. all: 60926 / Num. obs: 60737 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rsym value: 0.16 / Net I/σ(I): 11.6
Reflection shellResolution: 3.45→3.55 Å / Redundancy: 7.1 % / % possible all: 91.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RFT

2rft


Resolution: 3.45→49.066 Å / SU ML: 0.72 / σ(F): 1.99 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 1921 3.17 %
Rwork0.2573 --
obs0.2577 60657 99.61 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.363 Å2 / ksol: 0.265 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-24.1023 Å2-0 Å20 Å2
2---29.264 Å20 Å2
3---80.4014 Å2
Refinement stepCycle: LAST / Resolution: 3.45→49.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23220 0 1226 0 24446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124963
X-RAY DIFFRACTIONf_angle_d1.6133771
X-RAY DIFFRACTIONf_dihedral_angle_d15.7499444
X-RAY DIFFRACTIONf_chiral_restr0.0893988
X-RAY DIFFRACTIONf_plane_restr0.0094244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2588X-RAY DIFFRACTIONPOSITIONAL
12C2588X-RAY DIFFRACTIONPOSITIONAL0.393
13E2588X-RAY DIFFRACTIONPOSITIONAL0.38
14G2580X-RAY DIFFRACTIONPOSITIONAL0.439
15I2588X-RAY DIFFRACTIONPOSITIONAL0.395
16K2588X-RAY DIFFRACTIONPOSITIONAL0.39
21B1243X-RAY DIFFRACTIONPOSITIONAL
22D1243X-RAY DIFFRACTIONPOSITIONAL0.173
23F1243X-RAY DIFFRACTIONPOSITIONAL0.151
24H1243X-RAY DIFFRACTIONPOSITIONAL0.231
25J1243X-RAY DIFFRACTIONPOSITIONAL0.225
26L1243X-RAY DIFFRACTIONPOSITIONAL0.425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.53630.40991350.38094085X-RAY DIFFRACTION99
3.5363-3.63190.38661440.35464113X-RAY DIFFRACTION99
3.6319-3.73870.33221270.33214188X-RAY DIFFRACTION100
3.7387-3.85930.32141400.30714140X-RAY DIFFRACTION100
3.8593-3.99720.36211360.30024114X-RAY DIFFRACTION100
3.9972-4.15720.2851330.27064156X-RAY DIFFRACTION100
4.1572-4.34620.20911430.22984173X-RAY DIFFRACTION100
4.3462-4.57520.23881310.22584145X-RAY DIFFRACTION99
4.5752-4.86160.20421370.20314197X-RAY DIFFRACTION100
4.8616-5.23660.23731320.21314212X-RAY DIFFRACTION100
5.2366-5.76290.21041400.23294210X-RAY DIFFRACTION100
5.7629-6.59510.2541380.25214255X-RAY DIFFRACTION100
6.5951-8.30250.26471390.23754278X-RAY DIFFRACTION100
8.3025-49.07080.24891460.24724470X-RAY DIFFRACTION100
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)
11.11810.2428-0.60452.0171-0.67732.65160.0867-0.01950.37640.07590.16920.2519-0.21-0.1211-0.19130.3560.0889-0.00980.3003-0.01640.407635.7027278.7376134.9944
21.5074-0.1357-0.09591.69040.85911.0964-0.0112-0.76070.06361.62390.05310.3142-0.4113-0.33470.09591.83450.15160.1210.7919-0.11460.620634.2529267.9489187.5543
31.0434-0.04020.61791.6119-0.0142.6773-0.0642-0.0498-0.20390.00850.13210.30790.2247-0.149-0.02750.15710.0165-0.03940.28750.03230.503532.5626245.9465133.5819
41.2060.1971-0.3182.04450.11441.0687-0.0583-0.626-0.29721.4664-0.0661-0.19720.87240.04420.03311.44220.0606-0.090.59790.08880.552740.479247.7026186.9301
50.8079-0.1021-0.08552.37380.55843.28130.03070.04880.1350.16040.15-0.8202-0.07860.3297-0.09170.05080.0188-0.17960.396-0.15490.551562.5446259.5006134.368
61.2971-0.14980.54411.64050.14840.2007-0.2641-0.70110.22781.39010.032-0.3364-0.32780.17860.16341.38750.1211-0.30580.7711-0.10070.679754.9896263.3174187.4862
71.19770.1398-0.63551.6128-0.84652.8577-0.0175-0.1046-0.0428-0.08120.06850.50060.1549-0.416-0.01860.2260.0017-0.04260.42540.02490.713430.9365326.8775134.9738
81.69280.1559-0.18570.52130.43260.8193-0.2076-0.7255-0.42550.64510.00810.36430.6674-0.76120.30070.97460.08160.15191.16890.25740.824522.4678315.6507186.6755
91.67930.0705-0.91071.4907-0.03312.4794-0.0981-0.20150.19920.12970.2077-0.5623-0.1840.1647-0.0630.22820.0572-0.1220.456-0.08090.594459.7756339.0286145.1331
100.0074-1.0050.7788-0.27870.11420.79130.408-0.88970.59043.2331-0.30922.1143-0.2387-0.11180.01340.43880.3866-0.83351.09230.30930.030836.1445330.8521192.5028
110.9113-0.05890.00491.53120.30942.75690.0506-0.234-0.47190.00990.0761-0.13490.49560.2763-0.14560.37360.1262-0.03820.42380.10630.768156.3026306.6991140.5783
121.3422-0.0546-0.21121.4595-1.58180.1233-0.6045-0.9173-0.5241.19540.0807-0.27711.206-0.12980.12741.40270.44830.02671.04490.41450.800242.1793310.6809191.9714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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