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- PDB-4fqk: Influenza B/Brisbane/60/2008 hemagglutinin Fab CR8059 complex -

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Basic information

Entry
Database: PDB / ID: 4fqk
TitleInfluenza B/Brisbane/60/2008 hemagglutinin Fab CR8059 complex
Components
  • (Antibody CR8059 ...) x 2
  • (Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / Fab fragment / monoclonal / immunoglobulin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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
Haemagglutinin, influenzavirus B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.65 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: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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_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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Antibody CR8059 Heavy Chain
F: Antibody CR8059 Light Chain
H: Antibody CR8059 Heavy Chain
L: Antibody CR8059 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,99318
Polymers210,8318
Non-polymers4,16210
Water00
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR8059 Heavy Chain
L: Antibody CR8059 Light Chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR8059 Heavy Chain
L: Antibody CR8059 Light Chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR8059 Heavy Chain
L: Antibody CR8059 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,48927
Polymers316,24712
Non-polymers6,24315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Antibody CR8059 Heavy Chain
F: Antibody CR8059 Light Chain
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Antibody CR8059 Heavy Chain
F: Antibody CR8059 Light Chain
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Antibody CR8059 Heavy Chain
F: Antibody CR8059 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,48927
Polymers316,24712
Non-polymers6,24315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)189.200, 189.200, 319.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:6 or resseq 10:340 )
211chain 'C' and (resseq 1:6 or resseq 10:340 )
112chain 'L' and (resseq 3:7 or resseq 10:110 or resseq 113:115 or resseq 121:215 )
212chain 'F' and (resseq 3:7 or resseq 10:110 or resseq 113:115 or resseq 121:215 )
113chain 'B' and (resseq 368:459 or resseq 463:513 )
213chain 'D' and (resseq 368:459 or resseq 463:513 )
114chain 'H' and (resseq 2:99 )
214chain 'E' and (resseq 2:99 )

NCS ensembles :
ID
1
2
3
4

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Components

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Hemagglutinin ... , 2 types, 4 molecules ACBD

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


Mass: 37699.113 Da / Num. of mol.: 2 / 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.: 2 / 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

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Antibody , 2 types, 4 molecules EHFL

#3: Antibody Antibody CR8059 Heavy Chain


Mass: 25345.338 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Antibody CR8059 Light Chain


Mass: 23106.467 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 3 types, 10 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.: 6
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.: 2
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 / 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.: 2
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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Details

Has protein modificationY

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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: 5.22 Å3/Da / Density % sol: 76.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 5.65→50 Å / Num. all: 12751 / Num. obs: 12751 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 5.65→5.8 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.86 / % possible all: 99.8

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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 ENTRIES 4FQM AND 4FQJ

4fqm

4fqj


Resolution: 5.65→48.932 Å / SU ML: 2.25 / σ(F): 2 / Phase error: 35.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1269 9.98 %RANDOM
Rwork0.3061 ---
obs0.3079 12713 99.59 %-
all-13982 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.621 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-219.4109 Å2-0 Å20 Å2
2--219.4109 Å20 Å2
3---269.9402 Å2
Refinement stepCycle: LAST / Resolution: 5.65→48.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13806 0 274 0 14080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514401
X-RAY DIFFRACTIONf_angle_d1.58719527
X-RAY DIFFRACTIONf_dihedral_angle_d15.2865275
X-RAY DIFFRACTIONf_chiral_restr0.0882246
X-RAY DIFFRACTIONf_plane_restr0.0092473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2555X-RAY DIFFRACTIONPOSITIONAL
12C2555X-RAY DIFFRACTIONPOSITIONAL0.041
21L1528X-RAY DIFFRACTIONPOSITIONAL
22F1528X-RAY DIFFRACTIONPOSITIONAL0.039
31B1043X-RAY DIFFRACTIONPOSITIONAL
32D1043X-RAY DIFFRACTIONPOSITIONAL0.155
41H797X-RAY DIFFRACTIONPOSITIONAL
42E797X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.65-5.87630.37621430.35471286X-RAY DIFFRACTION100
5.8763-6.14330.29631330.33851258X-RAY DIFFRACTION100
6.1433-6.46650.34641440.33471274X-RAY DIFFRACTION100
6.4665-6.87060.33921450.34351292X-RAY DIFFRACTION100
6.8706-7.39940.37961360.30881262X-RAY DIFFRACTION100
7.3994-8.1410.29071420.30471279X-RAY DIFFRACTION100
8.141-9.3120.28021440.26281272X-RAY DIFFRACTION100
9.312-11.70550.24131470.24791267X-RAY DIFFRACTION99
11.7055-48.93340.40851350.34881254X-RAY DIFFRACTION98

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