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- PDB-4nm8: Crystal structure of broadly neutralizing antibody CR8043 bound t... -

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Basic information

Entry
Database: PDB / ID: 4nm8
TitleCrystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin
Components
  • (Antibody CR8043, ...) x 2
  • (Hemagglutinin ...) x 2
Keywordsviral protein/immune system / Viral fusion protein / immunoglobulin / virus attachment and entry / immune recognition / viral protein-immune system complex / Immunoglobulin'
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / viral budding from plasma membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / host cell surface receptor binding / immune response / 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 / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
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 ...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 / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Immunoglobulin kappa constant / Immunoglobulin kappa light chain / Ig-like domain-containing protein / Hemagglutinin / IgG H chain
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.0041 Å
AuthorsLee, P.S. / Wilson, I.A.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: A common solution to group 2 influenza virus neutralization.
Authors: Robert H E Friesen / Peter S Lee / Esther J M Stoop / Ryan M B Hoffman / Damian C Ekiert / Gira Bhabha / Wenli Yu / Jarek Juraszek / Wouter Koudstaal / Mandy Jongeneelen / Hans J W M Korse / ...Authors: Robert H E Friesen / Peter S Lee / Esther J M Stoop / Ryan M B Hoffman / Damian C Ekiert / Gira Bhabha / Wenli Yu / Jarek Juraszek / Wouter Koudstaal / Mandy Jongeneelen / Hans J W M Korse / Carla Ophorst / Els C M Brinkman-van der Linden / Mark Throsby / Mark J Kwakkenbos / Arjen Q Bakker / Tim Beaumont / Hergen Spits / Ted Kwaks / Ronald Vogels / Andrew B Ward / Jaap Goudsmit / Ian A Wilson /
Abstract: The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the ...The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the design of universal influenza vaccines. Only one human bnAb (CR8020) specifically recognizing group 2 influenza A viruses has been previously characterized that binds to a highly conserved epitope at the base of the hemagglutinin (HA) stem and has neutralizing activity against H3, H7, and H10 viruses. Here, we report a second group 2 bnAb, CR8043, which was derived from a different germ-line gene encoding a highly divergent amino acid sequence. CR8043 has in vitro neutralizing activity against H3 and H10 viruses and protects mice against challenge with a lethal dose of H3N2 and H7N7 viruses. The crystal structure and EM reconstructions of the CR8043-H3 HA complex revealed that CR8043 binds to a site similar to the CR8020 epitope but uses an alternative angle of approach and a distinct set of interactions. The identification of another antibody against the group 2 stem epitope suggests that this conserved site of vulnerability has great potential for design of therapeutics and vaccines.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.3Dec 6, 2017Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.content_type / _pdbx_database_related.db_id
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 / 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 / _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_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_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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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 Chain
B: Hemagglutinin HA2 Chain
C: Hemagglutinin HA1 Chain
D: Hemagglutinin HA2 Chain
E: Hemagglutinin HA1 Chain
F: Hemagglutinin HA2 Chain
L: Antibody CR8043, Light Chain
H: Antibody CR8043, Heavy Chain
M: Antibody CR8043, Light Chain
I: Antibody CR8043, Heavy Chain
N: Antibody CR8043, Light Chain
J: Antibody CR8043, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,37626
Polymers314,06012
Non-polymers4,31614
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)241.491, 142.355, 170.725
Angle α, β, γ (deg.)90.00, 133.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 Chain


Mass: 35506.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2 Chain


Mass: 20197.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7

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Antibody , 2 types, 6 molecules LMNHIJ

#3: Antibody Antibody CR8043, Light Chain / Immunoglobulin kappa light chain EU


Mass: 24228.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DOX7, UniProt: P01834*PLUS
#4: Antibody Antibody CR8043, Heavy Chain


Mass: 24753.713 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686I15212, DKFZp686P15220 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6N089, UniProt: S6C4S0*PLUS

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Sugars , 2 types, 14 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: 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.: 8
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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5, 3% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 34622 / Num. obs: 34622 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 92.5 Å2 / Rmerge(I) obs: 0.201 / Rsym value: 0.201 / Net I/σ(I): 6.4
Reflection shellResolution: 4→4.2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4271 / Rsym value: 0.826 / % possible all: 90.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FNK, 4NM4

4fnk

4nm4


Resolution: 4.0041→43.821 Å / SU ML: 0.55 / σ(F): 1.99 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 1730 5.01 %RANDOM
Rwork0.2397 ---
obs0.2423 34531 97.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.0041→43.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21392 0 280 0 21672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622207
X-RAY DIFFRACTIONf_angle_d1.22730148
X-RAY DIFFRACTIONf_dihedral_angle_d16.2768067
X-RAY DIFFRACTIONf_chiral_restr0.0783378
X-RAY DIFFRACTIONf_plane_restr0.0063860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0041-4.12180.33861410.29622365X-RAY DIFFRACTION85
4.1218-4.25480.31011360.26812767X-RAY DIFFRACTION99
4.2548-4.40670.3071420.25082774X-RAY DIFFRACTION99
4.4067-4.5830.28941520.23812708X-RAY DIFFRACTION98
4.583-4.79130.27741430.23732739X-RAY DIFFRACTION97
4.7913-5.04360.27371450.23542799X-RAY DIFFRACTION100
5.0436-5.35910.28961290.22462784X-RAY DIFFRACTION99
5.3591-5.7720.27721400.23522776X-RAY DIFFRACTION99
5.772-6.35130.32231240.24122753X-RAY DIFFRACTION98
6.3513-7.26670.31031580.24422800X-RAY DIFFRACTION100
7.2667-9.14160.27611690.22312746X-RAY DIFFRACTION98
9.1416-43.82370.28721510.23662790X-RAY DIFFRACTION97
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)
10.2559-0.1296-0.04280.5955-0.06950.5536-0.05850.04940.05590.02330.0035-0.2257-0.03370.19540.01930.1626-0.0617-0.00260.2801-0.01380.37979.930910.093241.1245
21.1024-0.3210.14350.8778-0.24741.1807-0.05230.28710.3905-0.2744-0.0278-0.0283-0.2659-0.10790.04310.42470.0879-0.17710.25730.01530.3722-28.679753.847937.2112
31.10240.26940.35650.65220.50560.4148-0.15070.57380.9215-0.22420.2584-0.2219-0.94830.0431-0.08921.5198-0.2449-0.03350.72010.30421.4158-20.178985.453326.9066
40.7092-0.1282-0.23790.68610.31030.87840.0271-0.27510.1150.27620.07730.1479-0.06720.00630.02460.48790.12480.17310.33220.02090.2369-27.4465-7.318582.4404
50.9357-0.0727-0.22860.2883-0.13370.2273-0.0078-0.9948-0.02960.8913-0.296-0.28880.3940.24330.26871.69780.1798-0.25141.47380.05630.6472-18.173-13.9497114.7687
61.22750.3815-0.19452.0885-0.3960.6185-0.04530.1503-0.2671-0.2715-0.0342-0.04190.4331-0.24750.02410.3633-0.1823-0.01070.3778-0.03010.3522-29.5611-15.9576.5667
70.5118-0.0549-0.18530.3623-0.10480.3854-0.01190.4195-0.7242-0.2388-0.0560.30940.78590.32090.0851.75480.0470.36951.041-0.54041.2374-21.8725-40.6146-16.1887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain E or chain F
2X-RAY DIFFRACTION2chain H and resid 1:121 or chain L and resid 1:114
3X-RAY DIFFRACTION3chain H and resid 122:213 or chain L and resid 115:211
4X-RAY DIFFRACTION4chain I and resid 1:121 or chain M and resid 1:114
5X-RAY DIFFRACTION5chain I and resid 122:213 or chain M and resid 115:211
6X-RAY DIFFRACTION6chain J and resid 1:121 or chain N and resid 1:114
7X-RAY DIFFRACTION7chain J and resid 122:213 or chain N and resid 115:211

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