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- PDB-3sdy: Crystal Structure of Broadly Neutralizing Antibody CR8020 Bound t... -

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Basic information

Entry
Database: PDB / ID: 3sdy
TitleCrystal Structure of Broadly Neutralizing Antibody CR8020 Bound to the Influenza A H3 Hemagglutinin
Components
  • (Antibody CR8020, ...) x 2
  • (Hemagglutinin ...) x 2
KeywordsViral Protein/Immune System / Viral fusion protein / immunoglobulin / Virus attachment and entry / immune recognition / Viral Protein-Immune System complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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
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 / Immunoglobulins ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: Science / Year: 2011
Title: A highly conserved neutralizing epitope on group 2 influenza A viruses.
Authors: Ekiert, D.C. / Friesen, R.H. / Bhabha, G. / Kwaks, T. / Jongeneelen, M. / Yu, W. / Ophorst, C. / Cox, F. / Korse, H.J. / Brandenburg, B. / Vogels, R. / Brakenhoff, J.P. / Kompier, R. / ...Authors: Ekiert, D.C. / Friesen, R.H. / Bhabha, G. / Kwaks, T. / Jongeneelen, M. / Yu, W. / Ophorst, C. / Cox, F. / Korse, H.J. / Brandenburg, B. / Vogels, R. / Brakenhoff, J.P. / Kompier, R. / Koldijk, M.H. / Cornelissen, L.A. / Poon, L.L. / Peiris, M. / Koudstaal, W. / Wilson, I.A. / Goudsmit, J.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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_chiral / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _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_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Apr 7, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 3.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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
H: Antibody CR8020, Heavy Chain
L: Antibody CR8020, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,30219
Polymers103,6304
Non-polymers4,67215
Water00
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: Antibody CR8020, Heavy Chain
L: Antibody CR8020, Light Chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: Antibody CR8020, Heavy Chain
L: Antibody CR8020, Light Chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: Antibody CR8020, Heavy Chain
L: Antibody CR8020, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,90557
Polymers310,88912
Non-polymers14,01645
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area64550 Å2
ΔGint-396 kcal/mol
Surface area117540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.750, 197.750, 197.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 chain


Mass: 35506.949 Da / Num. of mol.: 1 / Fragment: UNP residues 27-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968(H3N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2 chain


Mass: 20197.312 Da / Num. of mol.: 1 / Fragment: UNP residues 346-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968(H3N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7

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Antibody , 2 types, 2 molecules HL

#3: Antibody Antibody CR8020, Heavy Chain


Mass: 24344.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin heavy chain locus (IGH) / Cell line (production host): PER.C6 / Production host: Homo sapiens (human)
#4: Antibody Antibody CR8020, Light Chain


Mass: 23581.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin kappa chain locus (IGK) / Cell line (production host): PER.C6 / Production host: Homo sapiens (human)

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Sugars , 5 types, 5 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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
#9: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 1 types, 10 molecules

#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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Details

Has protein modificationY
Sequence detailsAS PER THE AUTHORS GLY IS THE CORRECT RESIDUE AT THIS POSITION

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 1.8M ammonium sulfate, 100mM sodium acetate 5.4, and 50mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 60262 / Num. obs: 60239 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Rsym value: 0.15 / Net I/σ(I): 27.7
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 20.9 % / Rsym value: 0.9969 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→46.61 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2661 5.02 %
Rwork0.2015 --
obs0.2031 53055 88.12 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.133 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.85→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 298 0 7465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097890
X-RAY DIFFRACTIONf_angle_d1.03910402
X-RAY DIFFRACTIONf_dihedral_angle_d22.6932854
X-RAY DIFFRACTIONf_chiral_restr0.1111197
X-RAY DIFFRACTIONf_plane_restr0.0041302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.90190.47751160.41971878X-RAY DIFFRACTION63
2.9019-2.95770.41031000.37182030X-RAY DIFFRACTION69
2.9577-3.01810.44021010.35532184X-RAY DIFFRACTION73
3.0181-3.08370.33641060.33322292X-RAY DIFFRACTION75
3.0837-3.15540.33411480.30522375X-RAY DIFFRACTION81
3.1554-3.23430.32591200.30852503X-RAY DIFFRACTION84
3.2343-3.32180.32891560.28222604X-RAY DIFFRACTION87
3.3218-3.41950.29881470.25942655X-RAY DIFFRACTION89
3.4195-3.52980.26271330.24592706X-RAY DIFFRACTION90
3.5298-3.65590.27291330.21332741X-RAY DIFFRACTION92
3.6559-3.80220.2751580.20172809X-RAY DIFFRACTION93
3.8022-3.97520.21381390.1792757X-RAY DIFFRACTION92
3.9752-4.18460.19581440.16372857X-RAY DIFFRACTION95
4.1846-4.44660.19511500.14382904X-RAY DIFFRACTION97
4.4466-4.78960.18181500.14332933X-RAY DIFFRACTION97
4.7896-5.27110.17241550.15192981X-RAY DIFFRACTION98
5.2711-6.03240.22281700.1892982X-RAY DIFFRACTION99
6.0324-7.59490.22581780.1853045X-RAY DIFFRACTION100
7.5949-46.61630.19711570.19493158X-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)
10.5247-0.10630.27720.14630.15270.69930.14970.2168-0.2787-0.0738-0.04570.03190.1555-0.0073-0.0010.64840.13750.04790.4734-0.05570.66216.099512.1411-10.3392
20.74270.0270.02610.5178-0.16030.6192-0.08520.03810.1428-0.11270.0343-0.1657-0.23520.1689-0.0040.41920.10980.17710.32190.13460.41440.154641.231825.3435
30.2203-0.06320.18110.0821-0.24431.49290.16290.09960.61950.29010.24240.1786-0.9965-0.13-0.24390.73130.05930.27090.4080.19540.892549.110470.76058.8243
40.0674-0.31020.19181.2633-0.68780.5244-0.0630.7441-0.1270.15330.17690.7054-0.0809-0.6514-0.01180.3811-0.2622-0.02171.29970.14320.899651.136971.7286-25.5101
50.87770.2225-1.45080.0939-0.29633.0493-0.0568-0.0255-0.4693-0.28430.287-0.32950.22570.4367-0.16680.5622-0.00290.11140.49640.09020.723960.534952.5792.8312
60.4085-0.19930.05120.18140.06370.12040.26650.69220.0937-0.0668-0.12870.2045-0.0308-0.27330.08290.1148-0.40720.14341.12570.44450.633967.172568.8433-28.9747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain H and resid 1:102
4X-RAY DIFFRACTION4chain H and resid 103:215
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:214

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