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- PDB-6ur5: Resurfaced influenza hemagglutinin in complex with a broadly neut... -

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Basic information

Entry
Database: PDB / ID: 6ur5
TitleResurfaced influenza hemagglutinin in complex with a broadly neutralizing antibody
Components
  • Antibody heavy chain
  • Antibody light chain
  • Influenza hemagglutinin HA1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / VIRAL PROTEIN / 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 / 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 (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 ...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 speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBajic, G. / Schmidt, A.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI89618-A1 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structure-Guided Molecular Grafting of a Complex Broadly Neutralizing Viral Epitope.
Authors: Bajic, G. / Maron, M.J. / Caradonna, T.M. / Tian, M. / Mermelstein, A. / Fera, D. / Kelsoe, G. / Kuraoka, M. / Schmidt, A.G.
History
DepositionOct 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 / _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
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Antibody heavy chain
B: Antibody light chain
C: Influenza hemagglutinin HA1
D: Influenza hemagglutinin HA1
G: Antibody heavy chain
H: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,4149
Polymers163,4026
Non-polymers2,0123
Water00
1
A: Antibody heavy chain
B: Antibody light chain
C: Influenza hemagglutinin HA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5804
Polymers81,7013
Non-polymers8791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Influenza hemagglutinin HA1
G: Antibody heavy chain
H: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8345
Polymers81,7013
Non-polymers1,1332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.270, 141.470, 166.870
Angle α, β, γ (deg.)90.000, 102.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules AGBH

#1: Antibody Antibody heavy chain


Mass: 26690.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody light chain


Mass: 22562.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 3 molecules CD

#3: Protein Influenza hemagglutinin HA1


Mass: 32447.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Homo sapiens (human) / References: UniProt: M1UPL4*PLUS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4[LFucpa1-6]DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3/a4-b1_a6-e1_b4-c1_b6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}[(6+1)][a-L-Fucp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4[LFucpa1-6]DGlcpNAcb1-4[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]/1-1-2-3-4-4/a4-b1_a6-f1_b4-c1_b6-e1_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]{}}[(6+1)][a-L-Fucp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate (pH 4.5), 20% (wt/vol) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 4→48.59 Å / Num. obs: 17321 / % possible obs: 97.5 % / Redundancy: 3.642 % / Biso Wilson estimate: 51.275 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.29 / Rrim(I) all: 0.34 / Χ2: 0.88 / Net I/σ(I): 4.51 / Num. measured all: 63077 / Scaling rejects: 230
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
4-4.23.2840.7341.677101241421620.5690.87589.6
4.2-4.33.7760.5752.343829101910140.7680.67399.5
4.3-4.43.8080.5052.7236149539490.8020.5999.6
4.4-4.53.7050.4043.1631018408370.8640.47299.6
4.5-53.7510.3533.7112580338733540.8910.41399
5-63.7230.316414146384038000.9050.36999
6-83.6630.284.5710959303729920.9360.32898.5
8-103.4560.1129.353701109810710.9850.13397.5
10-153.5440.07913.0428358218000.9940.09297.4
15-203.6090.07813.657292082020.9920.09197.1
20-303.510.0617.353651071040.9980.06997.2
30-403.3850.04718.038827260.9950.05496.3
40-462.6250.0418.7921780.9990.05100
46-48.5940.04121.7481420.04814.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA0

1ha0


Resolution: 4→48.59 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3218 992 5.73 %
Rwork0.2997 16322 -
obs0.301 17314 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.64 Å2 / Biso mean: 97.2961 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 4→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10781 0 135 0 10916
Biso mean--122.95 --
Num. residues----1416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.210.39631360.36142137227390
4.21-4.470.33661490.32642345249499
4.47-4.820.35861310.30372372250399
4.82-5.30.35311340.30392368250299
5.3-6.070.29751530.30642359251299
6.07-7.640.29731530.31362357251099
7.64-48.590.2761360.24652384252098

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