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- PDB-6p3r: crystal structure of human Fab H5.31 in complex with influenza A ... -

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Basic information

Entry
Database: PDB / ID: 6p3r
Titlecrystal structure of human Fab H5.31 in complex with influenza A H5N1 Vietnam hemagglutinin head domain
Components
  • Hemagglutinin
  • Human Fab H5.31 light chain
  • human Fab H5.31 heavy chain
KeywordsVIRAL PROTEIN / human monoclonal antibody / antigen-antibody complex / influenza A virus / H5N1 vietnam / hemagglutinin / head domain
Function / homology
Function and homology information


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
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDong, J. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U19AI117905-05 United States
CitationJournal: To Be Published
Title: Crystal structure of human Fab H5.31 in complex with influenza A H5N1 Vietnam hemagglutinin head domain
Authors: Dong, J. / Crowe, J.E.
History
DepositionMay 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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 / _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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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_entity_branch_descriptor / 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: human Fab H5.31 heavy chain
B: Human Fab H5.31 light chain
C: human Fab H5.31 heavy chain
D: Human Fab H5.31 light chain
E: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,94415
Polymers146,4366
Non-polymers4,5089
Water75742
1
A: human Fab H5.31 heavy chain
B: Human Fab H5.31 light chain
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6218
Polymers73,2183
Non-polymers2,4035
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: human Fab H5.31 heavy chain
D: Human Fab H5.31 light chain
E: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3237
Polymers73,2183
Non-polymers2,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.113, 234.472, 284.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein , 1 types, 2 molecules EL

#3: Protein Hemagglutinin


Mass: 25162.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/32/2004(H5N1))
Strain: A/chicken/Vietnam/32/2004(H5N1) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q1KHK2

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody human Fab H5.31 heavy chain


Mass: 24659.674 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 Human Fab H5.31 light chain


Mass: 23396.004 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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Sugars , 4 types, 6 molecules

#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.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1567.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpa1-4DGlcpNAca1-2DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAca1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][a-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}LINUCSPDB-CARE
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fructofuranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1567.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAca1-2DManpb1-6DManpb1-4DGlcpNAcb1-4[DFrufa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
#8: 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.: 3 / Source method: isolated from a natural 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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Non-polymers , 2 types, 45 molecules

#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 5.28 Å3/Da / Density % sol: 76.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.8 M K2HPO4, 0.6 M NaHPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3→49.52 Å / Num. obs: 61716 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Net I/σ(I): 16
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.508 / Num. unique obs: 8933

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNQ, 4GSD

4xnq

4gsd


Resolution: 3→47.469 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 3061 4.96 %
Rwork0.1923 --
obs0.1939 61688 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9620 0 297 42 9959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210172
X-RAY DIFFRACTIONf_angle_d0.72113901
X-RAY DIFFRACTIONf_dihedral_angle_d7.6276012
X-RAY DIFFRACTIONf_chiral_restr0.071610
X-RAY DIFFRACTIONf_plane_restr0.0041761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04690.4041520.362634X-RAY DIFFRACTION100
3.0469-3.09680.33781440.29952634X-RAY DIFFRACTION100
3.0968-3.15020.3321400.26492634X-RAY DIFFRACTION100
3.1502-3.20750.25431300.24572640X-RAY DIFFRACTION100
3.2075-3.26920.241470.23142651X-RAY DIFFRACTION100
3.2692-3.33590.26741480.23192634X-RAY DIFFRACTION100
3.3359-3.40840.25481360.23322639X-RAY DIFFRACTION100
3.4084-3.48760.29161320.23852681X-RAY DIFFRACTION100
3.4876-3.57480.24421380.21912627X-RAY DIFFRACTION100
3.5748-3.67150.22511330.20262657X-RAY DIFFRACTION100
3.6715-3.77950.27971610.20742640X-RAY DIFFRACTION100
3.7795-3.90140.25971370.19932658X-RAY DIFFRACTION100
3.9014-4.04080.23831290.18642661X-RAY DIFFRACTION100
4.0408-4.20240.19531440.16982654X-RAY DIFFRACTION100
4.2024-4.39360.21541540.15352661X-RAY DIFFRACTION100
4.3936-4.6250.16561480.14152632X-RAY DIFFRACTION100
4.625-4.91450.15511400.13542683X-RAY DIFFRACTION100
4.9145-5.29350.18711200.15592703X-RAY DIFFRACTION100
5.2935-5.82540.20791320.16852688X-RAY DIFFRACTION100
5.8254-6.66640.22611350.19722691X-RAY DIFFRACTION100
6.6664-8.39130.23261320.20512739X-RAY DIFFRACTION100
8.3913-47.47490.22931290.20732786X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.5454 Å / Origin y: -16.5227 Å / Origin z: -45.5183 Å
111213212223313233
T0.3642 Å20.1171 Å20.0081 Å2-0.5583 Å2-0.0146 Å2--0.4781 Å2
L0.8865 °2-0.0843 °2-0.0133 °2-1.0062 °20.2194 °2--0.9252 °2
S-0.069 Å °-0.1117 Å °-0.0933 Å °0.1879 Å °0.0773 Å °-0.0226 Å °0.2458 Å °0.1573 Å °0.0039 Å °
Refinement TLS groupSelection details: all

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