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- PDB-6iuv: Crystal structure of influenza A virus H5 hemagglutinin globular ... -

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Basic information

Entry
Database: PDB / ID: 6iuv
TitleCrystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody 3C11
Components
  • 3C11 Heavy Chain
  • 3C11 Light Chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / influenza virus / HPAI / H5N1 / neutralizing antibody / epitope / major vulnerable site / vaccine development
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.332 Å
AuthorsWang, P. / Zuo, Y. / Sun, J. / Zhang, L. / Wang, X.
Funding support China, 10items
OrganizationGrant numberCountry
National Natural Science Foundation of China81530065 China
National Natural Science Foundation of China81661128042 China
National Natural Science Foundation of China31470751 China
National Natural Science Foundation of ChinaU1405228 China
Ministry of Science and Technology (China)2016YFD0500307 China
Ministry of Science and Technology (China)2012ZX10001-004 China
Ministry of Science and Technology (China)2012ZX10001-006 China
Ministry of Science and Technology (China)2012ZX10001-009 China
Ministry of Science and Technology (China)2017ZX10201-101 China
Ministry of Science and Technology (China)2014CB542500-03 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structural and functional definition of a vulnerable site on the hemagglutinin of highly pathogenic avian influenza A virus H5N1.
Authors: Wang, P. / Zuo, Y. / Sun, J. / Zuo, T. / Zhang, S. / Guo, S. / Shi, X. / Liang, M. / Zhou, P. / Zhang, L. / Wang, X.
History
DepositionNov 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / _chem_comp.type / _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 2.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
L: 3C11 Light Chain
H: 3C11 Heavy Chain
B: Hemagglutinin
D: 3C11 Light Chain
C: 3C11 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0378
Polymers147,8956
Non-polymers1,1412
Water11,007611
1
A: Hemagglutinin
L: 3C11 Light Chain
H: 3C11 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5184
Polymers73,9483
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-12 kcal/mol
Surface area28900 Å2
MethodPISA
2
B: Hemagglutinin
D: 3C11 Light Chain
C: 3C11 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5184
Polymers73,9483
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-16 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.780, 62.236, 127.827
Angle α, β, γ (deg.)90.00, 117.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin /


Mass: 25436.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Hong Kong/482/97(H5N1))
Gene: H5, HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q77XR4
#2: Antibody 3C11 Light Chain


Mass: 23854.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody 3C11 Heavy Chain


Mass: 24656.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 3.05 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 2.0M (NH4)2SO4, phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 75703 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.3
Reflection shellResolution: 2.33→2.38 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 7413

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DUT

5dut


Resolution: 2.332→43.242 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.43
RfactorNum. reflection% reflection
Rfree0.2461 3637 4.8 %
Rwork0.2074 --
obs0.2092 75693 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.332→43.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10146 0 76 611 10833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910501
X-RAY DIFFRACTIONf_angle_d1.08414310
X-RAY DIFFRACTIONf_dihedral_angle_d6.1866238
X-RAY DIFFRACTIONf_chiral_restr0.0661585
X-RAY DIFFRACTIONf_plane_restr0.0081829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3318-2.36240.26641490.22112674X-RAY DIFFRACTION98
2.3624-2.39480.2641470.23112755X-RAY DIFFRACTION99
2.3948-2.4290.291440.22932690X-RAY DIFFRACTION99
2.429-2.46530.28381390.2342709X-RAY DIFFRACTION99
2.4653-2.50380.27991520.23942770X-RAY DIFFRACTION99
2.5038-2.54480.31451530.23722730X-RAY DIFFRACTION100
2.5448-2.58870.28431530.22982749X-RAY DIFFRACTION99
2.5887-2.63580.32931590.22942706X-RAY DIFFRACTION99
2.6358-2.68650.25841640.2292750X-RAY DIFFRACTION99
2.6865-2.74130.28571500.22752712X-RAY DIFFRACTION99
2.7413-2.80090.26641480.22512753X-RAY DIFFRACTION99
2.8009-2.8660.25551170.21972777X-RAY DIFFRACTION99
2.866-2.93770.30911440.2292781X-RAY DIFFRACTION99
2.9377-3.01710.26611170.23322775X-RAY DIFFRACTION99
3.0171-3.10580.27411280.23022792X-RAY DIFFRACTION100
3.1058-3.20610.20631170.21672764X-RAY DIFFRACTION100
3.2061-3.32060.25551220.21472803X-RAY DIFFRACTION100
3.3206-3.45350.26411380.20382800X-RAY DIFFRACTION100
3.4535-3.61060.23611330.20292747X-RAY DIFFRACTION100
3.6106-3.80090.24471500.19372783X-RAY DIFFRACTION100
3.8009-4.03880.24091140.18382848X-RAY DIFFRACTION100
4.0388-4.35040.20311060.17632814X-RAY DIFFRACTION100
4.3504-4.78770.15691350.16662825X-RAY DIFFRACTION100
4.7877-5.47930.18031410.18242811X-RAY DIFFRACTION100
5.4793-6.89880.24151520.21522831X-RAY DIFFRACTION100
6.8988-43.24940.27781650.21852907X-RAY DIFFRACTION100

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