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- PDB-5xku: Crystal structure of hemagglutinin globular head from an H7N9 inf... -

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Basic information

Entry
Database: PDB / ID: 5xku
TitleCrystal structure of hemagglutinin globular head from an H7N9 influenza virus in complex with a neutralizing antibody HNIgGA6
Components
  • HNIgGA6 heavy chain
  • HNIgGA6 light chain
  • Influenza a virus
KeywordsIMMUNE SYSTEM / Hemagglutinin / Complex / Antibody / Influenza A
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 / metal ion binding / 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: 1.78 Å
AuthorsChen, C. / Wang, J. / Wang, W. / Gao, X. / Cui, S. / Jin, Q.
Funding support China, 1items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2016-I2M-1-014 China
CitationJournal: J. Virol. / Year: 2018
Title: Structural Insight into a Human Neutralizing Antibody against Influenza Virus H7N9
Authors: Chen, C. / Liu, L. / Xiao, Y. / Cui, S. / Wang, J. / Jin, Q.
History
DepositionMay 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Influenza a virus
B: HNIgGA6 light chain
C: HNIgGA6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5494
Polymers84,3283
Non-polymers2211
Water8,773487
1
A: Influenza a virus
hetero molecules

B: HNIgGA6 light chain
C: HNIgGA6 heavy chain


Theoretical massNumber of molelcules
Total (without water)84,5494
Polymers84,3283
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_534y+1/2,-x-3/2,z-1/41
Buried area5140 Å2
ΔGint-24 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.983, 70.983, 283.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Influenza a virus


Mass: 35953.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: R4NN21*PLUS
#2: Antibody HNIgGA6 light chain


Mass: 23697.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pCBio (others)
#3: Antibody HNIgGA6 heavy chain


Mass: 24677.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pCBio (others)
#4: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.96 % / Description: rhombus
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium acetate hydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.78→47.318 Å / Num. obs: 70029 / % possible obs: 98.8 % / Redundancy: 7.07 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.22
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 7.24 % / Num. unique obs: 11241 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5J

4n5j


Resolution: 1.78→47.318 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.82
RfactorNum. reflection% reflection
Rfree0.2417 3464 4.95 %
Rwork0.2057 --
obs0.2075 70016 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→47.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 15 487 5361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074995
X-RAY DIFFRACTIONf_angle_d0.9316793
X-RAY DIFFRACTIONf_dihedral_angle_d12.3322971
X-RAY DIFFRACTIONf_chiral_restr0.059757
X-RAY DIFFRACTIONf_plane_restr0.006870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7801-1.80440.38231270.34792509X-RAY DIFFRACTION95
1.8044-1.83020.3761550.30752565X-RAY DIFFRACTION98
1.8302-1.85750.34641480.3012594X-RAY DIFFRACTION99
1.8575-1.88660.29921380.28682586X-RAY DIFFRACTION98
1.8866-1.91750.33781430.28592619X-RAY DIFFRACTION98
1.9175-1.95060.34091530.28162571X-RAY DIFFRACTION99
1.9506-1.9860.30811310.26242618X-RAY DIFFRACTION99
1.986-2.02420.28861190.26382640X-RAY DIFFRACTION99
2.0242-2.06560.27731350.27492631X-RAY DIFFRACTION99
2.0656-2.11050.28351380.25852606X-RAY DIFFRACTION99
2.1105-2.15960.29171330.25872659X-RAY DIFFRACTION99
2.1596-2.21360.27181440.25182610X-RAY DIFFRACTION99
2.2136-2.27340.29461290.24552671X-RAY DIFFRACTION99
2.2734-2.34030.31521350.24372661X-RAY DIFFRACTION99
2.3403-2.41580.2661120.24582668X-RAY DIFFRACTION99
2.4158-2.50220.27321310.23462662X-RAY DIFFRACTION99
2.5022-2.60240.26871470.23122673X-RAY DIFFRACTION99
2.6024-2.72080.27251380.22612684X-RAY DIFFRACTION99
2.7208-2.86420.27551260.22442674X-RAY DIFFRACTION99
2.8642-3.04360.24261320.2182730X-RAY DIFFRACTION100
3.0436-3.27860.22151540.19332653X-RAY DIFFRACTION99
3.2786-3.60840.23051500.19222753X-RAY DIFFRACTION100
3.6084-4.13030.20841450.17032740X-RAY DIFFRACTION99
4.1303-5.20270.17811490.15322773X-RAY DIFFRACTION99
5.2027-47.33490.22051520.17463002X-RAY DIFFRACTION99

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