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- PDB-6icx: Crystal structure of H7 hemagglutinin mutant AH-AGPL (V186G) from... -

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Basic information

Entry
Database: PDB / ID: 6icx
TitleCrystal structure of H7 hemagglutinin mutant AH-AGPL (V186G) from the influenza virus A/Anhui/1/2013 (H7N9)
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / influenza virus / H7N9 / Hemagglutinin
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsGao, G.F. / Xu, Y. / Qi, J.X.
CitationJournal: Cell Rep / Year: 2019
Title: Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin.
Authors: Xu, Y. / Peng, R. / Zhang, W. / Qi, J. / Song, H. / Liu, S. / Wang, H. / Wang, M. / Xiao, H. / Fu, L. / Fan, Z. / Bi, Y. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionSep 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 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 1.3Nov 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 1.4Oct 9, 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

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0585
Polymers55,3942
Non-polymers6643
Water1,35175
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17315
Polymers166,1826
Non-polymers1,9919
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area32530 Å2
ΔGint-117 kcal/mol
Surface area57980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.318, 115.318, 293.318
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 34951.480 Da / Num. of mol.: 1 / Mutation: V177G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2 chain


Mass: 20442.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21
#3: 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 genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsSequence reference R4NN21_9INFA was used according to author's suggestion. Author stated ...Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated hemagglutinin used in this studay, which was derived from AH1-H7N9 virus, was identical with R4NN21_9INFA.

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.91847 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91847 Å / Relative weight: 1
ReflectionResolution: 2.399→36.555 Å / Num. obs: 29523 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 21.69
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.633 / Num. unique obs: 2900 / Rsym value: 0.633

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KOL

4kol


Resolution: 2.399→32.098 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3004 1458 4.94 %
Rwork0.2659 --
obs0.2676 29515 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.399→32.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 42 75 3829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023832
X-RAY DIFFRACTIONf_angle_d0.5115185
X-RAY DIFFRACTIONf_dihedral_angle_d17.851428
X-RAY DIFFRACTIONf_chiral_restr0.041564
X-RAY DIFFRACTIONf_plane_restr0.003686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.399-2.48460.3791350.34182756X-RAY DIFFRACTION99
2.4846-2.5840.42041430.34552806X-RAY DIFFRACTION100
2.584-2.70160.37951370.34162803X-RAY DIFFRACTION100
2.7016-2.84390.35981550.32842796X-RAY DIFFRACTION100
2.8439-3.0220.36271590.3142805X-RAY DIFFRACTION100
3.022-3.25510.29511460.30012800X-RAY DIFFRACTION100
3.2551-3.58230.33441420.27322847X-RAY DIFFRACTION100
3.5823-4.09980.30411390.23862808X-RAY DIFFRACTION99
4.0998-5.16180.26091310.22442810X-RAY DIFFRACTION97
5.1618-32.0980.26221710.25272826X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -53.0135 Å / Origin y: 17.7424 Å / Origin z: 7.5925 Å
111213212223313233
T0.3008 Å20.0365 Å20.0181 Å2-0.2311 Å20.0902 Å2--0.4749 Å2
L1.4946 °20.4288 °2-0.2007 °2-1.7574 °20.7022 °2--0.5573 °2
S-0.0277 Å °-0.0306 Å °-0.1465 Å °0.0091 Å °0.266 Å °-0.2185 Å °-0.0155 Å °0.0926 Å °-0.1914 Å °
Refinement TLS groupSelection details: all

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