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- PDB-6id5: Crystal structure of H7 hemagglutinin mutant H7-SVPL ( A138S) fro... -

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Basic information

Entry
Database: PDB / ID: 6id5
TitleCrystal structure of H7 hemagglutinin mutant H7-SVPL ( A138S) 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: 2.6 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 8, 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 1.4Nov 6, 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: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1165
Polymers55,4522
Non-polymers6643
Water50428
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)168,34715
Polymers166,3566
Non-polymers1,9919
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area32280 Å2
ΔGint-115 kcal/mol
Surface area58050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.386, 115.386, 294.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-705-

HOH

21B-610-

HOH

31B-614-

HOH

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 35009.559 Da / Num. of mol.: 1 / Mutation: A138S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / 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 / Gene: HA / 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
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.: 28 / Source method: isolated from a natural source / Formula: H2O
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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.8M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 2% v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K
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: 2.6→50 Å / Num. obs: 23529 / % possible obs: 99.6 % / Redundancy: 6.4 % / Net I/σ(I): 20.16
Reflection shellResolution: 2.6→2.69 Å

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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: 2.6→36.585 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.9
RfactorNum. reflection% reflection
Rfree0.3103 1155 4.91 %
Rwork0.2588 --
obs0.2612 23527 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 42 28 3786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043836
X-RAY DIFFRACTIONf_angle_d0.7165191
X-RAY DIFFRACTIONf_dihedral_angle_d16.8471430
X-RAY DIFFRACTIONf_chiral_restr0.076566
X-RAY DIFFRACTIONf_plane_restr0.002686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5999-2.71820.41161470.35792729X-RAY DIFFRACTION99
2.7182-2.86140.35841510.33562753X-RAY DIFFRACTION100
2.8614-3.04060.34191280.32782802X-RAY DIFFRACTION100
3.0406-3.27530.32471220.31042795X-RAY DIFFRACTION100
3.2753-3.60460.32171510.27412802X-RAY DIFFRACTION100
3.6046-4.12560.27451490.23462791X-RAY DIFFRACTION100
4.1256-5.19540.26041690.21952784X-RAY DIFFRACTION99
5.1954-36.58820.34321380.24482916X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45340.2091-0.54881.4579-0.35691.27420.18120.07580.21980.303-0.03190.3125-0.12210.0752-0.00040.3192-0.03530.00260.3959-0.02350.537937.1859-37.20180.8329
21.39810.48390.24262.33330.83620.82380.4738-0.3223-0.33550.94530.0644-0.2745-0.18970.56540.08450.9789-0.2222-0.07430.6279-0.08820.450643.164-42.65529.0798
30.6572-0.6596-0.18630.89350.02010.18150.07740.42050.03520.0435-0.0460.2035-0.1017-0.253700.40650.0018-0.00580.4659-0.01680.563538.3835-31.8109-14.5924
40.31210.73431.39072.17642.97756.3851-0.2779-0.45480.4805-0.0842-0.5026-0.1462-0.3928-0.8372-1.8351.1329-0.0608-0.53640.67450.20510.774942.0598-23.5848-50.2093
50.187-0.08210.07110.09760.00210.0393-0.225-0.06860.2235-0.7858-0.1320.82910.161-0.8235-0.02661.5871-0.0256-0.37331.6132-0.03050.826834.6249-32.0507-55.32
60.052-0.086-0.01520.207-0.07990.09850.5514-0.1956-0.6072-0.59010.034-0.54730.6344-0.436100.8123-0.1491-0.02140.76610.01660.601442.2029-40.1596-36.8164
70.0108-0.01090.02580.01990.00390.0354-0.07670.2401-0.78190.05920.3340.4668-0.0022-0.305700.67240.0481-0.05990.5961-0.11010.57544.3615-41.6682-9.7917
80.25340.5206-0.41191.1573-0.95040.79540.3357-0.2290.36590.7174-0.3453-0.2891-0.28970.553-0.13730.5946-0.09310.17710.6074-0.21540.633844.6173-29.31388.0691
90.5477-0.27610.17481.065-0.25490.13050.09050.10790.2034-0.2756-0.16720.1150.0231-0.7305-0.01190.39550.0152-0.05060.45180.04430.453651.5707-30.9683-26.6384
100.01240.18360.15951.70331.17520.9951-0.2110.4932-0.0017-0.40260.90280.2124-0.0269-0.61441.76521.8559-0.2012-0.3991.80920.13520.471346.3267-31.9338-66.2356
110.30010.346-0.0640.6633-0.06120.0066-0.2620.7467-1.1222-0.0960.194-0.726-0.2553-0.536-0.01811.6985-0.002-0.31382.1654-0.18691.093743.0109-40.3316-68.6017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 316 )
4X-RAY DIFFRACTION4chain 'B' and (resid 328 through 337 )
5X-RAY DIFFRACTION5chain 'B' and (resid 338 through 358 )
6X-RAY DIFFRACTION6chain 'B' and (resid 359 through 376 )
7X-RAY DIFFRACTION7chain 'B' and (resid 377 through 386 )
8X-RAY DIFFRACTION8chain 'B' and (resid 387 through 395 )
9X-RAY DIFFRACTION9chain 'B' and (resid 396 through 446 )
10X-RAY DIFFRACTION10chain 'B' and (resid 447 through 466 )
11X-RAY DIFFRACTION11chain 'B' and (resid 467 through 490 )

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