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- PDB-6ida: Crystal structure of H7 hemagglutinin mutant H7-SVTQ ( A138S, P22... -

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Basic information

Entry
Database: PDB / ID: 6ida
TitleCrystal structure of H7 hemagglutinin mutant H7-SVTQ ( A138S, P221T, L226Q) 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 / 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 / metal ion binding
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: 3.104 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 9, 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

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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)56,1355
Polymers55,4712
Non-polymers6643
Water0
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)168,40415
Polymers166,4136
Non-polymers1,9919
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area32600 Å2
ΔGint-121 kcal/mol
Surface area58320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.594, 116.594, 297.139
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: 35028.520 Da / Num. of mol.: 1 / Mutation: A138S,P221T,L226Q
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 / N-Acetylglucosamine


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
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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 14316 / % possible obs: 99.5 % / Redundancy: 3.8 % / Net I/σ(I): 12.1
Reflection shellResolution: 3.1→3.22 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: 3.104→37.743 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.41
RfactorNum. reflection% reflection
Rfree0.2581 720 5.03 %
Rwork0.2152 --
obs0.2174 14309 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.104→37.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 42 0 3759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033836
X-RAY DIFFRACTIONf_angle_d0.9355190
X-RAY DIFFRACTIONf_dihedral_angle_d16.2741429
X-RAY DIFFRACTIONf_chiral_restr0.067566
X-RAY DIFFRACTIONf_plane_restr0.003686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1037-3.34320.31761650.27862624X-RAY DIFFRACTION98
3.3432-3.67940.32071410.24122678X-RAY DIFFRACTION100
3.6794-4.21120.24411360.21312717X-RAY DIFFRACTION100
4.2112-5.30340.22251400.19472742X-RAY DIFFRACTION100
5.3034-37.74580.2511380.20732828X-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)
10.88250.3232-0.04841.7362-1.02591.73470.13260.07650.15070.0834-0.08240.1770.036-0.267500.3797-0.01810.02340.4181-0.01980.6037-20.5127-4.3558-48.6511
20.23320.0799-0.04720.19030.18440.20240.3506-0.86540.05491.42590.3351.4555-0.0653-0.95380.00021.1415-0.15710.20891.131-0.01120.8913-26.3929-7.5267-18.762
30.94550.5810.16952.25810.16210.76850.6133-0.9385-0.51261.7911-0.0117-0.7301-0.13360.23410.02630.8888-0.2297-0.18530.8531-0.05280.6951-13.6141-10.9604-14.9404
40.2034-0.189-0.20220.476-0.45660.91930.0286-0.70450.16640.08660.9333-1.4885-0.91821.42860.0831.0141-0.1979-0.30950.8698-0.1120.9342-5.4239-6.6207-17.3073
50.32390.32360.32891.2880.0570.308-0.053-0.9672-0.67351.20040.2153-0.7467-0.08280.7271-0.03950.7364-0.0772-0.02020.8179-0.16220.7523-15.8543-1.9241-23.581
61.71961.6694-0.1582.1860.21180.25690.0159-0.2044-0.03580.3103-0.1675-0.37430.1816-0.0309-00.55620.05340.03080.4145-0.02750.5816-18.0505-12.0279-37.3021
71.5311-1.08030.6451.2523-1.11530.990.17140.4938-0.1678-0.0795-0.15610.2005-0.0597-0.2084-00.4969-0.01950.01730.5883-0.02230.544-16.26443.0713-68.0272
80.0543-0.3870.04291.6318-0.075-0.0053-0.216-1.09270.1618-1.7282-0.8321-0.326-0.4489-1.4714-0.11661.4724-0.1025-0.35631.33570.12280.7418-20.22724.1235-103.0172
90.1150.1465-0.16930.16650.05881.59080.05680.6915-0.1308-0.8006-0.35120.2452.063-0.2248-0.10860.9142-0.2869-0.19311.09040.01190.7563-16.9776-5.8706-90.6056
100.02630.04460.02220.06180.03180.03720.1772-0.0530.2753-0.43890.76260.5192-0.53080.22670.00030.6315-0.1368-0.03171.1595-0.20790.929-14.3905-9.652-66.2816
110.8165-0.08250.01810.4622-0.46840.43690.2307-0.54860.12591.1455-0.3456-0.1460.72930.6088-00.6778-0.01210.09950.6984-0.19550.7555-12.6713-0.443-45.6344
121.261-0.19891.0930.8590.08740.89510.02960.34650.2294-0.37820.01970.1331-0.6575-0.19310.00720.4276-0.0104-0.03190.52930.08820.3439-6.18042.0392-76.285
135.72234.6591-2.05795.8005-0.6071.3055-0.10022.49180.9927-2.26571.01161.7834-0.9904-0.72911.0521.7116-0.0315-0.58422.30820.07730.5018-14.2754-1.0915-115.28
140.072-0.01660.04620.0659-0.09420.1313-1.4656-1.09211.14432.10011.3737-1.8098-0.2950.144801.8233-0.0467-0.33361.672-0.16141.2189-13.6225-11.3364-116.3322
151.99638.5982.8189.4229-0.25972.20941.13421.2761-2.40440.8354-0.5541-1.58362.045-1.314-0.18221.62830.117-0.14552.4134-0.12480.9458-8.4547-3.6551-126.3898
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 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 186 )
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 211 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 275 )
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 316 )
8X-RAY DIFFRACTION8chain 'B' and (resid 328 through 352 )
9X-RAY DIFFRACTION9chain 'B' and (resid 353 through 376 )
10X-RAY DIFFRACTION10chain 'B' and (resid 377 through 381 )
11X-RAY DIFFRACTION11chain 'B' and (resid 382 through 395 )
12X-RAY DIFFRACTION12chain 'B' and (resid 396 through 446 )
13X-RAY DIFFRACTION13chain 'B' and (resid 447 through 474 )
14X-RAY DIFFRACTION14chain 'B' and (resid 475 through 483 )
15X-RAY DIFFRACTION15chain 'B' and (resid 484 through 490 )

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