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- PDB-6id8: Crystal structure of H7 hemagglutinin mutant H7-SVTL ( A138S, P22... -

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Basic information

Entry
Database: PDB / ID: 6id8
TitleCrystal structure of H7 hemagglutinin mutant H7-SVTL ( A138S, P221T) 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: 2.902 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
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)56,1205
Polymers55,4562
Non-polymers6643
Water00
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)168,35915
Polymers166,3686
Non-polymers1,9919
Water0
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 area31610 Å2
ΔGint-119 kcal/mol
Surface area59060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.243, 117.243, 294.129
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: 35013.547 Da / Num. of mol.: 1 / Mutation: A138S,P221T
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
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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0M Ammonium sulfate, 0.1M Sodium HEPES pH 7.5, 5% v/v PEG 400

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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: 2.9→50 Å / Num. obs: 16810 / % possible obs: 95.5 % / Redundancy: 4.1 % / Net I/σ(I): 21.42
Reflection shellResolution: 2.9→3 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: 2.902→38.434 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.58
RfactorNum. reflection% reflection
Rfree0.2712 781 4.65 %
Rwork0.2422 --
obs0.2436 16807 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.902→38.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 42 0 3758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023835
X-RAY DIFFRACTIONf_angle_d0.575189
X-RAY DIFFRACTIONf_dihedral_angle_d14.5361428
X-RAY DIFFRACTIONf_chiral_restr0.043567
X-RAY DIFFRACTIONf_plane_restr0.003685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9019-3.08360.34551500.31662597X-RAY DIFFRACTION95
3.0836-3.32160.31071200.2932638X-RAY DIFFRACTION95
3.3216-3.65560.35861360.26392636X-RAY DIFFRACTION95
3.6556-4.18410.3121270.23822662X-RAY DIFFRACTION95
4.1841-5.26930.22641320.21712707X-RAY DIFFRACTION97
5.2693-38.43730.23441160.23322786X-RAY DIFFRACTION95
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)
10.5695-0.0308-0.02442.09380.74251.77050.0857-0.0126-0.1227-0.4832-0.1633-0.1910.26630.02930.00220.54490.06250.04370.4533-0.00760.5806-52.647412.581-5.3495
22.27951.2636-0.10941.4253-0.4792.66660.17650.34150.1909-1.7205-0.27420.597-0.4224-0.19440.02081.49780.3077-0.1610.6275-0.00540.9066-62.047118.53-31.2717
30.7060.33480.2710.92330.13520.14580.2923-0.176-0.2093-0.2462-0.57070.01720.207-0.2930.0010.42020.0018-0.00640.4535-0.07290.5997-55.24198.8274-1.7435
40.5680.06340.35910.3688-0.27930.5003-0.315-0.15510.01250.03430.24010.1548-0.01560.360100.5391-0.01410.04810.55120.06280.6135-47.916721.237518.276
56.68580.9815-0.27740.1443-0.04020.01110.91520.24531.37580.8542-0.9947-0.4686-0.28961.1060.35941.5754-0.1437-0.18250.85620.2330.8601-42.460724.527349.6532
60.00750.0736-0.02130.5942-0.17830.05230.0148-1.0467-0.4213-0.2958-0.6622-1.02260.1352-0.8933-0.0231.6330.0889-0.35281.65460.36310.7874-47.19614.074154.5995
70.1465-0.0531-0.03520.01810.01250.00890.3663-0.2160.4377-0.3809-0.16840.47320.4817-0.355601.22860.0624-0.03240.950.16530.7492-57.480917.676335.8309
80.03240.0499-0.00320.0732-0.00460.0001-0.09470.5175-0.6673-0.37070.3261-0.2162-0.3232-0.913700.59010.01810.04850.90480.13440.9037-59.787218.06989.4872
90.27210.1643-0.0380.1730.030.04060.16861.15590.8919-1.3956-0.4126-0.0898-0.3785-0.2892-0.00130.88770.06620.12060.6063-0.03940.8425-49.154823.9648-8.342
101.30210.01571.36360.6641-0.18711.53680.1942-0.29150.13630.2172-0.0272-0.1443-0.33350.36140.1080.56120.0369-0.10010.4429-0.02070.5558-53.745229.472326.3542
110.6260.8351-0.40633.5258-2.08621.24730.4271-0.7442-0.05631.8060.22780.4145-0.2291-0.60870.44821.68990.2557-0.11511.69330.26350.538-54.65519.898665.629
123.26712.7461.38143.67781.52840.6827-1.41120.5248-0.1552-1.44711.0751-0.03970.7603-0.4045-0.4552.20320.45080.2051.79540.17850.6579-57.217324.937176.4611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 246 )
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 316 )
5X-RAY DIFFRACTION5chain 'B' and (resid 328 through 337 )
6X-RAY DIFFRACTION6chain 'B' and (resid 338 through 359 )
7X-RAY DIFFRACTION7chain 'B' and (resid 360 through 376 )
8X-RAY DIFFRACTION8chain 'B' and (resid 377 through 386 )
9X-RAY DIFFRACTION9chain 'B' and (resid 387 through 395 )
10X-RAY DIFFRACTION10chain 'B' and (resid 396 through 446 )
11X-RAY DIFFRACTION11chain 'B' and (resid 447 through 483 )
12X-RAY DIFFRACTION12chain 'B' and (resid 484 through 490 )

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