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- PDB-6idd: Crystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G1... -

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Basic information

Entry
Database: PDB / ID: 6idd
TitleCrystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G186V, T221P, Q226L) from the influenza virus A/Shanghai/1/2013 (H7N9)
ComponentsHemagglutinin
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 / membrane => GO:0016020 / 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
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 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

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Assembly

Deposited unit
A: Hemagglutinin
C: Hemagglutinin
E: Hemagglutinin
G: Hemagglutinin
I: Hemagglutinin
K: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,73915
Polymers332,7486
Non-polymers1,9919
Water8,629479
1
A: Hemagglutinin
E: Hemagglutinin
G: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,4808
Polymers166,3743
Non-polymers1,1065
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-43 kcal/mol
Surface area57290 Å2
MethodPISA
2
C: Hemagglutinin
I: Hemagglutinin
K: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2597
Polymers166,3743
Non-polymers8854
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-39 kcal/mol
Surface area57270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.181, 226.274, 116.780
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hemagglutinin /


Mass: 55457.949 Da / Num. of mol.: 6 / Mutation: S165N,N267D,H274Y,N392T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/MH01/2013(H7N9))
Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A088BEK2
#2: 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.: 9
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium HEPES pH 7.5, 14% w/v PEG 4000, 7% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 150579 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 11.37
Reflection shellResolution: 2.38→2.47 Å / Rmerge(I) obs: 0.864 / Num. unique obs: 13391 / Rsym value: 0.864

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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: 2.383→40.549 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 7454 4.96 %
Rwork0.2526 --
obs0.254 150368 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.383→40.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22786 0 0 479 23265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223250
X-RAY DIFFRACTIONf_angle_d0.45831439
X-RAY DIFFRACTIONf_dihedral_angle_d17.2238671
X-RAY DIFFRACTIONf_chiral_restr0.043405
X-RAY DIFFRACTIONf_plane_restr0.0034156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.383-2.40990.40021740.34633423X-RAY DIFFRACTION71
2.4099-2.43830.41132350.35754598X-RAY DIFFRACTION94
2.4383-2.4680.36862440.35064625X-RAY DIFFRACTION96
2.468-2.49930.38462420.35024788X-RAY DIFFRACTION98
2.4993-2.53210.37812560.34914768X-RAY DIFFRACTION99
2.5321-2.56680.36352550.34234849X-RAY DIFFRACTION99
2.5668-2.60350.38082660.34264887X-RAY DIFFRACTION100
2.6035-2.64230.43542660.34474774X-RAY DIFFRACTION100
2.6423-2.68360.37682460.33074888X-RAY DIFFRACTION100
2.6836-2.72760.3892430.33334816X-RAY DIFFRACTION100
2.7276-2.77460.39582490.32764891X-RAY DIFFRACTION100
2.7746-2.82510.33722450.32274783X-RAY DIFFRACTION100
2.8251-2.87940.31992550.30954897X-RAY DIFFRACTION100
2.8794-2.93820.36422360.31184843X-RAY DIFFRACTION100
2.9382-3.0020.35942400.30634878X-RAY DIFFRACTION99
3.002-3.07180.32692770.28514801X-RAY DIFFRACTION99
3.0718-3.14860.32982620.29184856X-RAY DIFFRACTION99
3.1486-3.23370.30922640.29294816X-RAY DIFFRACTION99
3.2337-3.32880.3342490.29394841X-RAY DIFFRACTION99
3.3288-3.43620.28392850.27864826X-RAY DIFFRACTION99
3.4362-3.5590.29352640.2664821X-RAY DIFFRACTION99
3.559-3.70140.29612370.24694791X-RAY DIFFRACTION99
3.7014-3.86970.28092200.2374868X-RAY DIFFRACTION99
3.8697-4.07360.24272430.21834835X-RAY DIFFRACTION99
4.0736-4.32850.22952530.20464840X-RAY DIFFRACTION99
4.3285-4.66230.21982600.19054827X-RAY DIFFRACTION98
4.6623-5.13060.20352530.19354773X-RAY DIFFRACTION98
5.1306-5.87110.20842400.20124809X-RAY DIFFRACTION98
5.8711-7.38970.23852310.21364815X-RAY DIFFRACTION98
7.3897-40.5490.20682640.19244687X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 148.6315 Å / Origin y: 6.2791 Å / Origin z: 133.4352 Å
111213212223313233
T0.2769 Å20.0269 Å2-0.0011 Å2-0.3274 Å20.0186 Å2--0.3736 Å2
L0.1679 °20.0281 °2-0.042 °2-0.448 °20.1227 °2--0.2367 °2
S-0.0128 Å °0.0041 Å °0.0204 Å °0.0427 Å °-0.0008 Å °0.0225 Å °-0.0151 Å °-0.0031 Å °0.0196 Å °
Refinement TLS groupSelection details: all

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