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- PDB-6wko: Structure of an influenza C virus hemagglutinin-esterase-fusion (... -

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Basic information

Entry
Database: PDB / ID: 6wko
TitleStructure of an influenza C virus hemagglutinin-esterase-fusion (HEF2) intermediate
ComponentsHemagglutinin-esterase-fusion glycoprotein
KeywordsVIRAL PROTEIN / viral fusion / fusion intermediate / influenza C virus / hemagglutinin-esterase-fusion
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / 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 / plasma membrane
Similarity search - Function
Haemagglutinin stalk, influenza C / Influenza C hemagglutinin stalk / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesInfluenza C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.401 Å
AuthorsSerrao, V.H.B. / Lee, J.E.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2019-057 Canada
Canadian Institutes of Health Research (CIHR)MOP-115066 Canada
CitationJournal: Cell Rep / Year: 2021
Title: Snapshot of an influenza virus glycoprotein fusion intermediate.
Authors: Serrao, V.H.B. / Cook, J.D. / Lee, J.E.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-esterase-fusion glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2922
Polymers10,2571
Non-polymers351
Water724
1
A: Hemagglutinin-esterase-fusion glycoprotein
hetero molecules

A: Hemagglutinin-esterase-fusion glycoprotein
hetero molecules

A: Hemagglutinin-esterase-fusion glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8766
Polymers30,7703
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area6510 Å2
ΔGint-65 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.142, 65.142, 65.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-601-

CL

21A-703-

HOH

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Components

#1: Protein Hemagglutinin-esterase-fusion glycoprotein / HEF


Mass: 10256.511 Da / Num. of mol.: 1 / Mutation: C583S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Strain: C/Johannesburg/1/1966 / Gene: HEF, HE / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8E060, sialate O-acetylesterase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 85 mM tri-sodium citrate pH 5.6, 29.75% (v/v) tert-butanol and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9397 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9397 Å / Relative weight: 1
ReflectionResolution: 2.4→65.14 Å / Num. obs: 3791 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 60.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.026 / Rrim(I) all: 0.12 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4921.61.8963910.7620.4141.941100
8.98-65.1416.50.0439110.010.04499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHASERphasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
DIALS1.12.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NKJ chain A

4nkj


Resolution: 2.401→46.062 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.51
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 191 5.06 %Random selection
Rwork0.1971 ---
obs0.2002 3776 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.77 Å2 / Biso mean: 77.2259 Å2 / Biso min: 36.86 Å2
Refinement stepCycle: final / Resolution: 2.401→46.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 1 4 667
Biso mean--92.98 57.27 -
Num. residues----90
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01667
X-RAY DIFFRACTIONf_angle_d0.972906
X-RAY DIFFRACTIONf_chiral_restr0.056113
X-RAY DIFFRACTIONf_plane_restr0.005117
X-RAY DIFFRACTIONf_dihedral_angle_d9.427406
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2546 191 -
Rwork0.1971 3585 -
obs--100 %
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)
13.0621-2.10691.27011.7774-2.38627.02010.31761.2309-0.4206-0.3427-0.36052.89632.5292-1.2287-0.15360.8496-0.30010.12841.1132-0.13160.9856-40.9392-1.910632.0954
25.37020.5408-1.66975.4129-1.78258.6358-0.37850.75350.3381-0.60040.48360.07820.0582-0.7189-0.13770.4865-0.0095-0.01020.53450.03660.579-29.57468.895320.7786
31.808-1.66760.92185.5606-5.68036.23690.20122.2224-0.1285-1.38682.67362.89370.9084-0.6887-2.78350.6659-0.1727-0.12390.9630.23360.7481-19.193316.56068.9859
44.12753.7338-3.87133.6615-3.67763.7859-0.16261.306-1.8177-1.9022-0.0052-0.21080.0174-0.02610.22610.6301-0.091-0.0120.6454-0.06210.5985-10.615221.92083.1628
54.93814.70011.75125.7744-0.52684.3276-0.7006-1.1250.4295-0.9921-0.10750.308-0.7211-0.78590.80090.4149-0.0718-0.04030.51870.02630.6392-3.838528.9127-3.0922
65.61920.40294.69548.3183-1.05774.1040.27110.98340.5297-1.00210.10970.08470.72790.69890.00310.58380.03250.0530.5402-0.05140.3774.251734.9247-12.1393
74.79412.9186-5.32584.9741-1.41997.0548-0.8152.7678-0.9236-1.3450.3523-1.3571-0.08020.62010.67110.5065-0.040.03120.8462-0.06480.861713.141133.6966-11.9925
85.2774.1169-2.91144.6269-0.46953.65631.7060.3934-0.80421.079-1.6053-0.76180.01380.7243-0.35920.80720.0014-0.02420.75550.01780.87697.67524.944-6.8788
99.29287.16215.25455.54124.09373.1121-1.36471.202-1.4556-1.75981.2284-0.6943-2.415-0.8788-0.16011.39180.235-0.18760.8331-0.15510.9113-0.184218.6012-2.7869
105.41453.9559-3.3989.31871.55924.651-0.8699-2.35051.02030.53030.52170.04841.7021.30290.62141.07720.3351-0.23091.09290.06461.086-2.983929.0477-16.4654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 496:501)A496 - 501
2X-RAY DIFFRACTION2(chain A and resid 502:520)A502 - 520
3X-RAY DIFFRACTION3(chain A and resid 521:525)A521 - 525
4X-RAY DIFFRACTION4(chain A and resid 526:535)A526 - 535
5X-RAY DIFFRACTION5(chain A and resid 536:541)A536 - 541
6X-RAY DIFFRACTION6(chain A and resid 542:552)A542 - 552
7X-RAY DIFFRACTION7(chain A and resid 553:561)A553 - 561
8X-RAY DIFFRACTION8(chain A and resid 562:569)A562 - 569
9X-RAY DIFFRACTION9(chain A and resid 570:576)A570 - 576
10X-RAY DIFFRACTION10(chain A and resid 577:585)A577 - 585

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