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- PDB-5opg: Structure of the Hantaan virus Gn glycoprotein ectodomain -

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Basic information

Entry
Database: PDB / ID: 5opg
TitleStructure of the Hantaan virus Gn glycoprotein ectodomain
Componentsenvelope glycoprotein Gn
KeywordsVIRAL PROTEIN / glycoprotein / Gn / hantavirus envelope / bunyavirus / viral entry / viral attachment
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virus-mediated perturbation of host defense response / virion membrane / signal transduction / membrane / metal ion binding
Similarity search - Function
: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal ...: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan orthohantavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRissanen, I. / Stass, R. / Zeltina, A. / Li, S. / Hepojoki, J. / Harlos, K. / Gilbert, R.J.C. / Huiskonen, J.T. / Bowden, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
CitationJournal: J. Virol. / Year: 2017
Title: Structural Transitions of the Conserved and Metastable Hantaviral Glycoprotein Envelope.
Authors: Rissanen, I. / Stass, R. / Zeltina, A. / Li, S. / Hepojoki, J. / Harlos, K. / Gilbert, R.J.C. / Huiskonen, J.T. / Bowden, T.A.
History
DepositionAug 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_common_name
Revision 1.2Oct 25, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jul 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 1.5Jan 17, 2024Group: 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: envelope glycoprotein Gn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8438
Polymers41,0611
Non-polymers7827
Water3,081171
1
A: envelope glycoprotein Gn
hetero molecules

A: envelope glycoprotein Gn
hetero molecules

A: envelope glycoprotein Gn
hetero molecules

A: envelope glycoprotein Gn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,37132
Polymers164,2444
Non-polymers3,12728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area14830 Å2
ΔGint-114 kcal/mol
Surface area51810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.906, 110.906, 180.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein envelope glycoprotein Gn


Mass: 41060.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hantaan orthohantavirus / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A0A077D153
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.6 M ammonium sulphate, 0.1 M citrate pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→78.42 Å / Num. obs: 30998 / % possible obs: 100 % / Redundancy: 38.2 % / Biso Wilson estimate: 34.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.032 / Rrim(I) all: 0.198 / Net I/σ(I): 14.8 / Num. measured all: 1184141 / Scaling rejects: 534
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.2136.42.25322590.8830.3772.285100
9.62-78.4232.70.04241910.0070.04299.8

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FXU

5fxu


Resolution: 2.15→59.207 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2266 1574 5.1 %
Rwork0.2005 --
obs0.2019 30848 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.47 Å2 / Biso mean: 48.3992 Å2 / Biso min: 20.05 Å2
Refinement stepCycle: final / Resolution: 2.15→59.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 48 171 2797
Biso mean--68.9 47.14 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022703
X-RAY DIFFRACTIONf_angle_d0.4473673
X-RAY DIFFRACTIONf_chiral_restr0.044413
X-RAY DIFFRACTIONf_plane_restr0.004459
X-RAY DIFFRACTIONf_dihedral_angle_d10.3091624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.21940.30461260.29732619274599
2.2194-2.29870.35121500.28292575272598
2.2987-2.39080.33251460.26872595274199
2.3908-2.49960.33061480.2562608275699
2.4996-2.63140.28441500.241726232773100
2.6314-2.79620.30041390.228926482787100
2.7962-3.01210.27091430.220326502793100
3.0121-3.31520.26791420.197226712813100
3.3152-3.79490.17441460.176126852831100
3.7949-4.78080.14541330.149727412874100
4.7808-59.22950.19971510.187328593010100
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)
14.8899-1.23112.69871.9903-1.22132.2087-0.01020.4433-0.1459-0.62250.04380.06540.18370.1021-0.0340.4877-0.1016-0.02670.51430.14650.30624.078635.330852.8096
21.04560.61110.31090.71660.93421.6568-0.25430.17240.4976-0.10230.0185-0.0143-0.5289-0.06050.27370.3183-0.068-0.00950.310.10480.369916.99234.90369.5335
33.4615-0.98161.5432.1973-0.48822.3557-0.20960.45040.4178-0.1793-0.09630.0672-0.38350.24840.30590.385-0.0597-0.02640.30140.11970.3584.997739.016763.3709
46.33853.07481.10693.5997-1.03124.037-0.64041.06460.5097-0.95720.42080.32830.2836-0.01810.18110.6866-0.0913-0.01260.58980.0730.3706-3.022332.666947.2081
52.96441.07580.64612.38460.50724.7348-0.09140.04210.0465-0.24510.02690.08170.0787-0.32690.04320.25020.0058-0.02720.19040.04820.2429-8.036828.253771.6048
65.6231-3.0179-1.89742.60190.15531.48330.02560.0885-0.2186-0.01590.1234-0.00430.05240.5225-0.12010.2957-0.03230.01660.24590.06820.301313.241623.293375.088
73.01751.03582.27231.37870.20515.0453-0.0137-0.0055-0.0593-0.1308-0.0211-0.02540.1937-0.2307-0.02480.2836-0.01210.03230.24250.0440.24371.38226.165271.3162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 54 )A21 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 96 )A55 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 153 )A97 - 153
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 201 )A154 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 275 )A202 - 275
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 324 )A276 - 324
7X-RAY DIFFRACTION7chain 'A' and (resid 325 through 371 )A325 - 371

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