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- PDB-5g47: Structure of Gc glycoprotein from severe fever with thrombocytope... -

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Basic information

Entry
Database: PDB / ID: 5g47
TitleStructure of Gc glycoprotein from severe fever with thrombocytopenia syndrome virus in the trimeric postfusion conformation
ComponentsSFTSV GC
KeywordsVIRAL PROTEIN / PHLEBOVIRUS / VIRAL MEMBRANE FUSION / GLYCOPROTEIN / CLASS II VIRAL FUSION / BUNYAVIRUS / HUAIYANGSHAN VIRUS / EMERGING VIRUS / ZOONOSIS
Function / homologyPhlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / virion component => GO:0044423 / membrane => GO:0016020 / Membrane glycoprotein polyprotein
Function and homology information
Biological speciesSEVERE FEVER WITH THROMBOCYTOPENIA SYNDROME VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsHalldorsson, S. / Behrens, A.J. / Harlos, K. / Huiskonen, J.T. / Elliott, R.M. / Crispin, M. / Brennan, B. / Bowden, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of a Phleboviral Envelope Glycoprotein Reveals a Consolidated Model of Membrane Fusion.
Authors: Halldorsson, S. / Behrens, A. / Harlos, K. / Huiskonen, J.T. / Elliott, R.M. / Crispin, M. / Brennan, B. / Bowden, T.A.
History
DepositionMay 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct / struct_biol / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval ..._entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SFTSV GC
B: SFTSV GC
C: SFTSV GC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8637
Polymers143,1643
Non-polymers6994
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-54 kcal/mol
Surface area50170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.360, 152.270, 160.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21B-2015-

HOH

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Components

#1: Protein SFTSV GC


Mass: 47721.203 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, RESIDUES 563-996
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SEVERE FEVER WITH THROMBOCYTOPENIA SYNDROME VIRUS
Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: R4V2Q5
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 4.6
Details: 45% PENTAERYTHRIOTOL 426, 0.1 M SODIUM ACETATE AT PH 4.6

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.008
DetectorType: DECTRIS PILATUS3 M6 / Detector: PIXEL / Date: Apr 18, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.45→108.51 Å / Num. obs: 66293 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 61.36 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.7
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.45→108.511 Å / SU ML: 0.35 / σ(F): 1.33 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 3096 4.7 %
Rwork0.1936 --
obs0.1954 66125 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→108.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9582 0 43 101 9726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029849
X-RAY DIFFRACTIONf_angle_d0.513347
X-RAY DIFFRACTIONf_dihedral_angle_d10.4866000
X-RAY DIFFRACTIONf_chiral_restr0.0441509
X-RAY DIFFRACTIONf_plane_restr0.0031704
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)
12.82861.63171.01861.6810.57271.03250.1957-0.79040.14660.1559-0.35940.0774-0.1071-0.30020.13630.44640.06670.04220.6031-0.05580.385-25.9167-16.1167-9.8874
21.79621.74940.61093.17031.95341.91130.22130.3889-0.531-0.8107-0.35780.98120.2056-0.61440.01150.90120.0451-0.3170.8794-0.21781.3048-73.9659-51.8401-49.3255
32.22620.92711.41111.49071.20241.57880.2066-0.3224-0.35770.1133-0.17850.2510.1836-0.252-0.05690.4163-0.00480.01960.54980.06060.4921-48.1992-35.0763-25.8513
42.0250.5347-0.02232.45970.2040.52170.1029-0.4236-0.62170.2278-0.1424-0.14190.2052-0.15230.05250.5492-0.05530.01250.76450.18480.568-24.8711-38.3432-9.436
52.61150.98991.33382.6038-0.33253.2157-0.55770.17130.2614-0.09140.2379-0.3056-0.49370.05970.26530.5821-0.0424-0.04640.4392-0.0220.4513-10.4575-4.2399-21.4572
61.88740.64710.74890.75660.24390.8985-0.29440.7088-0.3193-0.74720.32920.3147-0.1924-0.033-0.00360.8699-0.0813-0.15990.7886-0.07520.6372-45.5871-41.443-59.0404
71.37950.9460.58421.67660.32920.4169-0.19370.3983-0.043-0.54070.22690.1243-0.1920.12080.03350.6973-0.0082-0.03390.4588-0.01440.3517-31.2235-23.4717-45.4629
81.89761.1841-0.22653.10631.17431.8031-0.29230.4598-0.0282-0.78560.08040.4372-0.2108-0.08410.19150.7160.0032-0.16010.6551-0.01950.6016-44.3408-33.7462-50.6697
94.01711.07693.10080.72390.74522.4085-0.41220.14250.446-0.71140.17110.1799-0.2420.05620.25850.73150.0164-0.00130.41690.06980.4058-27.0641-13.4064-33.8913
103.56930.91190.34020.94880.7172.073-0.2944-0.6890.6087-0.1732-0.18110.5355-0.2932-0.84010.4240.6590.1791-0.10230.7964-0.08410.7174-39.0836-5.5941-22.8192
112.85051.34931.18242.95461.22581.8801-0.0533-0.68030.7645-0.0886-0.40310.7365-0.0134-1.07560.39720.67310.191-0.10251.16-0.21410.9721-49.4528-10.66-22.0653
122.18051.62490.8792.80081.3541.0636-0.03510.0538-0.5889-0.2441-0.01180.01750.0202-0.13490.02340.43670.0299-0.02890.37380.02430.5989-32.1744-49.1772-33.7975
133.00511.59221.38871.85020.8921.00080.02110.1489-0.8134-0.14760.1969-0.2630.04150.0696-0.23360.39720.01820.02240.39340.01720.6687-26.4606-45.3942-33.6366
141.41311.82411.94022.79682.19762.8725-0.07860.2155-0.5274-0.01580.2972-0.41580.16370.4706-0.15190.4783-0.00180.04960.5039-0.00050.6908-14.5248-33.4605-28.4648
152.49831.49971.31672.35591.13553.9118-0.47561.1133-0.591-0.85450.6956-0.4934-0.30890.6732-0.14960.7798-0.15690.20810.7614-0.14690.6558-9.9064-23.2577-44.7075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 563 THROUGH 640 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 641 THROUGH 703 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 704 THROUGH 863 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 864 THROUGH 996 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 563 THROUGH 614 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 615 THROUGH 696 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 697 THROUGH 769 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 770 THROUGH 863 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 864 THROUGH 895 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 896 THROUGH 954 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 955 THROUGH 996 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 563 THROUGH 726 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 727 THROUGH 863 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 864 THROUGH 894 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 895 THROUGH 996 )

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