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- PDB-5ljy: Structure of hantavirus envelope glycoprotein Gc in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5ljy
TitleStructure of hantavirus envelope glycoprotein Gc in complex with scFv A5
Components
  • Envelopment polyprotein
  • scFvA5
KeywordsVIRAL PROTEIN / Hantavirus / Glycoprotein / Viral fusion
Function / homology
Function and homology information


suppression by virus of host autophagy / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endocytosis involved in viral entry into host cell / host cell surface / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / virus-mediated perturbation of host defense response ...suppression by virus of host autophagy / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endocytosis involved in viral entry into host cell / host cell surface / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COBALT HEXAMMINE(III) / Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsGuardado-Calvo, P. / Stettner, E. / Jeffers, S.A. / Rey, F.A.
CitationJournal: Plos Pathog. / Year: 2016
Title: Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc.
Authors: Guardado-Calvo, P. / Bignon, E.A. / Stettner, E. / Jeffers, S.A. / Perez-Vargas, J. / Pehau-Arnaudet, G. / Tortorici, M.A. / Jestin, J.L. / England, P. / Tischler, N.D. / Rey, F.A.
History
DepositionJul 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelopment polyprotein
H: scFvA5
L: scFvA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9785
Polymers112,5953
Non-polymers3822
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-4 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.623, 148.795, 37.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Envelopment polyprotein / Glycoprotein precursor / M polyprotein / glycoprotein Gc


Mass: 54339.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hantaan virus (strain 76-118) / Gene: GP / Plasmid: pMT / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P08668
#2: Antibody scFvA5


Mass: 29127.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 60 mM Na-HEPES 7.5, 40 mM hexamine cobalt chloride salt, 13.45% (w/v) PEG 4K, 7.4% (v/v) 2-propanol, and 1% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→29.76 Å / Num. obs: 13990 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 50.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Net I/σ(I): 14
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.886 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1471refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→29.268 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 993 7.13 %
Rwork0.2125 --
obs0.2165 13932 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 21 2 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054705
X-RAY DIFFRACTIONf_angle_d1.1036362
X-RAY DIFFRACTIONf_dihedral_angle_d14.0481680
X-RAY DIFFRACTIONf_chiral_restr0.042701
X-RAY DIFFRACTIONf_plane_restr0.004812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.15820.34761580.31451810X-RAY DIFFRACTION99
3.1582-3.35580.39041420.26451757X-RAY DIFFRACTION100
3.3558-3.61440.33251460.24171820X-RAY DIFFRACTION100
3.6144-3.97740.27091360.22591831X-RAY DIFFRACTION100
3.9774-4.55110.24371280.1851851X-RAY DIFFRACTION100
4.5511-5.72680.21041140.17451898X-RAY DIFFRACTION100
5.7268-29.26970.25191690.20971972X-RAY DIFFRACTION100
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)
12.93652.80571.78164.66523.04932.40620.0324-0.27040.39240.2038-0.39010.28110.0584-0.11690.00070.57980.01160.02760.56920.03750.625155.883189.895755.9406
24.15065.08732.22948.12033.64111.9773-0.0016-0.0437-0.2530.0025-0.0079-0.6731-0.00730.0426-0.00070.57660.03240.04690.59870.11190.674865.701897.216258.9804
34.8595-1.0292-1.12771.66572.15722.7529-0.2072-0.1269-0.03720.80470.1332-0.73430.03230.02020.00010.67640.0082-0.12710.6861-0.13560.567217.880747.590841.0683
45.9903-0.3131-0.74314.78811.55091.49760.0388-0.06990.0353-0.43280.3255-0.9393-0.74270.50330.00040.9336-0.25420.03070.7533-0.13420.841275.8399142.399577.7044
57.59770.806-1.76764.52172.27361.8932-0.1382-0.3281-0.69210.04080.1123-0.70660.0204-0.2560.0030.7065-0.0563-0.10840.57250.1340.474960.2932126.536681.7671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 414 )
4X-RAY DIFFRACTION4chain 'H'
5X-RAY DIFFRACTION5chain 'L'

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