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- PDB-5lk2: Structure of hantavirus envelope glycoprotein Gc in postfusion co... -

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Basic information

Entry
Database: PDB / ID: 5lk2
TitleStructure of hantavirus envelope glycoprotein Gc in postfusion conformation in presence of 300 mM KCL
ComponentsEnvelopment polyprotein
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 / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
: / Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuardado-Calvo, P. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9244
Polymers54,2921
Non-polymers6333
Water6,161342
1
A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,77312
Polymers162,8753
Non-polymers1,8989
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area15680 Å2
ΔGint11 kcal/mol
Surface area47210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.329, 107.329, 128.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-505-

NA

21A-870-

HOH

31A-876-

HOH

41A-915-

HOH

51A-929-

HOH

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Components

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


Mass: 54291.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hantaan virus / Gene: GP / Plasmid: pMT / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P08668
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES 6.5, 10.77%(v/v) PEG 8000, 7% (v/v) glycerol, 300 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.6→37.61 Å / Num. obs: 72553 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.84 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LJZ

5ljz


Resolution: 1.6→37.61 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.99
RfactorNum. reflection% reflection
Rfree0.2081 3562 4.91 %
Rwork0.1755 --
obs0.1771 72552 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 40 342 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063076
X-RAY DIFFRACTIONf_angle_d1.0474160
X-RAY DIFFRACTIONf_dihedral_angle_d12.5561109
X-RAY DIFFRACTIONf_chiral_restr0.043464
X-RAY DIFFRACTIONf_plane_restr0.005531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5987-1.62060.22371330.17522623X-RAY DIFFRACTION96
1.6206-1.64380.24961490.16242760X-RAY DIFFRACTION100
1.6438-1.66830.22331440.15922802X-RAY DIFFRACTION100
1.6683-1.69440.21821350.15172753X-RAY DIFFRACTION100
1.6944-1.72220.22351480.15032746X-RAY DIFFRACTION100
1.7222-1.75190.23661570.15692764X-RAY DIFFRACTION100
1.7519-1.78370.21551490.15012755X-RAY DIFFRACTION100
1.7837-1.8180.21191420.15132770X-RAY DIFFRACTION100
1.818-1.85510.19811080.15432806X-RAY DIFFRACTION100
1.8551-1.89550.23031150.15312770X-RAY DIFFRACTION100
1.8955-1.93960.2356900.16242803X-RAY DIFFRACTION100
1.9396-1.98810.19311590.16042807X-RAY DIFFRACTION100
1.9881-2.04180.18991450.15132732X-RAY DIFFRACTION100
2.0418-2.10190.18941020.15732829X-RAY DIFFRACTION100
2.1019-2.16970.19961580.16452744X-RAY DIFFRACTION100
2.1697-2.24730.19621910.16282678X-RAY DIFFRACTION100
2.2473-2.33720.22221440.17372778X-RAY DIFFRACTION100
2.3372-2.44360.2088930.17662820X-RAY DIFFRACTION100
2.4436-2.57240.20461700.18322747X-RAY DIFFRACTION100
2.5724-2.73350.20431320.19092767X-RAY DIFFRACTION100
2.7335-2.94450.21171840.1912711X-RAY DIFFRACTION100
2.9445-3.24070.22311560.19052764X-RAY DIFFRACTION100
3.2407-3.70930.18871490.17942757X-RAY DIFFRACTION100
3.7093-4.67190.1991820.17862733X-RAY DIFFRACTION100
4.6719-37.62480.22581270.19632771X-RAY DIFFRACTION100

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