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- PDB-5lk1: Structure of hantavirus envelope glycoprotein Gc in postfusion co... -

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Basic information

Entry
Database: PDB / ID: 5lk1
TitleStructure of hantavirus envelope glycoprotein Gc in postfusion conformation in presence of 200 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 / fusion of virus membrane with host endosome membrane ...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 / 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
Similarity search - Domain/homology
: / Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / chem_comp ...atom_site / 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 / _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

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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
Water5,675315
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_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area16360 Å2
ΔGint8 kcal/mol
Surface area50730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.289, 107.289, 127.539
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-865-

HOH

31A-866-

HOH

41A-906-

HOH

51A-912-

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 / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
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, 200 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: 1.7→37.55 Å / Num. obs: 56962 / % possible obs: 94.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 15.3 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3 / CC1/2: 0.84 / % possible all: 91.1

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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: 1.7→37.55 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.19
RfactorNum. reflection% reflection
Rfree0.2032 2800 4.92 %
Rwork0.1772 --
obs0.1786 56962 94.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 40 315 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113393
X-RAY DIFFRACTIONf_angle_d1.2874602
X-RAY DIFFRACTIONf_dihedral_angle_d12.7991226
X-RAY DIFFRACTIONf_chiral_restr0.062507
X-RAY DIFFRACTIONf_plane_restr0.007595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6994-1.72870.25351090.20172616X-RAY DIFFRACTION91
1.7287-1.76010.23141370.19492684X-RAY DIFFRACTION94
1.7601-1.79390.22051270.18872721X-RAY DIFFRACTION94
1.7939-1.83060.19681370.18212688X-RAY DIFFRACTION94
1.8306-1.87040.2088780.18172825X-RAY DIFFRACTION97
1.8704-1.91390.20011010.17512799X-RAY DIFFRACTION97
1.9139-1.96170.21371310.18052788X-RAY DIFFRACTION97
1.9617-2.01480.20422010.1712727X-RAY DIFFRACTION97
2.0148-2.07410.20181610.17472723X-RAY DIFFRACTION96
2.0741-2.1410.21221610.17342768X-RAY DIFFRACTION96
2.141-2.21750.20351780.1722656X-RAY DIFFRACTION95
2.2175-2.30630.23531220.18412690X-RAY DIFFRACTION94
2.3063-2.41120.24561510.18862754X-RAY DIFFRACTION95
2.4112-2.53830.21771330.18382736X-RAY DIFFRACTION96
2.5383-2.69730.2221300.19482790X-RAY DIFFRACTION96
2.6973-2.90550.18811150.18422744X-RAY DIFFRACTION95
2.9055-3.19780.20941660.18382614X-RAY DIFFRACTION92
3.1978-3.66010.19431470.17032639X-RAY DIFFRACTION93
3.6601-4.61010.18091750.16292631X-RAY DIFFRACTION93
4.6101-37.55870.18441400.16692569X-RAY DIFFRACTION89
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)
10.38610.1089-0.00170.3884-0.16440.05140.0881-0.3399-0.010.2145-0.04290.034-0.083-0.02930.02260.1897-0.0227-0.01370.2465-0.02520.093-48.4637100.652739.2167
20.0818-0.007-0.00620.00740.01490.04190.1886-0.3084-0.13990.25280.4155-0.04330.0811-0.2354-0.00020.79170.00520.02290.6534-0.09150.3091-53.4689110.393156.9081
30.3379-0.2656-0.15170.9350.00380.1867-0.0501-0.09040.16030.06860.0325-0.0165-0.1360.1669-0.0360.0878-0.02420.01310.1104-0.02980.1108-51.9989110.875411.3722
40.02460.051-0.0267-0.03040.0054-0.0074-0.3470.6028-0.2164-1.50740.1531-0.45060.26020.6133-0.3871.3207-0.02120.38120.6252-0.00870.525-46.4276107.319-36.8665
50.8858-0.2092-0.40660.9879-0.2090.3045-0.2929-0.34130.6968-0.22170.0677-0.7686-0.06550.0911-0.37820.126-0.10120.171-0.18450.1510.0909-51.118109.8366-7.0897
60.6143-0.32980.35350.2459-0.28370.29480.1256-0.07880.14670.26590.1655-0.349-0.2070.35630.11940.2498-0.0653-0.00790.2323-0.08810.1774-46.9019109.948533.2896
70.37960.09010.14740.30240.18170.74080.0131-0.01370.0844-0.01190.0225-0.0321-0.11710.0952-00.11070.00030.00690.0645-0.01570.1289-50.6349105.02156.4993
80.920.13390.25040.37660.00570.0619-0.17060.79450.0325-1.9186-0.00420.3612-1.0938-0.2229-0.5471.08630.0553-0.10880.38740.07610.1118-56.7648101.7262-33.5895
90.4485-0.23920.01830.4337-0.51190.22870.0046-0.11570.15770.10750.0342-0.0001-0.1158-0.04510.08280.1212-0.00570.00830.0989-0.04660.0961-52.9127106.063319.5466
100.52770.20520.6770.65520.44930.5023-0.0370.0942-0.00540.076-0.0398-0.1087-0.14560.28460.50850.1096-0.043-0.04660.1676-0.00040.1551-28.332103.867519.6938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:40)
2X-RAY DIFFRACTION2(chain A and resid 41:53)
3X-RAY DIFFRACTION3(chain A and resid 54:80)
4X-RAY DIFFRACTION4(chain A and resid 81:130)
5X-RAY DIFFRACTION5(chain A and resid 131:151)
6X-RAY DIFFRACTION6(chain A and resid 152:172)
7X-RAY DIFFRACTION7(chain A and resid 173:241)
8X-RAY DIFFRACTION8(chain A and resid 242:262)
9X-RAY DIFFRACTION9(chain A and resid 263:322)
10X-RAY DIFFRACTION10(chain A and resid 323:415)

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