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- PDB-5j9h: Crystal structure of Glycoprotein C from Puumala virus in the pos... -

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Basic information

Entry
Database: PDB / ID: 5j9h
TitleCrystal structure of Glycoprotein C from Puumala virus in the post-fusion conformation (pH 8.0)
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Hantavirus / membrane fusion / conformational changes / enveloped viruses / virus entry
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 / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane ...: / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / 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 / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesPuumala virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWillensky, S. / Dessau, M.
CitationJournal: Plos Pathog. / Year: 2016
Title: Crystal Structure of Glycoprotein C from a Hantavirus in the Post-fusion Conformation.
Authors: Willensky, S. / Bar-Rogovsky, H. / Bignon, E.A. / Tischler, N.D. / Modis, Y. / Dessau, M.
History
DepositionApr 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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

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Assembly

Deposited unit
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6693
Polymers48,9861
Non-polymers6832
Water18010
1
A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0079
Polymers146,9593
Non-polymers2,0486
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18570 Å2
ΔGint-42 kcal/mol
Surface area48750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.521, 138.521, 138.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 48986.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puumala virus (strain P360) / Strain: P360 / Gene: GP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41266
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.46 Å3/Da / Density % sol: 49.93 % / Description: Sharp and rounded edges, cubic crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% PEG 400 0.2 M Lithium sulphate 0.1 M Tris buffer pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→49 Å / Num. obs: 15391 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 60.944 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.43
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.530.7832.15199.6
2.53-2.550.7262.31199.7
2.55-2.60.6962.42199.5
2.6-2.650.5792.86199.7
2.65-2.70.5173.42199.4
2.7-2.80.4214.1199.7
2.8-3.20.2037.78199.8
3.2-3.60.08915.85199.6
3.6-40.06322.19199.8
4-50.04628.79199.4
5-60.04429.78199.4
6-70.04329.67199.3
7-80.03831.94198.8
8-90.0432.81197.2
9-200.03535.01198.8
200.04231.82186.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J81

5j81


Resolution: 2.5→49 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.287 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.709 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 780 5.1 %RANDOM
Rwork0.2085 ---
obs0.211 14611 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 144.14 Å2 / Biso mean: 67.716 Å2 / Biso min: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.5→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 44 10 3203
Biso mean--94.11 55.22 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193281
X-RAY DIFFRACTIONr_bond_other_d0.0020.022996
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9594466
X-RAY DIFFRACTIONr_angle_other_deg0.85636947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3865412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94424.574129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35515529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6631510
X-RAY DIFFRACTIONr_chiral_restr0.070.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
X-RAY DIFFRACTIONr_mcbond_it0.834.9641651
X-RAY DIFFRACTIONr_mcbond_other0.834.9621650
X-RAY DIFFRACTIONr_mcangle_it1.4927.4432062
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 56 -
Rwork0.322 1064 -
all-1120 -
obs--99.64 %
Refinement TLS params.Method: refined / Origin x: 10.85 Å / Origin y: -9.719 Å / Origin z: 2.287 Å
111213212223313233
T0.0278 Å2-0.0262 Å2-0.0256 Å2-0.0742 Å20.005 Å2--0.1035 Å2
L0.8356 °2-0.0474 °2-0.0547 °2-0.6622 °2-0.038 °2--0.6226 °2
S-0.0026 Å °-0.145 Å °-0.0569 Å °0.0274 Å °0.0112 Å °-0.2054 Å °-0.0564 Å °0.15 Å °-0.0086 Å °

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