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- PDB-5j81: Crystal structure of Glycoprotein C from Puumala virus in the pos... -

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Basic information

Entry
Database: PDB / ID: 5j81
TitleCrystal structure of Glycoprotein C from Puumala virus in the post-fusion conformation (pH 6.0)
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / membrane fusion / virus / glycoprotein / class II
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-mediated suppression of host innate immune response / symbiont entry into host cell / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell ...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-mediated suppression of host innate immune response / symbiont entry into host cell / virus-mediated perturbation of host defense response / 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 / 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
ACETATE ION / Envelopment polyprotein
Similarity search - Component
Biological speciesPuumala virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 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 7, 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / 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.occupancy / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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

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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)50,0545
Polymers48,9861
Non-polymers1,0684
Water6,612367
1
A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,16315
Polymers146,9593
Non-polymers3,20412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19780 Å2
ΔGint-39 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.430, 96.430, 247.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1638-

HOH

21A-1644-

HOH

31A-1664-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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

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Non-polymers , 4 types, 370 molecules

#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 50.09 % / Description: Sharp edges rhombohedrons
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 2000 MME, 0.1 M MES pH 6.0, 0.2 M (NH4)2SO4

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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: 1.8→50 Å / Num. obs: 41365 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.93 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.65
Reflection shell
Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible allRmerge(I) obs
1.8-1.91.38199.9
1.9-22.5811000.845
2-2.24.5611000.49
2.2-2.58.3211000.265
2.5-2.814.69199.90.142
2.8-3.224.2811000.082
3.2-3.637.511000.053
3.6-442.48199.40.046
4-4.548.57199.90.039
4.5-549.37199.90.036
5-648.6911000.038
6-744.29199.80.041
7-849.2411000.035
8-952.1511000.031
9-1052.7611000.03
1054.74197.20.028

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→48.215 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.2088 2103 5.08 %
Rwork0.1828 --
obs0.1841 41357 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.99 Å2 / Biso mean: 25.3894 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 1.8→48.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 70 367 3570
Biso mean--57.17 33.72 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093301
X-RAY DIFFRACTIONf_angle_d0.8934490
X-RAY DIFFRACTIONf_chiral_restr0.05511
X-RAY DIFFRACTIONf_plane_restr0.004563
X-RAY DIFFRACTIONf_dihedral_angle_d11.7871985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.8420.43161590.470725692728
1.842-1.8880.36981240.341826032727
1.888-1.93910.32851430.278425652708
1.9391-1.99610.25931530.23225792732
1.9961-2.06060.24191420.214125862728
2.0606-2.13420.23881270.20126062733
2.1342-2.21970.21471480.198225902738
2.2197-2.32070.21341330.192626072740
2.3207-2.4430.23531110.190426182729
2.443-2.59610.20751660.184626022768
2.5961-2.79650.24161220.182826282750
2.7965-3.07790.22261360.17926182754
3.0779-3.52310.18211520.165726382790
3.5231-4.43830.18881330.147426792812
4.4383-48.23230.17131540.173327662920
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)
10.20470.0707-0.01580.3228-0.02880.02330.0721-0.2146-0.0190.1927-0.02620.02990.03410.06680.04050.09070.0116-0.01160.12120.02580.01057.946150.4877135.5243
20.2852-0.001-0.04180.3199-0.00730.01170.0111-0.0658-0.05970.1313-0.0416-0.22140.06610.09210.00730.07640.0181-0.00510.05890.00060.040116.876648.8102123.4473
30.1273-0.1069-0.0520.18890.18180.47760.06040.0746-0.0406-0.0563-0.0097-0.14830.03720.13170.25780.05480.01790.06910.08590.00780.033312.869851.188990.8191
40.2652-0.0015-0.03610.2576-0.02590.1882-0.0119-0.2006-0.3720.1685-0.0453-0.13970.1630.04110.03620.0950.09180.0185-0.10720.04930.12543.834630.8243116.5079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 666 through 701 )A666 - 701
2X-RAY DIFFRACTION2chain 'A' and (resid 702 through 735 )A702 - 735
3X-RAY DIFFRACTION3chain 'A' and (resid 736 through 965 )A736 - 965
4X-RAY DIFFRACTION4chain 'A' and (resid 966 through 1076 )A966 - 1076

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