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- PDB-5zl2: Crystal structure of Bourbon virus envelope glycoprotein at pH8.0 -

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Basic information

Entry
Database: PDB / ID: 5zl2
TitleCrystal structure of Bourbon virus envelope glycoprotein at pH8.0
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / BOUV / glycoprotein
Function / homologyBaculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein / viral envelope / virion membrane / membrane / Envelope glycoprotein
Function and homology information
Biological speciesBourbon virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsQi, J.X. / Peng, R.C. / Wu, Y. / Gao, F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31741041 China
National Natural Science Foundation of China81301465 China
CitationJournal: To Be Published
Title: The postfusion structure of human-infecting Bourbon virus envelope glycoprotein implicates the host adaptation properties of thogotoviruses
Authors: Bai, C.Z. / Qi, J.X. / Wu, Y. / Wang, X.J. / Gao, G.F. / Peng, R.C. / Gao, F.
History
DepositionMar 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
C: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)158,7953
Polymers158,7953
Non-polymers00
Water2,090116
1
A: Envelope glycoprotein

A: Envelope glycoprotein

A: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)158,7953
Polymers158,7953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area28850 Å2
ΔGint-237 kcal/mol
Surface area50480 Å2
MethodPISA
2
B: Envelope glycoprotein

B: Envelope glycoprotein

B: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)158,7953
Polymers158,7953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area29010 Å2
ΔGint-244 kcal/mol
Surface area50060 Å2
MethodPISA
3
C: Envelope glycoprotein

C: Envelope glycoprotein

C: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)158,7953
Polymers158,7953
Non-polymers00
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 area28930 Å2
ΔGint-239 kcal/mol
Surface area50870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.255, 102.255, 134.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Envelope glycoprotein


Mass: 52931.625 Da / Num. of mol.: 3 / Fragment: UNP residues 19-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bourbon virus / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A140H4W8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, pH 8.0 and 30%(v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.48
ReflectionResolution: 2.7→50 Å / Num. obs: 42840 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.961 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.085 / Net I/σ(I): 8.579
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.09 / CC1/2: 0.662 / Rpim(I) all: 0.483

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→47.79 Å / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2397 1736 4.99 %
Rwork0.2014 --
obs0.304332 34756 80.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.703→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9267 0 0 116 9383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039510
X-RAY DIFFRACTIONf_angle_d0.62112882
X-RAY DIFFRACTIONf_dihedral_angle_d20.3033504
X-RAY DIFFRACTIONf_chiral_restr0.041386
X-RAY DIFFRACTIONf_plane_restr0.0041650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7044-2.7840.3053360.2962903X-RAY DIFFRACTION25
2.784-2.87380.3104690.29441202X-RAY DIFFRACTION34
2.8738-2.97640.2552860.27931688X-RAY DIFFRACTION47
2.9764-3.09550.27681090.27212453X-RAY DIFFRACTION68
3.0955-3.23620.27061120.2643100X-RAY DIFFRACTION87
3.2362-3.40670.24751590.25513343X-RAY DIFFRACTION93
3.4067-3.61980.25181940.2563353X-RAY DIFFRACTION94
3.6198-3.89880.24251860.26133400X-RAY DIFFRACTION95
3.8988-4.29030.26412110.26993384X-RAY DIFFRACTION94
4.2903-4.90910.27491440.28853426X-RAY DIFFRACTION96
4.9091-6.17720.32982120.34493362X-RAY DIFFRACTION94
6.1772-31.43160.43111580.41463425X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 19.6296 Å / Origin y: 26.1858 Å / Origin z: -23.1632 Å
111213212223313233
T0.0643 Å2-0.0077 Å2-0.0063 Å2-0.0573 Å20.0094 Å2--0.0007 Å2
L0.0161 °2-0.0083 °2-0.0062 °2-0.0036 °20.0109 °2--0.0036 °2
S-0.0071 Å °-0.0028 Å °-0.0133 Å °-0.0054 Å °-0.0043 Å °0.0045 Å °-0.0247 Å °0.0082 Å °-0.0008 Å °
Refinement TLS groupSelection details: all

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