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- PDB-5zkx: The postfusion structure of human-infecting Bourbon virus envelop... -

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Basic information

Entry
Database: PDB / ID: 5zkx
TitleThe postfusion structure of human-infecting Bourbon virus envelope glycoprotein
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / BOUV / glycoprotein
Function / homologyBaculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein / symbiont-mediated perturbation of host process / viral envelope / virion membrane / membrane / Envelope glycoprotein
Function and homology information
Biological speciesBourbon virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQi, J.X. / Wu, Y. / Peng, R.C. / Gao, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31741041 China
National Natural Science Foundation of China81301465 China
National Natural Science Foundation of China81621091 China
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Postfusion structure of human-infecting Bourbon virus envelope glycoprotein.
Authors: Bai, C. / Qi, J. / Wu, Y. / Wang, X. / Gao, G.F. / Peng, R. / Gao, F.
History
DepositionMar 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 7, 2020Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._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
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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: Envelope glycoprotein
B: Envelope glycoprotein
C: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)158,7953
Polymers158,7953
Non-polymers00
Water7,638424
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_525-y,x-y-3,z1
crystal symmetry operation3_855-x+y+3,-x,z1
Buried area28920 Å2
ΔGint-235 kcal/mol
Surface area51070 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_515-y,x-y-4,z1
crystal symmetry operation3_955-x+y+4,-x,z1
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_625-y+1,x-y-3,z1
crystal symmetry operation3_965-x+y+4,-x+1,z1
Buried area29610 Å2
ΔGint-240 kcal/mol
Surface area50340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.947, 101.947, 134.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-649-

HOH

31C-611-

HOH

41C-618-

HOH

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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.: 424 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium malonate, pH 7.0 and 12%(w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 69252 / % possible obs: 99.6 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rpim(I) all: 0.061 / Net I/σ(I): 12.205
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.477 / Num. unique obs: 6728 / CC1/2: 0.754 / Rpim(I) all: 0.333 / % possible all: 96.8

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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
Starting model: 5XEA

5xea


Resolution: 2.3→47.666 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.54
RfactorNum. reflection% reflection
Rfree0.2007 3015 5.17 %
Rwork0.1739 --
obs0.1774 58301 83.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9217 0 0 424 9641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049459
X-RAY DIFFRACTIONf_angle_d0.62112812
X-RAY DIFFRACTIONf_dihedral_angle_d20.6663482
X-RAY DIFFRACTIONf_chiral_restr0.0411378
X-RAY DIFFRACTIONf_plane_restr0.0041640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33970.2764760.2851309X-RAY DIFFRACTION38
2.3397-2.38220.2886810.28331374X-RAY DIFFRACTION39
2.3822-2.42810.3568890.28121470X-RAY DIFFRACTION42
2.4281-2.47760.2729820.27421687X-RAY DIFFRACTION49
2.4776-2.53150.28871000.26191864X-RAY DIFFRACTION54
2.5315-2.59040.29931150.25062141X-RAY DIFFRACTION61
2.5904-2.65510.30481410.25022698X-RAY DIFFRACTION78
2.6551-2.72690.30711860.23293173X-RAY DIFFRACTION91
2.7269-2.80720.27471600.21543331X-RAY DIFFRACTION95
2.8072-2.89770.26081890.20643288X-RAY DIFFRACTION95
2.8977-3.00130.24721810.19343309X-RAY DIFFRACTION95
3.0013-3.12140.21781890.18393257X-RAY DIFFRACTION95
3.1214-3.26350.21581730.17983291X-RAY DIFFRACTION95
3.2635-3.43550.18851710.17253333X-RAY DIFFRACTION95
3.4355-3.65070.19681830.16213282X-RAY DIFFRACTION95
3.6507-3.93240.18731790.15133308X-RAY DIFFRACTION95
3.9324-4.32790.14541490.14373291X-RAY DIFFRACTION96
4.3279-4.95360.14291800.12233316X-RAY DIFFRACTION95
4.9536-6.23880.15051580.15343303X-RAY DIFFRACTION95
6.2388-47.67570.16281810.17073313X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 183.1044 Å / Origin y: -89.0949 Å / Origin z: -22.8575 Å
111213212223313233
T0.0976 Å20.005 Å20.0027 Å2-0.1273 Å20.0013 Å2--0.0354 Å2
L0.0121 °20.0034 °20.0135 °2-0.0104 °20.005 °2---0.0004 °2
S-0.0027 Å °-0.0001 Å °-0.0019 Å °-0.0109 Å °-0.0002 Å °0.0024 Å °-0.0101 Å °0.0012 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

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