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- PDB-6hj5: Crystal structure of Whitewater Arroyo virus GP1 glycoprotein at ... -

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Basic information

Entry
Database: PDB / ID: 6hj5
TitleCrystal structure of Whitewater Arroyo virus GP1 glycoprotein at pH 5.6
ComponentsPre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Attachment / glycoprotein
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesWhitewater Arroyo mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsPryce, R. / Ng, W.M. / Zeltina, A. / Watanabe, Y. / El Omari, K. / Wagner, A. / Bowden, T.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (United Kingdom)MR/N002091/1 United Kingdom
CitationJournal: J. Virol. / Year: 2019
Title: Structure-Based Classification Defines the Discrete Conformational Classes Adopted by the Arenaviral GP1.
Authors: Pryce, R. / Ng, W.M. / Zeltina, A. / Watanabe, Y. / El Omari, K. / Wagner, A. / Bowden, T.A.
History
DepositionAug 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3164
Polymers18,6521
Non-polymers6643
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint12 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.040, 109.040, 70.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

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Components

#1: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 18652.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Whitewater Arroyo mammarenavirus / Gene: GPC, GP-C / Cell (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q911P0
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10.1 mg/ml protein, 0.2 M potassium sodium tartrate, 2 M ammonium sulphate and 0.1 M tri-sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→55 Å / Num. obs: 15428 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Net I/σ(I): 18
Reflection shellResolution: 2.08→2.13 Å / Rmerge(I) obs: 2.213

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→54.52 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.45
RfactorNum. reflection% reflection
Rfree0.207 722 4.69 %
Rwork0.1772 --
obs0.1786 15403 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→54.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 42 83 1295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071247
X-RAY DIFFRACTIONf_angle_d0.861703
X-RAY DIFFRACTIONf_dihedral_angle_d13.197735
X-RAY DIFFRACTIONf_chiral_restr0.057199
X-RAY DIFFRACTIONf_plane_restr0.004217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0802-2.24090.25841360.23032862X-RAY DIFFRACTION100
2.2409-2.46640.24021330.20232879X-RAY DIFFRACTION100
2.4664-2.82330.22011430.18252900X-RAY DIFFRACTION100
2.8233-3.55690.2031530.17582924X-RAY DIFFRACTION100
3.5569-54.53870.19321570.16533116X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 44.3741 Å / Origin y: 48.0565 Å / Origin z: 30.6422 Å
111213212223313233
T0.2812 Å20.0054 Å20.0824 Å2-0.2724 Å2-0.044 Å2--0.3264 Å2
L3.0381 °2-1.0298 °20.6226 °2-3.3377 °2-0.1759 °2--2.5599 °2
S-0.023 Å °-0.2631 Å °0.3814 Å °0.0816 Å °0.0895 Å °-0.1113 Å °-0.3519 Å °-0.0378 Å °-0.0545 Å °
Refinement TLS groupSelection details: all

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