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- PDB-5i72: Crystal structure of the oligomeric form of the Lassa virus matri... -

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Basic information

Entry
Database: PDB / ID: 5i72
TitleCrystal structure of the oligomeric form of the Lassa virus matrix protein Z
ComponentsRING finger protein Z
KeywordsVIRAL PROTEIN / arenavirus / Lassa virus / matrix / Z / oligomer
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral budding from plasma membrane / virion component / host cell perinuclear region of cytoplasm / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
RING finger protein Z, zinc finger / RING finger protein Z, arenaviridae / Protein Z, RING-type zinc finger superfamily / P-11 zinc finger
Similarity search - Domain/homology
RING finger protein Z
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHastie, K. / Zandonatti, M. / Liu, T. / Li, S. / Woods Jr, V. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI2008031 United States
CitationJournal: J.Virol. / Year: 2016
Title: Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z.
Authors: Hastie, K.M. / Zandonatti, M. / Liu, T. / Li, S. / Woods, V.L. / Saphire, E.O.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RING finger protein Z
B: RING finger protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4326
Polymers12,1712
Non-polymers2624
Water00
1
A: RING finger protein Z
B: RING finger protein Z
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)74,59436
Polymers73,02412
Non-polymers1,57024
Water0
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
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area16200 Å2
ΔGint-151 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.961, 116.961, 82.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 2
211chain BB1 - 2

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Components

#1: Protein RING finger protein Z / Protein Z / Zinc-binding protein


Mass: 6085.327 Da / Num. of mol.: 2 / Fragment: unp residues 25-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
Strain: Mouse/Sierra Leone/Josiah/1976 / Production host: Escherichia coli (E. coli) / References: UniProt: O73557
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 4.49 Å3/Da / Density % sol: 72.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 300-400mM ammonium sulfate, 100mM HEPES pH 7.5 and 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2827 Å
DetectorType: 3 x 3 CCD array (ADSC Q315R) / Detector: CCD / Date: Feb 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.9→38.221 Å / Num. obs: 9325 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 86.73 Å2 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.083 / Χ2: 0.93 / Net I/σ(I): 10.2 / Num. measured all: 47129 / Scaling rejects: 2357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRrim(I) allΧ2Rejects% possible all
2.9-34.730.392.848469550.441.14331100
3-3.124.770.3043.746309140.3411.13271100
3.12-3.274.760.2884.347189300.3231.1629299.8
3.27-3.444.810.1935.547639390.2171.0625199.7
3.44-3.654.780.1447.146959340.1620.9722799.9
3.65-3.944.80.1019.746599260.1130.8621699.9
3.94-4.334.90.06713.747309330.0740.7715799.8
4.33-4.964.90.0541746729240.0610.6714099.9
4.96-6.244.880.06116.847329390.0680.7214699.8
6.24-38.214.680.05221.346849310.0590.8232699.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→38.221 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 433 4.65 %
Rwork0.1904 8884 -
obs0.1913 9317 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.25 Å2 / Biso mean: 89.7017 Å2 / Biso min: 52.25 Å2
Refinement stepCycle: final / Resolution: 2.9→38.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 4 0 826
Biso mean--94.76 --
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011859
X-RAY DIFFRACTIONf_angle_d1.3711166
X-RAY DIFFRACTIONf_chiral_restr0.045130
X-RAY DIFFRACTIONf_plane_restr0.007142
X-RAY DIFFRACTIONf_dihedral_angle_d15.928318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A468X-RAY DIFFRACTION5.105TORSIONAL
12B468X-RAY DIFFRACTION5.105TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9018-3.32140.27291330.27429893122100
3.3214-4.18380.19961520.208929383090100
4.1838-38.22440.20151480.16412957310599

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