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- PDB-2m1s: NMR assignment of the arenaviral protein Z from Lassa fever virus -

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Basic information

Entry
Database: PDB / ID: 2m1s
TitleNMR assignment of the arenaviral protein Z from Lassa fever virus
ComponentsRING finger protein Z
KeywordsTRANSCRIPTION / RING / negative regulator of eIF4E
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
Double Stranded RNA Binding Domain - #310 / RING finger protein Z, zinc finger / RING finger protein Z, arenaviridae / Protein Z, RING-type zinc finger superfamily / P-11 zinc finger / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RING finger protein Z
Similarity search - Component
Biological speciesLassa virus Josiah
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsVolpon, L. / Osborne, M.J. / Borden, K.L.B.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural characterization of the Z RING-eIF4E complex reveals a distinct mode of control for eIF4E
Authors: Volpon, L. / Osborne, M.J. / Capul, A.A. / de la Torre, J.C. / Borden, K.L.B.
#1: Journal: Biomol. NMR Assignments / Year: 2008
Title: NMR assignment of the arenaviral protein Z from Lassa fever virus
Authors: Volpon, L. / Osborne, M.J. / Borden, K.L.B.
History
DepositionDec 6, 2012Deposition site: BMRB / Processing site: RCSB
SupersessionJan 30, 2013ID: 2KO5
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RING finger protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8193
Polymers10,6881
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 10688.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus Josiah / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: Z / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O73557
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1313D 1H-15N TOCSY
1413D 1H-15N NOESY
1533D 1H-13C NOESY
1623D HN(CA)CB
1723D CBCA(CO)NH
1833D (H)CCH-TOCSY
1923D HNCO
11023D HBHA(CO)NH
11122D (HB)CB(CGCD)HD
11222D (HB)CB(CGCDCE)HE
11323D C(CO)NH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-100% 15N] LFV-Z, 20 mM potassium phosphate, 200 mM sodium chloride, 3 mM sodium azide, 0.05 mM zinc sulfate, 0.05 mM TCEP, 7 % D2O, 93 % H2O, 93% H2O/7% D2O93% H2O/7% D2O
20.2 mM [U-100% 13C; U-100% 15N] LFV-Z, 20 mM potassium phosphate, 200 mM sodium chloride, 3 mM sodium azide, 0.05 mM zinc sulfate, 0.05 mM TCEP, 7 % D2O, 93 % H2O, 93% H2O/7% D2O93% H2O/7% D2O
30.2 mM [U-100% 13C; U-100% 15N] LFV-Z, 20 mM potassium phosphate, 200 mM sodium chloride, 3 mM sodium azide, 0.05 mM zinc sulfate, 0.05 mM TCEP, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMLFV-Z-1[U-100% 15N]1
20 mMpotassium phosphate-21
200 mMsodium chloride-31
3 mMsodium azide-41
0.05 mMzinc sulfate-51
0.05 mMTCEP-61
7 %D2O-71
93 %H2O-81
0.2 mMLFV-Z-9[U-100% 13C; U-100% 15N]2
20 mMpotassium phosphate-102
200 mMsodium chloride-112
3 mMsodium azide-122
0.05 mMzinc sulfate-132
0.05 mMTCEP-142
7 %D2O-152
93 %H2O-162
0.2 mMLFV-Z-17[U-100% 13C; U-100% 15N]3
20 mMpotassium phosphate-183
200 mMsodium chloride-193
3 mMsodium azide-203
0.05 mMzinc sulfate-213
0.05 mMTCEP-223
100 %D2O-233
Sample conditionsIonic strength: 0.25 / pH: 7.2 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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