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- PDB-5a3g: Structure of herpesvirus nuclear egress complex subunit M50 -

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Basic information

Entry
Database: PDB / ID: 5a3g
TitleStructure of herpesvirus nuclear egress complex subunit M50
ComponentsM50
KeywordsVIRAL PROTEIN / NUCLEAR EGRESS
Function / homologyHerpesvirus viron egress-type / Herpesvirus virion protein U34 / membrane => GO:0016020 / host cell nucleus / Uncharacterized protein M50 / M50 protein
Function and homology information
Biological speciesMURID HERPESVIRUS 1 (Murine cytomegalovirus)
MethodSOLUTION NMR / SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS SIMULATION, RDC, WATERBOX REFINEMENT
AuthorsLeigh, K.E. / Boeszoermenyi, A. / Mansueto, M.S. / Sharma, M. / Filman, D.J. / Coen, D.M. / Wagner, G. / Hogle, J.M. / Arthanari, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of a Herpesvirus Nuclear Egress Complex Subunit Reveals an Interaction Groove that is Essential for Viral Replication
Authors: Leigh, K.E. / Sharma, M. / Mansueto, M.S. / Boeszoermenyi, A. / Filman, D.J. / Hogle, J.M. / Wagner, G. / Coen, D.M. / Arthanari, H.
History
DepositionJun 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M50


Theoretical massNumber of molelcules
Total (without water)19,4021
Polymers19,4021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein M50


Mass: 19402.285 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-168
Source method: isolated from a genetically manipulated source
Details: GENERATED AFTER CLEAVAGE FROM AN INTEIN AFFINITY TAG RESULTING IN AN ADDITIONAL THREE RESIDUES (ALA-GLY-HIS) BEFORE THE STARTING METHIONINE RESIDUE.
Source: (gene. exp.) MURID HERPESVIRUS 1 (Murine cytomegalovirus)
Strain: SMITH / Plasmid: IMPACT-CN PTYB12 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: H2A365, UniProt: D3XDN8*PLUS
Sequence detailsADDITIONAL 3 RESIDUES (ALA-GLY-HIS) IN SAMPLE SEQUENCE BEFORE THE BEGINNING METHIONINE LEFT FROM ...ADDITIONAL 3 RESIDUES (ALA-GLY-HIS) IN SAMPLE SEQUENCE BEFORE THE BEGINNING METHIONINE LEFT FROM THE CLEAVAGE OF THE INTEIN AFFINITY TAG. THE REMAINING SEQUENCE IS RESIDUES 1-168 OF M50 GIVING A TOTAL OF 171 RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N TROSY
121TROSY HNCA
131TROSY HN(CA)CB
141TROSY HN(CA)CO
151TROSY HNCO
161TROSY HN(CO)CA
271RDC HNCO
38115N NOESYHSQC
49113C HSQC
510113C NOESYHSQC
6111C(CO)NH
7121(H)CCH-TOCSY
7131H(CCO)NH
814113C ILV NOESY
815115N ILV NOESY
916113C ILV HSQC
91714D 13C HMQC- NOESY-HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE AND NOESY-BASED NMR EXPERIMENTS ON 13C,15N-LABELED M50 ( RESIDUES 1-168).

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Sample preparation

Details
Solution-IDContents
193% H2O/7% D2O, M50 230 UMOL/L
293% H2O/7% D2O, M50 230 UMOL/L
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1175.0 6.5 1.0 atm291.15 K
2175.0 6.5 1.0 atm291.15 K
3175.0 6.5 1.0 atm291.15 K
4175.0 6.5 1.0 atm291.15 K
5175.0 6.5 1.0 atm291.15 K
6175.0 6.5 1.0 atm291.15 K
7175.0 6.5 1.0 atm291.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7501
Varian INOVAVarianINOVA6002
9003

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Processing

NMR software
NameVersionDeveloperClassification
AmberCASE, CHEATHAM, MERZ, ROITBERG, SIMMERLING, LUO, WANG, WALKER,refinement
CYANA3structure solution
NMRDraw11structure solution
TALOS+1.2009.0605.17structure solution
CcpNmr Analysis2.4structure solution
NMRPipe11structure solution
hmsIST2.11structure solution
CARA1.8.4structure solution
RefinementMethod: SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS SIMULATION, RDC, WATERBOX REFINEMENT
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 15

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