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- PDB-2miz: Structure of the m04/gp34 mouse Cytomegalovirus Immunoevasin core... -

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Basic information

Entry
Database: PDB / ID: 2miz
TitleStructure of the m04/gp34 mouse Cytomegalovirus Immunoevasin core domain
Componentsm04 immunoevasin
KeywordsVIRAL PROTEIN / MHC class-I regulation / Immunoglobulin-like fold / Natural Killer decoy / missing-self / Rosetta modelling / ILV labelling / Residual Dipolar Couplings
Function / homologyImmunoglobulin-like - #2900 / Gp34-like superfamily / Immune evasion protein / Immune evasion protein / membrane => GO:0016020 / Immunoglobulin-like / Sandwich / Mainly Beta / M04 immunoevasin
Function and homology information
Biological speciesMurine cytomegalovirus (Murine cytomegalovirus)
MethodSOLUTION NMR / RASREC
Model detailslowest Rosetta energy, model1
AuthorsSgourakis, N.G. / Natarajan, K. / Margulies, D.H. / Bax, A.
CitationJournal: Structure / Year: 2014
Title: The Structure of Mouse Cytomegalovirus m04 Protein Obtained from Sparse NMR Data Reveals a Conserved Fold of the m02-m06 Viral Immune Modulator Family.
Authors: Sgourakis, N.G. / Natarajan, K. / Ying, J. / Vogeli, B. / Boyd, L.F. / Margulies, D.H. / Bax, A.
History
DepositionDec 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: m04 immunoevasin


Theoretical massNumber of molelcules
Total (without water)22,8001
Polymers22,8001
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000target function
RepresentativeModel #1lowest energy

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Components

#1: Protein m04 immunoevasin


Mass: 22799.732 Da / Num. of mol.: 1 / Mutation: I66V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine cytomegalovirus (Murine cytomegalovirus)
Strain: K181 / Gene: m04 / Production host: Escherichia coli (E. coli) / References: UniProt: A2Q6L0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY-HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO
2642D 1H-15N ARTSY
1732D 1H-15N ARTSY
1853D 1H-13C NOESY aliphatic (HCH)
1953D 1H-13C NOESY aliphatic (CCH)
11052D 1H-13C HMQC methyl
11153D 1H-15N NOESY (HCH)
11253D 1H-15N NOESY (HCN)
11363D 1H-15N NOESY (HNH)
11463D 1H-15N NOESY (NNH)
1152SIM-HMCM(CGCBCA)CO
1162HMCM(CG)CBCA

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM mM sodium phosphate, 5 % [U-99% 2H] D2O, 50 mM sodium chloride, 0.2-0.5 mM [U-13C; U-15N; U-2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
220mM mM sodium phosphate, 5 % [U-99% 2H] D2O, 50 mM sodium chloride, 0.2-0.5 mM [U-13C; U-15N; U-2H; ILVmethyl-1H] protein, 95% H2O/5% D2O95% H2O/5% D2O
320mM mM sodium phosphate, 5 % [U-99% 2H] D2O, 50 mM sodium chloride, 0.2-0.5 mM [U-15N; U-2H] protein, 5.5 % Ac/Bis-Ac, 20 % DADMAC, 95% H2O/5% D2O95% H2O/5% D2O
420mM mM sodium phosphate, 5 % [U-99% 2H] D2O, 200 mM sodium chloride, 0.2-0.5 mM [U-15N; U-2H] protein, 7.5 % Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
520mM mM sodium phosphate, 5 % [U-99% 2H] D2O, 50 mM sodium chloride, 0.2-0.5 mM [ILVmethyl-13C; U-15N; U-2H; ILVmethyl-1H] protein, 95% H2O/5% D2O95% H2O/5% D2O
620mM mM sodium phosphate, 5 % [U-99% 2H] D2O, 50 mM sodium chloride, 0.2-0.5 mM [U-15N; U-2H] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMsodium phosphate-11
5 %D2O-2[U-99% 2H]1
50 mMsodium chloride-31
mMentity-4[U-13C; U-15N; U-2H]0.2-0.51
20 mMsodium phosphate-52
5 %D2O-6[U-99% 2H]2
50 mMsodium chloride-72
mMentity-8[U-13C; U-15N; U-2H; ILVmethyl-1H]0.2-0.52
20 mMsodium phosphate-93
5 %D2O-10[U-99% 2H]3
50 mMsodium chloride-113
mMentity-12[U-15N; U-2H]0.2-0.53
5.5 %Ac/Bis-Ac-133
20 %DADMAC-143
20 mMsodium phosphate-154
5 %D2O-16[U-99% 2H]4
200 mMsodium chloride-174
mMentity-18[U-15N; U-2H]0.2-0.54
7.5 %Pf1 phage-194
20 mMsodium phosphate-205
5 %D2O-21[U-99% 2H]5
50 mMsodium chloride-225
mMentity-23[ILVmethyl-13C; U-15N; U-2H; ILVmethyl-1H]0.2-0.55
20 mMsodium phosphate-246
5 %D2O-25[U-99% 2H]6
50 mMsodium chloride-266
mMentity-27[U-15N; U-2H]0.2-0.56
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.110 6.5 ambient 285 K
20.260 6.5 ambient 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker AvanceBrukerAvance6002
Bruker AvanceBrukerAvance8003
Bruker AvanceBrukerAvance6004

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Processing

NMR software
NameVersionDeveloperClassification
nmrPipeDelaglio, Zhengrong and Baxdata analysis
sparkyGoddardchemical shift assignment
TOPSPIN3.1Bruker Biospincollection
CS-Rosetta3Shen, Vernon, Baker and Baxstructure solution
CS-Rosettarefinement
RefinementMethod: RASREC / Software ordinal: 1
Details: The high degree of order obtained for residues 21-22 and 175-176 in the deposited ensemble is inconsistent with the chemical shift-derived order parameters (<0.7) that suggest some residual mobility for these residues
NMR constraintsNOE constraints total: 67 / NOE intraresidue total count: 0 / NOE long range total count: 67 / NOE medium range total count: 0 / NOE sequential total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 1.5 Å / Maximum upper distance constraint violation: 4 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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