BMRB Entry 19699

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19699
MolProbity Validation Chart

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Title:
Structure of the m04/gp34 mouse Cytomegalovirus Immunoevasin core domain
Deposition date:
2013-12-21
Original release date:
2014-07-14
Authors:
Sgourakis, Nikolaos; Natarajan, Kannan; Margulies, David; Bax, Ad
Citation:

Citation: Sgourakis, Nikolaos; Natarajan, Kannan; Margulies, David; Bax, Ad. "The murine Cytomegalovirus gp34/m04 protein contains a core domain with novel structure revealed by solution NMR"  .

Assembly members:

Assembly members:
entity, polymer, 156 residues, 17494.967 Da.

Natural source:

Natural source:   Common Name: Maize chlorotic mottle virus   Taxonomy ID: 12138   Superkingdom: Virus   Kingdom: not available   Genus/species: Machlomovirus Maize chlorotic mottle virus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: plasmid

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: RHSLGCYFKGINPTKVPSSD PRTVLKCTLPDVKVNASWTL EWVVVNLHTSVDVTSYYESS PNSEPRFLRAILNFTPMHGL RTKNLLKVKDGFQVDNSTDN GNGGNLYVYPNATTGSADSV RCRLRMCPWTSNSKMTAPDE EMLRKMSEVLNLPNYG

Data sets:
Data typeCount
13C chemical shifts411
15N chemical shifts143
1H chemical shifts143

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1gp34/m041

Entities:

Entity 1, gp34/m04 156 residues - 17494.967 Da.

1   ARGHISSERLEUGLYCYSTYRPHELYSGLY
2   ILEASNPROTHRLYSVALPROSERSERASP
3   PROARGTHRVALLEULYSCYSTHRLEUPRO
4   ASPVALLYSVALASNALASERTRPTHRLEU
5   GLUTRPVALVALVALASNLEUHISTHRSER
6   VALASPVALTHRSERTYRTYRGLUSERSER
7   PROASNSERGLUPROARGPHELEUARGALA
8   ILELEUASNPHETHRPROMETHISGLYLEU
9   ARGTHRLYSASNLEULEULYSVALLYSASP
10   GLYPHEGLNVALASPASNSERTHRASPASN
11   GLYASNGLYGLYASNLEUTYRVALTYRPRO
12   ASNALATHRTHRGLYSERALAASPSERVAL
13   ARGCYSARGLEUARGMETCYSPROTRPTHR
14   SERASNSERLYSMETTHRALAPROASPGLU
15   GLUMETLEUARGLYSMETSERGLUVALLEU
16   ASNLEUPROASNTYRGLY

Samples:

3D: sodium phosphate 20mM mM; D2O, [U-99% 2H], 5%; sodium chloride 50 mM; gp34/m04, [U-13C; U-15N; U-2H], 0.2 – 0.5 mM; H2O 95

ILV_CC: sodium phosphate 20mM mM; D2O, [U-99% 2H], 5%; sodium chloride 50 mM; gp34/m04, [U-13C; U-15N; U-2H; ILVmethyl-1H], 0.2 – 0.5 mM; H2O 95

GEL: sodium phosphate 20mM mM; D2O, [U-99% 2H], 5%; sodium chloride 50 mM; gp34/m04, [U-15N; U-2H], 0.2 – 0.5 mM; Ac/Bis-Ac 5.5%; DADMAC 20%; H2O 95

Pf1: sodium phosphate 20mM mM; D2O, [U-99% 2H], 5%; sodium chloride 200 mM; gp34/m04, [U-15N; U-2H], 0.2 – 0.5 mM; Pf1 phage 7.5%; H2O 95

ILV_NOE: sodium phosphate 20mM mM; D2O, [U-99% 2H], 5%; sodium chloride 50 mM; gp34/m04, [ILVmethyl-13C; U-15N; U-2H; ILVmethyl-1H], 0.2 – 0.5 mM; H2O 95

2D: sodium phosphate 20mM mM; D2O, [U-99% 2H], 5%; sodium chloride 50 mM; gp34/m04, [U-15N; U-2H], 0.2 – 0.5 mM; H2O 95

sample_conditions_1: ionic strength: 0.110 M; pH: 6.5; pressure: 1 atm; temperature: 285 K

sample_conditions_2: ionic strength: 0.260 M; pH: 6.5; pressure: 1 atm; temperature: 285 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSY-HSQC3Disotropicsample_conditions_1
3D HNCA3Disotropicsample_conditions_1
3D HNCACB3Disotropicsample_conditions_1
3D HNCO3Disotropicsample_conditions_1
3D HN(CA)CO3Disotropicsample_conditions_1
2D 1H-15N ARTSYPf1anisotropicsample_conditions_2
2D 1H-15N ARTSYGELanisotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (HCH)ILV_NOEisotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (CCH)ILV_NOEisotropicsample_conditions_1
2D 1H-13C HMQC methylILV_NOEisotropicsample_conditions_1
3D 1H-15N NOESY (HCH)ILV_NOEisotropicsample_conditions_1
3D 1H-15N NOESY (HCN)ILV_NOEisotropicsample_conditions_1
3D 1H-15N NOESY (HNH)2Disotropicsample_conditions_1
3D 1H-15N NOESY (NNH)2Disotropicsample_conditions_1
SIM-HMCM(CGCBCA)COILV_CCisotropicsample_conditions_1
HMCM(CG)CBCAILV_CCisotropicsample_conditions_1

Software:

nmrPipe, Delaglio, Zhengrong and Bax - data analysis

sparky, Goddard - chemical shift assignment

TOPSPIN v3.1, Bruker Biospin - collection

CS-Rosetta v3.0, Shen, Vernon, Baker and Bax - structure solution

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks