BMRBj - BMREntryMaster

Found 1 Document (0.762 seconds)

BMRB: 27249

3J70

Backbone amide and AILV methyl chemical shift assignments for H2-Dd, a murine class I major histocompatibility molecule heavy chain

Authors

Sgourakis, N.G., McShan, A.C., Natarajan, K., Kumirov, V.K., Margulies, D.H., Nerli, S., Badstuebner, M.

Assembly

pMHC

Entity

1. H2-Dd (polymer, Thiol state: all disulfide bound), 277 monomers, 32222.53 Da Detail

MSHSLRYFVT AVSRPGFGEP RYMEVGYVDN TEFVRFDSDA ENPRYEPRAR WIEQEGPEYW ERETRRAKGN EQSFRVDLRT ALRYYNQSAG GSHTLQWMAG CDVESDGRLL RGYWQFAYDG CDYIALNEDL KTWTAADMAA QITRRKWEQA GAAERDRAYL EGECVEWLRR YLKNGNATLL RTDPPKAHVT HHRRPEGDVT LRCWALGFYP ADITLTWQLN GEELTQEMEL VETRPAGDGT FQKWASVVVP LGKEQKYTCH VEHEGLPEPL TLRWGKE

2. Beta-2 microglobulin (polymer, Thiol state: all disulfide bound), 100 monomers, 11862.21 Da Detail

MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLSQ PKIVKWDRDM

3. P18-I10 (polymer, Thiol state: not present), 10 monomers, 1073.249 Da Detail

RGPGRAFVTI

Total weight

45157.99 Da

Max. entity weight

32222.53 Da

Source organism

Mus musculus , Homo sapiens , Human immunodeficiency virus 1

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 69.5 %, Completeness: 37.4 %, Completeness (bb): 56.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	37.4 % (1715 of 4586)	25.1 % (601 of 2394)	48.8 % (870 of 1784)	59.8 % (244 of 408)
Backbone	56.1 % (1281 of 2284)	39.3 % (307 of 782)	64.6 % (732 of 1134)	65.8 % (242 of 368)
Sidechain	25.1 % (667 of 2662)	18.4 % (297 of 1612)	36.4 % (368 of 1010)	5.0 % (2 of 40)
Aromatic	4.6 % (23 of 500)	6.4 % (16 of 250)	3.0 % (7 of 237)	0.0 % (0 of 13)
Methyl	59.9 % (212 of 354)	61.0 % (108 of 177)	58.8 % (104 of 177)

1. H2-Dd

2. Beta-2 microglobulin

MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLSQ PKIVKWDRDM

3. P18-I10

RGPGRAFVTI

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details labeled at the heavy chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	[U-13C; U-15N; U-2H]	1 mM
2	Beta-2 microglobulin	natural abundance	1 mM
3	P18-I10	natural abundance	1 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details selectively 13C methyl labeled with sidechain and backbone carbons 13C labeled

#	Name	Isotope labeling	Concentration
7	H2-Dd	[U-15N; U-2H; U-13C-all methyl carbons]	1 mM
8	P18-I10	natural abundance	1 mM
9	Beta-2 microglobulin	natural abundance	1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.46 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.46 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.15 ppm, Outliers: 2 Detail

Release date

2017-09-10

Citation

Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle
McShan, A.C., Natarajan, K., Kumirov, V.K., Flores-Solis, D., Jiang, J., Badstubner, M., Toor, J.S., Bagshaw, C.R., Kovrigin, E.L., Margulies, D.H., Sgourakis, N.G.
Nat. Chem. Biol. (2018), 14, 811-820, PubMed 29988068 , DOI 10.1038/s41589-018-0096-2 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 30350 released on 2017-11-09
    Title Solution NMR Structure of Unbound P18-I10
  BMRB: 27248 released on 2017-09-10
    Title Backbone amide and AILV methyl chemical shift assignments for Beta2-microglobulin, a human class I major histocompatibility molecule light chain

Related entities 1. H2-Dd, : 93 entities Detail

Related entities 2. Beta-2 microglobulin, : 3 : 89 entities Detail

Related entities 3. P18-I10, : 1 : 22 : 1 entities Detail

Interaction partners 3. P18-I10, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N TROSY-HSQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details labeled at the heavy chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	[U-13C; U-15N; U-2H]	1 mM
2	Beta-2 microglobulin	natural abundance	1 mM
3	P18-I10	natural abundance	1 mM

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details labeled at the heavy chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	[U-13C; U-15N; U-2H]	1 mM
2	Beta-2 microglobulin	natural abundance	1 mM
3	P18-I10	natural abundance	1 mM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details labeled at the heavy chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	[U-13C; U-15N; U-2H]	1 mM
2	Beta-2 microglobulin	natural abundance	1 mM
3	P18-I10	natural abundance	1 mM

4 3D HN(CA)CB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details labeled at the heavy chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	[U-13C; U-15N; U-2H]	1 mM
2	Beta-2 microglobulin	natural abundance	1 mM
3	P18-I10	natural abundance	1 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

6 3D Hm-CmHm SOFAST NOESY HMQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

7 2D 1H-13C SOFAST HMQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

8 3D Cm-CmHm SOFAST HMQC NOESY HMQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

9 3D Hn-CmHm SOFAST NOESY HMQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

10 3D Cm-NHn SOFAST HMQC NOESY HMQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details Specifically labeled at Ala, Ile, Leu and Val methyls

#	Name	Isotope labeling	Concentration
4	H2-Dd	[U-15N; U-2H; U-13C; AILV]	1 mM
5	P18-I10	natural abundance	1 mM
6	Beta-2 microglobulin	natural abundance	1 mM

11 3D HMCM[CG]CBCA

Instrument

Bruker Avance - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details selectively 13C methyl labeled with sidechain and backbone carbons 13C labeled

#	Name	Isotope labeling	Concentration
7	H2-Dd	[U-15N; U-2H; U-13C-all methyl carbons]	1 mM
8	P18-I10	natural abundance	1 mM
9	Beta-2 microglobulin	natural abundance	1 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr27249_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr27249_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1564		94.2 (chain: 1, length: 277)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 277, Sequence coverage: 94.2%
- Total number of assignments
  - ¹³C chemical shifts: 801
  - ¹H chemical shifts: 530
  - ¹⁵N chemical shifts: 233
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1261	801	63.5
¹H chemical shifts	1696	332	19.6
¹⁵N chemical shifts	321	233	72.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	554	482	87.0
¹H chemical shifts	563	233	41.4
¹⁵N chemical shifts	264	233	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	707	319	45.1
¹H chemical shifts	1133	99	8.7
¹⁵N chemical shifts	57	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	131	96	73.3
¹H chemical shifts	131	99	75.6

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Found 1 Document (0.762 seconds)

BMRB: 27249

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. H2-Dd, : 93 entities Detail

Related entities 2. Beta-2 microglobulin, : 3 : 89 entities Detail

Related entities 3. P18-I10, : 1 : 22 : 1 entities Detail

Interaction partners 3. P18-I10, : 1 interactors Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 5 contents Detail