BMRBj - BMREntryMaster

Found 1 Document (0.697 seconds)

BMRB: 27248

3J70

Backbone amide and AILV methyl chemical shift assignments for Beta2-microglobulin, a human class I major histocompatibility molecule light 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

Human immunodeficiency virus 1 , Mus musculus , Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 27.1 %, Completeness: 10.5 %, Completeness (bb): 17.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	10.5 % (482 of 4586)	6.4 % (154 of 2394)	13.2 % (235 of 1784)	22.8 % (93 of 408)
Backbone	17.1 % (391 of 2284)	13.0 % (102 of 782)	17.3 % (196 of 1134)	25.3 % (93 of 368)
Sidechain	6.8 % (181 of 2662)	3.3 % (53 of 1612)	12.7 % (128 of 1010)	0.0 % (0 of 40)
Aromatic	0.0 % (0 of 500)	0.0 % (0 of 250)	0.0 % (0 of 237)	0.0 % (0 of 13)
Methyl	22.3 % (79 of 354)	22.6 % (40 of 177)	22.0 % (39 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 light chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	natural abundance	1 mM
2	Beta-2 microglobulin	[U-100% 13C; U-100% 15N]	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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

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: 27249 released on 2017-09-10
    Title Backbone amide and AILV methyl chemical shift assignments for H2-Dd, a murine class I major histocompatibility molecule heavy 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 9 experiments Detail

1 2D 1H-15N TROSY-HSQC

Instrument

Bruker Avance - 800 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

2 2D 1H-13C SOFAST HMQC

Instrument

Bruker Avance - 800 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	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 light chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	natural abundance	1 mM
2	Beta-2 microglobulin	[U-100% 13C; U-100% 15N]	1 mM
3	P18-I10	natural abundance	1 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

5 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 light chain light chain and peptide are natural abundance

#	Name	Isotope labeling	Concentration
1	H2-Dd	natural abundance	1 mM
2	Beta-2 microglobulin	[U-100% 13C; U-100% 15N]	1 mM
3	P18-I10	natural abundance	1 mM

6 3D Hm-CmHm SOFAST NOESY HMQC

Instrument

Bruker Avance - 600 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

7 3D Cm-CmHm SOFAST HMQC NOESY HMQC

Instrument

Bruker Avance - 800 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

8 3D Hn-CmHm SOFAST NOESY HMQC

Instrument

Bruker Avance - 800 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

9 3D Cm-NHn SOFAST HMQC NOESY HMQC

Instrument

Bruker Avance - 800 MHz

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	natural abundance	1 mM
5	Beta-2 microglobulin	[U-15N; U-2H; U-13C; AILV]	1 mM
6	P18-I10	natural abundance	1 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr27248_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: bmr27248_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	504		99.0 (chain: 2, length: 100)
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: 2, Chain length: 100, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 195
  - ¹³C chemical shifts: 219
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: 2
- 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: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	639	125	19.6
¹³C chemical shifts	478	219	45.8
¹⁵N chemical shifts	110	90	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	90	45.5
¹³C chemical shifts	200	99	49.5
¹⁵N chemical shifts	95	90	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	441	35	7.9
¹³C chemical shifts	278	120	43.2
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	35	74.5
¹³C chemical shifts	47	35	74.5

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Found 1 Document (0.697 seconds)

BMRB: 27248

Sample #1

Sample #2

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 9 experiments Detail

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Chemical shift validation 5 contents Detail