BMRB Entry 27632

Name: Backbone amide and AILV methyl chemical shift assignments for HLA-A*01:01, a human class I major histocompatibility molecule heavy chain
Published: 2018-11-01

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PDB ID: 6mpp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR27632
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Backbone amide and AILV methyl chemical shift assignments for HLA-A01:01, a human class I major histocompatibility molecule heavy chain PubMed: 31796585*

Deposition date: 2018-09-26 Original release date: 2018-11-01

Authors: McShan, Andrew; Sgourakis, Nik

Citation: McShan, Andrew; Devlin, Christine; Overall, Sarah; Park, Jihye; Toor, Jugmohit; Moschidi, Danai; Flores-Solis, David; Choi, Hannah; Tripathi, Sarvind; Procko, Erik; Sgourakis, Nikolaos. "Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection" Proc. Natl. Acad. Sci. U.S.A. 116, 25602-25613 (2019).

Assembly members:
HLA-A*01:01, polymer, 280 residues, Formula weight is not available
NRAS_Q61K_peptide, polymer, 10 residues, Formula weight is not available
human_beta2m, polymer, 100 residues, Formula weight is not available

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
HLA-A*01:01: GSHSMRYFFTSVSRPGRGEP RFIAVGYVDDTQFVRFDSDA ASQKMEPRAPWIEQEGPEYW DQETRNMKAHSQTDRANLGT LRGYYNQSEDGSHTIQIMYG CDVGPDGRFLRGYRQDAYDG KDYIALNEDLRSWTAADMAA QITKRKWEAVHAAEQRRVYL EGRCVNGLRRYLENGKETLQ RTDPPKTHMTHHHISDHEAT LRCWALGFYPAEITLTWQRD GEDQTQDTELVETRPAGDGT FQKWAAVVVPSGEEQRYTCH VQHEGLPKPLTLRWELSSQP
NRAS_Q61K_peptide: ILDTAGKEEY
human_beta2m: MIQRTPKIQVYSRHPAENGK SNFLNCYVSGFHPSDIEVDL LKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYA CRVNHVTLSQPKIVKWDRDM

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	786
15N chemical shifts	247
1H chemical shifts	557

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Heavy chain	1
2	Peptide	2
3	Light chain	3

Entities:

Entity 1, Heavy chain 280 residues - Formula weight is not available

1	GLY	SER	HIS	SER	MET	ARG	TYR	PHE	PHE	THR
2	SER	VAL	SER	ARG	PRO	GLY	ARG	GLY	GLU	PRO
3	ARG	PHE	ILE	ALA	VAL	GLY	TYR	VAL	ASP	ASP
4	THR	GLN	PHE	VAL	ARG	PHE	ASP	SER	ASP	ALA
5	ALA	SER	GLN	LYS	MET	GLU	PRO	ARG	ALA	PRO
6	TRP	ILE	GLU	GLN	GLU	GLY	PRO	GLU	TYR	TRP
7	ASP	GLN	GLU	THR	ARG	ASN	MET	LYS	ALA	HIS
8	SER	GLN	THR	ASP	ARG	ALA	ASN	LEU	GLY	THR
9	LEU	ARG	GLY	TYR	TYR	ASN	GLN	SER	GLU	ASP
10	GLY	SER	HIS	THR	ILE	GLN	ILE	MET	TYR	GLY
11	CYS	ASP	VAL	GLY	PRO	ASP	GLY	ARG	PHE	LEU
12	ARG	GLY	TYR	ARG	GLN	ASP	ALA	TYR	ASP	GLY
13	LYS	ASP	TYR	ILE	ALA	LEU	ASN	GLU	ASP	LEU
14	ARG	SER	TRP	THR	ALA	ALA	ASP	MET	ALA	ALA
15	GLN	ILE	THR	LYS	ARG	LYS	TRP	GLU	ALA	VAL
16	HIS	ALA	ALA	GLU	GLN	ARG	ARG	VAL	TYR	LEU
17	GLU	GLY	ARG	CYS	VAL	ASN	GLY	LEU	ARG	ARG
18	TYR	LEU	GLU	ASN	GLY	LYS	GLU	THR	LEU	GLN
19	ARG	THR	ASP	PRO	PRO	LYS	THR	HIS	MET	THR
20	HIS	HIS	HIS	ILE	SER	ASP	HIS	GLU	ALA	THR
21	LEU	ARG	CYS	TRP	ALA	LEU	GLY	PHE	TYR	PRO
22	ALA	GLU	ILE	THR	LEU	THR	TRP	GLN	ARG	ASP
23	GLY	GLU	ASP	GLN	THR	GLN	ASP	THR	GLU	LEU
24	VAL	GLU	THR	ARG	PRO	ALA	GLY	ASP	GLY	THR
25	PHE	GLN	LYS	TRP	ALA	ALA	VAL	VAL	VAL	PRO
26	SER	GLY	GLU	GLU	GLN	ARG	TYR	THR	CYS	HIS
27	VAL	GLN	HIS	GLU	GLY	LEU	PRO	LYS	PRO	LEU
28	THR	LEU	ARG	TRP	GLU	LEU	SER	SER	GLN	PRO

Entity 2, Peptide 10 residues - Formula weight is not available

1

ILE

LEU

ASP

THR

ALA

GLY

LYS

GLU

TYR

Entity 3, Light chain 100 residues - Formula weight is not available

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET

Samples:

sample_1: HLA-A*01:01, [U-100% 13C; U-100% 15N], 500 uM; NRAS Q61K peptide 500 uM; human beta2m 500 uM

sample_2: HLA-A*01:01, 13C AILV methyl [U-15N], 500 uM; NRAS Q61K peptide 500 uM; human beta2m 500 uM

sample_conditions_1: ionic strength: 50 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker Avance 800 MHz

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

1	GLY	SER	HIS	SER	MET	ARG	TYR	PHE	PHE	THR
2	SER	VAL	SER	ARG	PRO	GLY	ARG	GLY	GLU	PRO
3	ARG	PHE	ILE	ALA	VAL	GLY	TYR	VAL	ASP	ASP
4	THR	GLN	PHE	VAL	ARG	PHE	ASP	SER	ASP	ALA
5	ALA	SER	GLN	LYS	MET	GLU	PRO	ARG	ALA	PRO
6	TRP	ILE	GLU	GLN	GLU	GLY	PRO	GLU	TYR	TRP
7	ASP	GLN	GLU	THR	ARG	ASN	MET	LYS	ALA	HIS
8	SER	GLN	THR	ASP	ARG	ALA	ASN	LEU	GLY	THR
9	LEU	ARG	GLY	TYR	TYR	ASN	GLN	SER	GLU	ASP
10	GLY	SER	HIS	THR	ILE	GLN	ILE	MET	TYR	GLY
11	CYS	ASP	VAL	GLY	PRO	ASP	GLY	ARG	PHE	LEU
12	ARG	GLY	TYR	ARG	GLN	ASP	ALA	TYR	ASP	GLY
13	LYS	ASP	TYR	ILE	ALA	LEU	ASN	GLU	ASP	LEU
14	ARG	SER	TRP	THR	ALA	ALA	ASP	MET	ALA	ALA
15	GLN	ILE	THR	LYS	ARG	LYS	TRP	GLU	ALA	VAL
16	HIS	ALA	ALA	GLU	GLN	ARG	ARG	VAL	TYR	LEU
17	GLU	GLY	ARG	CYS	VAL	ASN	GLY	LEU	ARG	ARG
18	TYR	LEU	GLU	ASN	GLY	LYS	GLU	THR	LEU	GLN
19	ARG	THR	ASP	PRO	PRO	LYS	THR	HIS	MET	THR
20	HIS	HIS	HIS	ILE	SER	ASP	HIS	GLU	ALA	THR
21	LEU	ARG	CYS	TRP	ALA	LEU	GLY	PHE	TYR	PRO
22	ALA	GLU	ILE	THR	LEU	THR	TRP	GLN	ARG	ASP
23	GLY	GLU	ASP	GLN	THR	GLN	ASP	THR	GLU	LEU
24	VAL	GLU	THR	ARG	PRO	ALA	GLY	ASP	GLY	THR
25	PHE	GLN	LYS	TRP	ALA	ALA	VAL	VAL	VAL	PRO
26	SER	GLY	GLU	GLU	GLN	ARG	TYR	THR	CYS	HIS
27	VAL	GLN	HIS	GLU	GLY	LEU	PRO	LYS	PRO	LEU
28	THR	LEU	ARG	TRP	GLU	LEU	SER	SER	GLN	PRO

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET

1	GLY	SER	HIS	SER	MET	ARG	TYR	PHE	PHE	THR
2	SER	VAL	SER	ARG	PRO	GLY	ARG	GLY	GLU	PRO
3	ARG	PHE	ILE	ALA	VAL	GLY	TYR	VAL	ASP	ASP
4	THR	GLN	PHE	VAL	ARG	PHE	ASP	SER	ASP	ALA
5	ALA	SER	GLN	LYS	MET	GLU	PRO	ARG	ALA	PRO
6	TRP	ILE	GLU	GLN	GLU	GLY	PRO	GLU	TYR	TRP
7	ASP	GLN	GLU	THR	ARG	ASN	MET	LYS	ALA	HIS
8	SER	GLN	THR	ASP	ARG	ALA	ASN	LEU	GLY	THR
9	LEU	ARG	GLY	TYR	TYR	ASN	GLN	SER	GLU	ASP
10	GLY	SER	HIS	THR	ILE	GLN	ILE	MET	TYR	GLY
11	CYS	ASP	VAL	GLY	PRO	ASP	GLY	ARG	PHE	LEU
12	ARG	GLY	TYR	ARG	GLN	ASP	ALA	TYR	ASP	GLY
13	LYS	ASP	TYR	ILE	ALA	LEU	ASN	GLU	ASP	LEU
14	ARG	SER	TRP	THR	ALA	ALA	ASP	MET	ALA	ALA
15	GLN	ILE	THR	LYS	ARG	LYS	TRP	GLU	ALA	VAL
16	HIS	ALA	ALA	GLU	GLN	ARG	ARG	VAL	TYR	LEU
17	GLU	GLY	ARG	CYS	VAL	ASN	GLY	LEU	ARG	ARG
18	TYR	LEU	GLU	ASN	GLY	LYS	GLU	THR	LEU	GLN
19	ARG	THR	ASP	PRO	PRO	LYS	THR	HIS	MET	THR
20	HIS	HIS	HIS	ILE	SER	ASP	HIS	GLU	ALA	THR
21	LEU	ARG	CYS	TRP	ALA	LEU	GLY	PHE	TYR	PRO
22	ALA	GLU	ILE	THR	LEU	THR	TRP	GLN	ARG	ASP
23	GLY	GLU	ASP	GLN	THR	GLN	ASP	THR	GLU	LEU
24	VAL	GLU	THR	ARG	PRO	ALA	GLY	ASP	GLY	THR
25	PHE	GLN	LYS	TRP	ALA	ALA	VAL	VAL	VAL	PRO
26	SER	GLY	GLU	GLU	GLN	ARG	TYR	THR	CYS	HIS
27	VAL	GLN	HIS	GLU	GLY	LEU	PRO	LYS	PRO	LEU
28	THR	LEU	ARG	TRP	GLU	LEU	SER	SER	GLN	PRO

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET