BMRB Entry 27441

Name: Long-range effects induced by peptide-MHC binding to a human T cell receptor: Implications for the initiation of T cell signaling
Published: 2018-08-22

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27441

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Long-range effects induced by peptide-MHC binding to a human T cell receptor: Implications for the initiation of T cell signaling PubMed: 30135211

Deposition date: 2018-03-30 Original release date: 2018-08-22

Authors: He, Yanan; Rangarajan, Sneha; Chen, Yihong; Kerzic, Melissa; Ma, Buyong; Gowthaman, Ragul; Pierce, Brian; Nussinov, Ruth; Mariuzza, Roy; Orban, John

Citation: Rangarajan, Sneha; He, Yanan; Chen, Yihong; Kerzic, Melissa; Ma, Buyong; Gowthaman, Ragul; Pierce, Brian; Nussinov, Ruth; Mariuzza, Roy; Orban, John. "Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites" J. Biol. Chem. 293, 15991-16005 (2018).

Assembly members:
A6TCR_beta, polymer, 245 residues, Formula weight is not available
A6TCR_alpha, polymer, 206 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-26b

Entity Sequences (FASTA):
A6TCR_beta: NAGVTQTPKFQVLKTGQSMT LQCAQDMNHEYMSWYRQDPG MGLRLIHYSVGAGITDQGEV PNGYNVSRSTTEDFPLRLLS AAPSQTSVYFCASRPGLAGG RPEQYFGPGTRLTVTEDLKN VFPPEVAVFEPSEAEISHTQ KATLVCLATGFYPDHVELSW WVNGKEVHSGVCTDPQPLKE QPALNDSRYALSSRLRVSAT FWQDPRNHFRCQVQFYGLSE NDEWTQDRAKPVTQIVSAEA WGRAD
A6TCR_alpha: MQKEVEQNSGPLSVPEGAIA SLNCTYSDRGSQSFFWYRQY SGKSPELIMSIYSNGDKEDG RFTAQLNKASQYVSLLIRDS QPSDSATYLCAVTTDSWGKL QFGAGTQVVVTPDIQNPDPA VYQLRDSKSSDKSVCLFTDF DSQTNVSQSKDSDVYITDKC VLDMRSMDFKSNSAVAWSNK SDFACANAFNNSIIPEDTFF PSPESS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	536
15N chemical shifts	162
1H chemical shifts	162

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	A6TCR beta	1
2	A6TCR alpha	2

Entities:

Entity 1, A6TCR beta 245 residues - Formula weight is not available

1

ASN

ALA

GLY

VAL

THR

GLN

THR

PRO

LYS

PHE

2

GLN

VAL

LEU

LYS

THR

GLY

GLN

SER

MET

THR

3

LEU

GLN

CYS

ALA

GLN

ASP

MET

ASN

HIS

GLU

4

TYR

MET

SER

TRP

TYR

ARG

GLN

ASP

PRO

GLY

5

MET

GLY

LEU

ARG

LEU

ILE

HIS

TYR

SER

VAL

6

GLY

ALA

GLY

ILE

THR

ASP

GLN

GLY

GLU

VAL

7

PRO

ASN

GLY

TYR

ASN

VAL

SER

ARG

SER

THR

8

THR

GLU

ASP

PHE

PRO

LEU

ARG

LEU

SER

9

ALA

PRO

SER

GLN

THR

SER

VAL

TYR

PHE

10

CYS

ALA

SER

ARG

PRO

GLY

LEU

ALA

GLY

11

ARG

PRO

GLU

GLN

TYR

PHE

GLY

PRO

GLY

THR

12

ARG

LEU

THR

VAL

THR

GLU

ASP

LEU

LYS

ASN

13

VAL

PHE

PRO

GLU

VAL

ALA

VAL

PHE

GLU

14

PRO

SER

GLU

ALA

GLU

ILE

SER

HIS

THR

GLN

15

LYS

ALA

THR

LEU

VAL

CYS

LEU

ALA

THR

GLY

16

PHE

TYR

PRO

ASP

HIS

VAL

GLU

LEU

SER

TRP

17

TRP

VAL

ASN

GLY

LYS

GLU

VAL

HIS

SER

GLY

18

VAL

CYS

THR

ASP

PRO

GLN

PRO

LEU

LYS

GLU

19

GLN

PRO

ALA

LEU

ASN

ASP

SER

ARG

TYR

ALA

20

LEU

SER

ARG

LEU

ARG

VAL

SER

ALA

THR

21

PHE

TRP

GLN

ASP

PRO

ARG

ASN

HIS

PHE

ARG

22

CYS

GLN

VAL

GLN

PHE

TYR

GLY

LEU

SER

GLU

23

ASN

ASP

GLU

TRP

THR

GLN

ASP

ARG

ALA

LYS

24

PRO

VAL

THR

GLN

ILE

VAL

SER

ALA

GLU

ALA

25

TRP

GLY

ARG

ALA

ASP

Entity 2, A6TCR alpha 206 residues - Formula weight is not available

1

MET

GLN

LYS

GLU

VAL

GLU

GLN

ASN

SER

GLY

2

PRO

LEU

SER

VAL

PRO

GLU

GLY

ALA

ILE

ALA

3

SER

LEU

ASN

CYS

THR

TYR

SER

ASP

ARG

GLY

4

SER

GLN

SER

PHE

TRP

TYR

ARG

GLN

TYR

5

SER

GLY

LYS

SER

PRO

GLU

LEU

ILE

MET

SER

6

ILE

TYR

SER

ASN

GLY

ASP

LYS

GLU

ASP

GLY

7

ARG

PHE

THR

ALA

GLN

LEU

ASN

LYS

ALA

SER

8

GLN

TYR

VAL

SER

LEU

ILE

ARG

ASP

SER

9

GLN

PRO

SER

ASP

SER

ALA

THR

TYR

LEU

CYS

10

ALA

VAL

THR

ASP

SER

TRP

GLY

LYS

LEU

11

GLN

PHE

GLY

ALA

GLY

THR

GLN

VAL

12

THR

PRO

ASP

ILE

GLN

ASN

PRO

ASP

PRO

ALA

13

VAL

TYR

GLN

LEU

ARG

ASP

SER

LYS

SER

14

ASP

LYS

SER

VAL

CYS

LEU

PHE

THR

ASP

PHE

15

ASP

SER

GLN

THR

ASN

VAL

SER

GLN

SER

LYS

16

ASP

SER

ASP

VAL

TYR

ILE

THR

ASP

LYS

CYS

17

VAL

LEU

ASP

MET

ARG

SER

MET

ASP

PHE

LYS

18

SER

ASN

SER

ALA

VAL

ALA

TRP

SER

ASN

LYS

19

SER

ASP

PHE

ALA

CYS

ALA

ASN

ALA

PHE

ASN

20

ASN

SER

ILE

PRO

GLU

ASP

THR

PHE

21

PRO

SER

PRO

GLU

SER

Samples:

sample_1: A6TCR_beta, [U-13C; U-15N; U-2H], 250 mM; sodium phosphate 50 mM; sodium chloride 100 mM; Pefabloc 0.1 mg/mL

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACO	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - chemical shift assignment, collection, data analysis, processing

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 600 MHz

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