5M02: PDB entry 5M02

Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV. Determined by X-ray diffraction at 1.75 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Mus musculus, Lymphocytic choriomeningitis virus
Chains: 5
Atoms: 6,998
Mol. weight: 96.91 kDa
Released: 20 Dec 2017

Explore 5M02 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M02 contains 23 α-helices and 73 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-179	15
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain G: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	8
β-strand	17-21	5	9
α-helix	25	1
β-strand	26-32	7	8
β-strand	39-45	7	9
β-strand	52-58	7	9
β-strand	63-66	4	8
β-strand	69-74	6	8
β-strand	79-84	6	8
α-helix	89-91	3
β-strand	93-96	4	9
β-strand	98-99	2	10
β-strand	100	1	9
α-helix	105-106	2
β-strand	107-108	2	10
β-strand	112-117	6	9
β-strand	126-131	6	11
β-strand	139-144	6	11
α-helix	151-153	3
β-strand	160-162	3	11
β-strand	166-170	5	11
β-strand	175-184	10	11
α-helix	191-194	4

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	8-12	5	13
β-strand	17-23	7	12
β-strand	29-36	8	13
β-strand	39-47	9	13
β-strand	54-55	2	13
β-strand	63-65	3	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	85-92	8	13
α-helix	98-100	3
β-strand	101-102	2	13
β-strand	106-111	6	13
α-helix	114-116	3
β-strand	118	1	14
α-helix	119-120	2
β-strand	121-125	5	15
β-strand	126	1	11
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	15
β-strand	148	1	14
β-strand	152-158	7	16
β-strand	161-163	3	16
β-strand	167-169	3	15
β-strand	174-177	4	15
β-strand	180-190	11	15
α-helix	191-194	4
β-strand	200-207	8	16
β-strand	210	1	17
β-strand	224	1	17
β-strand	226-233	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A	protein	276	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B	protein	119	Mus musculus	P01887 (AlphaFold model)
Protein Trav14-1,T-cell receptor alpha chain C region	G	protein	205	Mus musculus	A0A0G2JF94 (AlphaFold model), P01849 (AlphaFold model)
T-cell receptor beta chain V region C5,T-cell receptor beta-2 chain C region	H	protein	238	Mus musculus	P01851, P04213
Lcmv-derived GP33 altered peptide ligand pf	P	protein	9	Lymphocytic choriomeningitis virus

Sequence of entity 1 (A), FASTA

>5M02_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

Sequence of entity 2 (B), FASTA

>5M02_2 Beta-2-microglobulin (chains B)
MARSVTLVFLVLVSLTGLMGIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQML
KNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (G), FASTA

>5M02_3 Protein Trav14-1,T-cell receptor alpha chain C region (chains G)
QQKEKHDQQQVRQSPQSLTVWEGGTTVLTCSYEDSTFNYFPWYQQFPGEGPALLISILSV
SDKKEDGRFTTFFNKREKKLSLHIIDSQPGDSATYFCAALYGNEKITFGAGTKLTIKPNI
QNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGA
IAWSNQTSFTCQDIFKETNATYPSS

Sequence of entity 4 (H), FASTA

>5M02_4 T-cell receptor beta chain V region C5,T-cell receptor beta-2 chain C region (chains H)
AVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPD
GYKASRPSQENFSLILELASLSQTAVYFCASSDAGGRNTLYFGAGTRLSVLEDLRNVTPP
KVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYS
YSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADC

Sequence of entity 5 (P), FASTA

>5M02_5 LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND PF (chains P)
KAPFNFATM

Primary citation

Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant. Allerbring, E., Duru, A., Sun, R. et al. To be published.

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…

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