4NHU: The M33 TCR p3M33l/H-2 Ld Complex

The M33 TCR p3M33l/H-2 Ld Complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 9,829
Mol. weight: 150.89 kDa
Released: 6 May 2015

Explore 4NHU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NHU contains 33 α-helices and 100 β-strands across 6 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: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	9-13	5	2
β-strand	18-20	3	1
β-strand	23-24	2	1
β-strand	31-37	7	2
β-strand	44-49	6	2
β-strand	55-57	3	1
α-helix	59-61	3
β-strand	63-67	5	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	87-93	7	2
α-helix	99	1
β-strand	100-101	2	2
β-strand	105-110	6	2
α-helix	111	1
β-strand	119-125	7	3
β-strand	132-137	6	3
β-strand	154-155	2	3
β-strand	159-163	5	3
β-strand	168-176	9	3
β-strand	198	1	3

Chain B: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-14	5	5
β-strand	19-25	7	4
β-strand	31-38	8	5
β-strand	42-49	8	5
β-strand	56-57	2	5
β-strand	65-67	3	4
β-strand	73-78	6	4
α-helix	83-85	3
β-strand	87-94	8	5
β-strand	100-101	2	5
β-strand	105-110	6	5
α-helix	113-115	3
β-strand	117	1	6
β-strand	120-125	6	3
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	3
β-strand	147	1	6
β-strand	151-157	7	7
β-strand	160-162	3	7
β-strand	166-168	3	3
β-strand	173-174	2	3
β-strand	184-193	10	3
α-helix	194-197	4
β-strand	203-210	8	7
β-strand	213	1	8
α-helix	224-225	2
β-strand	227	1	8
β-strand	229-236	8	7

Chain C: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	10
β-strand	9-13	5	11
β-strand	18-20	3	10
β-strand	23-24	2	10
β-strand	31-37	7	11
β-strand	44-49	6	11
β-strand	55-57	3	10
α-helix	59-61	3
β-strand	63-67	5	10
β-strand	72-77	6	10
α-helix	82-84	3
β-strand	87-93	7	11
α-helix	99	1
β-strand	100-101	2	11
β-strand	105-110	6	11
β-strand	119-125	7	12
β-strand	132-137	6	12
α-helix	146-148	3
β-strand	153-155	3	12
β-strand	159-163	5	12
β-strand	168-177	10	12
β-strand	198	1	12

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	31-38	8	14
β-strand	42-49	8	14
β-strand	56-57	2	14
β-strand	65-67	3	13
β-strand	73-78	6	13
α-helix	83-85	3
β-strand	87-94	8	14
β-strand	100-101	2	14
β-strand	105-110	6	14
α-helix	113-115	3
β-strand	117	1	15
β-strand	120-125	6	12
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	12
β-strand	147	1	15
β-strand	151-157	7	16
β-strand	160-162	3	16
β-strand	166-168	3	12
β-strand	173-174	2	12
β-strand	184-193	10	12
α-helix	194-197	4
β-strand	203-210	8	16
β-strand	213	1	17
β-strand	227	1	17
β-strand	229-236	8	16

Chain E: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	9
α-helix	20	1
β-strand	21-28	8	9
β-strand	31-37	7	9
β-strand	46-47	2	9
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	9
β-strand	109-118	10	9
β-strand	121-126	6	9
β-strand	133-135	3	9
α-helix	138-149	12
α-helix	153-160	8
α-helix	163-171	9
α-helix	199-201	3

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-150	13
α-helix	153-161	9
α-helix	163-171	9
α-helix	199-201	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2C m33 alpha VmCh chimera	A, C	protein	219	Mus musculus, Homo sapiens	P01738 (AlphaFold model), P01848 (AlphaFold model)
2C m33 beta VmCh chimera	B, D	protein	254	Mus musculus, Homo sapiens	A0A5B9 (AlphaFold model), P04213 (AlphaFold model)
H-2 class I histocompatibility antigen, L-D alpha chain	E, G	protein	204	Mus musculus	P01897

Sequence of entity 1 (A, C), FASTA

>4NHU_1 2C m33 alpha VmCh chimera (chains A, C)
ADPGQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQLLLKYYSGDPVV
QGVNGFEAEFSKSNSSFHLRKASVHWSDSAVYFCAVSLHRPALTFGSGTKVIVLPNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESSSRGGLEVLFQ

Sequence of entity 2 (B, D), FASTA

>4NHU_2 2C m33 beta VmCh chimera (chains B, D)
ADPGEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTE
KGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGGGTLYFGAGTRLSVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRADSRGGLEVLFQ

Sequence of entity 3 (E, G), FASTA

>4NHU_3 H-2 class I histocompatibility antigen, L-D alpha chain (chains E, G)
MGPHSMRYFETAVSRPGLGEPRYISVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEY
WERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYD
GCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEALHRYLKNGNATL
LGSLVPRGSGGGGGGAPWNPAMMI

Primary citation

Interrogating TCR Signal Strength and Cross-Reactivity by Yeast Display of pMHC. Birnbaum, M.E., Adams, J.J., Garcia, K.C. To be published.

Other PDB entries of the same protein (UniProt P01738 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex
1MWA 2.4 Å, 2C/H-2KBM3/DEV8 allogeneic complex
2ICW 2.41 Å, Crystal structure of a complete ternary complex between TCR, superantigen, and…
1I9E 2.5 Å, TCR domain
1TCR 2.5 Å, Murine T-cell antigen receptor 2C clone
4MXQ 2.6 Å, 42F3 TCR pCPC5/H-2Ld Complex
1G6R 2.8 Å, A functional hot spot for antigen recognition in a superagonist tcr/mhc complex
4N0C 2.9 Å, 42F3 TCR pCPE3/H-2Ld complex
3E3Q 2.95 Å, Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9
2CKB 3.0 Å, Structure of the 2C/KB/DEV8 complex
4N5E 3.06 Å, 42F3 TCR pCPA12/H-2Ld complex
4MVB 3.09 Å, 42F3 pCPB7/H-2Ld Complex

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