1NAM: BM3.3 T Cell Receptor alpha-Chain

Murine alloreactive scFv TCR-peptide-MHC class I molecule complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 11 Mar 2003.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Mus musculus
Chains: 5
Atoms: 5,091
Mol. weight: 71 kDa
Released: 11 Mar 2003

Explore 1NAM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NAM contains 11 α-helices and 51 β-strands across 5 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: 2 helices, 12 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	43-50	8	2
β-strand	58-59	2	1
β-strand	62-67	6	1
α-helix	68-70	3
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-93	8	2
β-strand	104-106	3	2
β-strand	110-115	6	2

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	10-13	4	4
β-strand	19-25	7	3
β-strand	31-37	7	4
β-strand	43-49	7	4
β-strand	55-60	6	3
β-strand	63-69	7	3
β-strand	74-80	7	3
β-strand	86-95	8	4
α-helix	103-106	3
β-strand	107-108	2	4
β-strand	112-116	5	4

Chain H: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	5
β-strand	21-28	8	5
β-strand	31-37	7	5
β-strand	46-47	2	5
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	5
β-strand	109-118	10	5
β-strand	121-126	6	5
β-strand	133-135	3	5
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-179	17
β-strand	183	1	6
β-strand	186-191	6	7
β-strand	201-208	8	7
β-strand	209	1	6
β-strand	214-218	5	8
β-strand	223	1	8
β-strand	229-230	2	7
β-strand	234-235	2	7
β-strand	241-247	7	7
β-strand	258-262	5	8
β-strand	270-272	3	8

Chain L: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6-9	4	9
β-strand	24-30	7	9
β-strand	35-39	5	10
α-helix	52-54	3
β-strand	55-56	2	9
β-strand	62-67	6	9
β-strand	79	1	11
β-strand	80-84	5	10
β-strand	91	1	10
β-strand	94	1	11

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BM3.3 T Cell Receptor alpha-Chain	A	protein	116	Mus musculus	Q5R1F1 (AlphaFold model)
BM3.3 T Cell Receptor beta-Chain	B	protein	113	Mus musculus	P04214 (AlphaFold model)
H-2 class I histocompatibility antigen, K-B alpha chain precursor	H	protein	275	Mus musculus	P01901 (AlphaFold model)
Nucleocapsid	P	protein	8		P11212
Beta-2-microglobulin	L	protein	100	Mus musculus	P01887

Sequence of entity 1 (A), FASTA

>1NAM_1 BM3.3 T Cell Receptor alpha-Chain (chains A)
QKVTQTQTSISVMEKTTVTMDCVYETQDSSYFLFWYKQTASGEIVFLIRQDSYKKENATV
GHYSLNFQKPKSSIGLIITATQIEDSAVYFCAMRGDYGGSGNKLIFGTGTLLSVKP

Sequence of entity 2 (B), FASTA

>1NAM_2 BM3.3 T Cell Receptor beta-Chain (chains B)
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSADRVGNTLYFGEGSRLIVV

Sequence of entity 3 (H), FASTA

>1NAM_3 H-2 class I histocompatibility antigen, K-B alpha chain precursor (chains H)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE

Sequence of entity 4 (P), FASTA

>1NAM_4 Nucleocapsid (chains P)
RGYVYQGL

Sequence of entity 5 (L), FASTA

>1NAM_5 Beta-2-microglobulin (chains L)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Primary citation

CDR3 loop flexibility contributes to the degeneracy of TCR recognition. Reiser, J.-B., Darnault, C., Gregoire, C. et al. Nat Immunol (2003) 4:241-247. DOI 10.1038/ni891 · PubMed

Other PDB entries of the same protein (UniProt Q5R1F1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FO0 2.5 Å, Murine alloreactive scFv TCR-peptide-MHC class I molecule complex
2OL3 2.9 Å, crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule

Browse structure collections

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