2OL3: BM3.3 ScFV TCR

crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule. Determined by X-ray diffraction at 2.9 Å resolution. Released 3 Apr 2007.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Mus musculus
Chains: 5
Atoms: 5,073
Mol. weight: 73.81 kDa
Ligands: NAG
Released: 3 Apr 2007

Explore 2OL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OL3 contains 11 α-helices and 54 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: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	9-13	5	2
β-strand	18-20	3	3
β-strand	23	1	1
β-strand	31-37	7	2
β-strand	43-50	8	2
α-helix	56-57	2
β-strand	58-59	2	3
β-strand	62-64	3	3
β-strand	67	1	1
α-helix	68-70	3
β-strand	72	1	1
β-strand	75-77	3	3
β-strand	86-93	8	2
β-strand	104-106	3	2
β-strand	110-115	6	2

Chain B: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-25	7	4
β-strand	31-38	8	5
β-strand	43-49	7	5
β-strand	55-60	6	4
β-strand	63-69	7	4
β-strand	74-80	7	4
β-strand	86-95	8	5
β-strand	107-108	2	5
β-strand	112-116	5	5

Chain H: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	6
α-helix	20	1
β-strand	21-28	8	6
β-strand	31-37	7	6
β-strand	46-47	2	6
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	6
β-strand	109-118	10	6
β-strand	122-126	5	6
β-strand	133-135	3	6
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-179	16
β-strand	183	1	7
β-strand	186-192	7	8
β-strand	198-208	11	8
β-strand	209	1	7
β-strand	214-219	6	9
β-strand	222-223	2	9
β-strand	229-230	2	8
β-strand	234-235	2	8
β-strand	241-250	10	8
α-helix	253-256	4
β-strand	257-262	6	9
β-strand	270-272	3	9

Chain L: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	10
β-strand	6-11	6	11
β-strand	21-30	10	11
β-strand	31	1	10
β-strand	35-39	5	12
β-strand	51	1	11
α-helix	52-54	3
β-strand	55-56	2	11
β-strand	62-70	9	11
β-strand	79-84	6	12
β-strand	91-94	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BM3.3 T-cell receptor alpha-chain	A	protein	142	Mus musculus	Q5R1F1 (AlphaFold model)
BM3.3 T-cell receptor beta-chain	B	protein	113	Mus musculus	P04214 (AlphaFold model)
Allogeneic H-2KBM8 MHC class I molecule	H	protein	279	Mus musculus	P01901 (AlphaFold model)
Beta-2-microglobulin	L	protein	100	Mus musculus	P01887 (AlphaFold model)
Naturally processed octapeptide PBM8	P	protein	8		Q91YE7

Sequence of entity 1 (A), FASTA

>2OL3_1 BM3.3 T-CELL RECEPTOR ALPHA-CHAIN (chains A)
QKVTQTQTSISVMEKTTVTMDCVYETQDSSYFLFWYKQTASGEIVFLIRQDSYKKENATV
GHYSLNFQKPKSSIGLIITATQIEDSAVYFCAMRGDYGGSGNKLIFGTGTLLSVKPGSAD
DAKKDAAKKDDAKKDAAKKDGS

Sequence of entity 2 (B), FASTA

>2OL3_2 BM3.3 T-CELL RECEPTOR BETA-CHAIN (chains B)
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSADRVGNTLYFGEGSRLIVV

Sequence of entity 3 (H), FASTA

>2OL3_3 ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE (chains H)
GPHSLRYFVTAVSRPGLGEPRFISVGYVDNTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPPS

Sequence of entity 4 (L), FASTA

>2OL3_4 Beta-2-microglobulin (chains L)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 5 (P), FASTA

>2OL3_5 NATURALLY PROCESSED OCTAPEPTIDE PBM8 (chains P)
SQYYYNSL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides? Mazza, C., Auphan-Anezin, N., Gregoire, C. et al. EMBO J (2007) 26:1972-1983. DOI 10.1038/sj.emboj.7601605 · 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
1NAM 2.7 Å, Murine alloreactive scFv TCR-peptide-MHC class I molecule complex

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