3VFM: HLA B*3508 LPEP155A, HLA mutant Ala155

crystal structure of HLA B*3508 LPEP155A, HLA mutant Ala155. Determined by X-ray diffraction at 1.9 Å resolution. Released 7 Mar 2012.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,724
Mol. weight: 45.23 kDa
Released: 7 Mar 2012

Explore 3VFM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VFM contains 16 α-helices and 30 β-strands across 3 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
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	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
α-helix	182	1
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	229-230	2	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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
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
α-helix	46	1
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 C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	9-12	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	C5MK56 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
LPEP peptide from EBV, LPEPLPQGQLTAY	C	protein	13

Sequence of entity 1 (A), FASTA

>3VFM_1 MHC class I antigen (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEARRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>3VFM_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>3VFM_3 LPEP peptide from EBV, LPEPLPQGQLTAY (chains C)
LPEPLPQGQLTAY

Primary citation

The Energetic Basis Underpinning T-cell Receptor Recognition of a Super-bulged Peptide Bound to a Major Histocompatibility Complex Class I Molecule. Liu, Y.C., Chen, Z., Burrows, S.R. et al. J Biol Chem (2012) 287:12267-12276. DOI 10.1074/jbc.M112.344689 · PubMed

Other PDB entries of the same protein (UniProt C5MK56 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VFN 1.5 Å, crystal structure of HLA B*3508LPEP151A, HLA mutant Ala151
4PRE 1.65 Å, Crystal structure of a HLA-B*35:08-HPVG-Q5
3VFO 1.7 Å, crystal structure of HLA B*3508 LPEP157A, HLA mutant Ala157
4PRB 1.75 Å, Crystal structure of a HLA-B*35:08-HPVG-A4
4PRD 1.75 Å, Crystal structure of a HLA-B*35:08-HPVG-D5
3VFP 1.85 Å, crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158
3VFR 1.85 Å, crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala
4PRA 1.85 Å, Crystal structure of a HLA-B*35:01-HPVG-Q5
4JRX 2.3 Å, Crystal Structure of CA5 TCR-HLA B*3505-LPEP complex
4PRI 2.4 Å, Crystal structure of TK3 TCR-HLA-B*35:08-HPVG complex
4PRH 2.5 Å, Crystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex
4PRP 2.5 Å, Crystal structure of TK3 TCR-HLA-B*35:01-HPVG-Q5 complex

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