2J8U: PDB entry 2J8U

Large CDR3a loop alteration as a function of MHC mutation. Determined by X-ray diffraction at 2.88 Å resolution. Released 16 Oct 2007.

Method: X-ray diffraction
Resolution: 2.88 Å
Organisms: Homo sapiens, HOMO SAPIENS, MUS MUSCULUS
Chains: 10
Atoms: 13,128
Mol. weight: 186.54 kDa
Released: 16 Oct 2007

Explore 2J8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2J8U contains 48 α-helices and 148 β-strands across 8 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
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
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	222-224	3	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: 2 helices, 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
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 E: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	8
β-strand	9-13	5	9
α-helix	17	1
β-strand	18-20	3	10
β-strand	22-25	4	8
β-strand	31-37	7	9
β-strand	44-48	5	9
β-strand	63-64	2	10
β-strand	67	1	8
β-strand	72	1	8
β-strand	75-77	3	10
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	104-106	3	9
β-strand	110-115	6	9
α-helix	116	1
β-strand	124-129	6	11
β-strand	139-144	6	11
α-helix	151-155	5
β-strand	161-162	2	11
α-helix	163-165	3
β-strand	166-168	3	11
β-strand	177-183	7	11
α-helix	191-194	4

Chain F: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	31-38	8	13
β-strand	41-51	11	13
β-strand	54-57	4	13
β-strand	66-68	3	14
β-strand	74	1	12
β-strand	76-79	4	14
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	107-108	2	13
β-strand	112-116A	6	13
β-strand	126-130	5	15
β-strand	131	1	11
α-helix	132-133	2
α-helix	134-140	7
β-strand	142-152	11	15
β-strand	157-163	7	16
β-strand	166-168	3	16
β-strand	172-174	3	15
β-strand	179-182	4	15
β-strand	189-199	11	15
α-helix	200-203	4
β-strand	209-216	8	16
β-strand	219	1	17
α-helix	230-231	2
β-strand	233	1	17
β-strand	235-242	8	16

Chain H: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	19
α-helix	184-185	2
β-strand	186-192	7	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	214-219	6	21
β-strand	222-224	3	21
β-strand	228-230	3	20
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-250	10	20
α-helix	254-256	3
β-strand	257-262	6	21
β-strand	270-273	4	21

Chain I: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
α-helix	4-5	2
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	44-45	2	24
α-helix	46	1
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
β-strand	91-94	4	24

Chain L: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	25
β-strand	9-13	5	26
α-helix	17	1
β-strand	18-20	3	27
β-strand	22-24	3	25
β-strand	31-37	7	26
β-strand	44-48	5	26
β-strand	62-64	3	27
β-strand	67	1	25
β-strand	72	1	25
β-strand	75-77	3	27
α-helix	82-84	3
β-strand	87-93	7	26
β-strand	104-106	3	26
β-strand	110-115	6	26
α-helix	116	1
β-strand	124-129	6	28
β-strand	139-144	6	28
α-helix	151-155	5
β-strand	161-162	2	28
α-helix	163-165	3
β-strand	166-170	5	28
β-strand	175-183	9	28
α-helix	191-193	3

Chain M: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	29
β-strand	10-14	5	30
β-strand	19-21	3	31
β-strand	22-25	4	29
β-strand	31-38	8	30
β-strand	41-51	11	30
β-strand	54-57	4	30
β-strand	65-68	4	31
β-strand	74	1	29
β-strand	76-79	4	31
α-helix	84-86	3
β-strand	88-95	8	30
β-strand	107-108	2	30
β-strand	112-116A	6	30
α-helix	119-121	3
β-strand	123	1	32
β-strand	126-130	5	33
β-strand	131	1	28
α-helix	132-133	2
α-helix	134-140	7
β-strand	142-152	11	33
β-strand	153	1	32
β-strand	157-163	7	34
β-strand	166-168	3	34
β-strand	172-174	3	33
β-strand	179-182	4	33
β-strand	189-199	11	33
α-helix	200-204	5
β-strand	209-216	8	34
β-strand	219	1	35
α-helix	230-231	2
β-strand	233	1	35
β-strand	235-242	8	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, H	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, I	protein	100	Homo sapiens	P61769 (AlphaFold model)
Self-peptide P1049	C, J	protein	9	HOMO SAPIENS	Q9NPA0 (AlphaFold model)
Ahiii TCR alpha chain	E, L	protein	194	MUS MUSCULUS	P01849 (AlphaFold model)
Ahiii TCR beta chain	F, M	protein	238	MUS MUSCULUS	P04213

Sequence of entity 1 (A, H), FASTA

>2J8U_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, H)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRAVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, I), FASTA

>2J8U_2 Beta-2-microglobulin (chains B, I)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, J), FASTA

>2J8U_3 SELF-PEPTIDE P1049 (chains C, J)
ALWGFFPVL

Sequence of entity 4 (E, L), FASTA

>2J8U_4 AHIII TCR ALPHA CHAIN (chains E, L)
MDSVTQTEGLVTLTEGLPVMLNCTYQSTYSPFLFWYVQHLNEAPKLLLKSFTDNKRPEHQ
GFHATLHKSSSSFHLQKSSAQLSDSALYYCALFLASSSFSKLVFGQGTSLSVVPNIQNPE
PAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKTVLDMKAMDSKSNGAIAWS
NQTSFTCQDIFKET

Sequence of entity 5 (F, M), FASTA

>2J8U_5 AHIII TCR BETA CHAIN (chains F, M)
MEAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGD
IPDGYKASRPSQENFSLILELASLSQTAVYFCASSDWVSYEQYFGPGTRLTVLEDLRNVT
PPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESN
YSYALSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRA

Primary citation

Single MHC mutation eliminates enthalpy associated with T cell receptor binding. Miller, P.J., Pazy, Y., Conti, B. et al. J Mol Biol (2007) 373:315-327. DOI 10.1016/j.jmb.2007.07.028 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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