4JFF: PDB entry 4JFF

Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR. Determined by X-ray diffraction at 2.43 Å resolution. Released 29 May 2013.

Method: X-ray diffraction
Resolution: 2.43 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,874
Mol. weight: 95.37 kDa
Released: 29 May 2013

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

Secondary structure: helices and β-sheets

4JFF contains 23 α-helices and 74 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	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	152-158	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	1	3
β-strand	189-195	7	4
β-strand	198-208	11	4
β-strand	209	1	2
β-strand	214-218	5	5
β-strand	230	1	4
α-helix	231-233	3
β-strand	234-235	2	4
β-strand	241-250	10	4
β-strand	258-262	5	5
α-helix	269	1
β-strand	270-272	3	5

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	45	1	8
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	9

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	10
β-strand	11-14	4	11
α-helix	18	1
β-strand	19-25	7	10
β-strand	32-38	7	11
β-strand	45-50	6	11
β-strand	54-58	5	10
β-strand	61-66	6	10
β-strand	71-76	6	10
α-helix	81-83	3
β-strand	85-92	8	11
β-strand	97-99	3	11
β-strand	103-108	6	11
β-strand	117-121	5	12
β-strand	122-123	2	13
β-strand	130-135	6	12
α-helix	141-143	3
β-strand	152-153	2	12
α-helix	154-156	3
β-strand	157-161	5	12
β-strand	166-175	10	12
β-strand	193-194	2	12

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-14	5	15
β-strand	19-26	8	14
β-strand	32-38	7	15
β-strand	45-51	7	15
β-strand	54-55	2	15
β-strand	65-70	6	14
β-strand	73-78	6	14
α-helix	83-85	3
β-strand	87-94	8	15
β-strand	98	1	9
β-strand	102-105	4	15
β-strand	109-114	6	15
α-helix	117-119	3
β-strand	121	1	16
α-helix	122-123	2
β-strand	124-129	6	13
α-helix	130-131	2
α-helix	132-137	6
β-strand	140-150	11	13
β-strand	151	1	16
β-strand	155-161	7	17
β-strand	164-165	2	17
β-strand	170-172	3	13
β-strand	177-178	2	13
β-strand	188-197	10	13
α-helix	198-201	4
β-strand	207-214	8	17
β-strand	217	1	18
α-helix	228-229	2
β-strand	231	1	18
β-strand	233-240	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma motif	C	protein	10	Homo sapiens	Q16655 (AlphaFold model)
High Affinity TCR Alpha Chain	D	protein	197	Homo sapiens	P01848 (AlphaFold model)
High Affinity TCR Beta Chain	E	protein	245	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>4JFF_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>4JFF_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4JFF_3 Melanoma motif (chains C)
ELAGIGILTV

Sequence of entity 4 (D), FASTA

>4JFF_4 High Affinity TCR Alpha Chain (chains D)
KQEVEQNSGPLSVPEGAIASLNCTYSFLGSQSFFWYRQYSGKSPELIMFTYREGDKEDGR
FTAQLNKASQHVSLLIRDSQPSDSATYLCAVNDGGRLTFGDGTTLTVKPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFF

Sequence of entity 5 (E), FASTA

>4JFF_5 High Affinity TCR Beta Chain (chains E)
MSQTIHQWPATLVQPVGSPLSLECTVEGTSNPNLYWYRQAAGRGPQLLFYWGPFGQISSE
VPQNLSASRPQDRQFILSSKKLLLSDSGFYLCAWSETGLGMGGWQFGEGSRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Primary citation

T-cell receptor specificity maintained by altered thermodynamics. Madura, F., Rizkallah, P.J., Miles, K.M. et al. J Biol Chem (2013) 288:18766-18775. DOI 10.1074/jbc.M113.464560 · 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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