2F54: HLA class I histocompatibility antigen

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity. Determined by X-ray diffraction at 2.7 Å resolution. Released 25 Apr 2006.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,259
Mol. weight: 188.12 kDa
Released: 25 Apr 2006

Explore 2F54 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2F54 contains 43 α-helices and 145 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: 9 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	57-85	29
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	159-164	6
α-helix	165-174	10
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222	1	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	253-256	4
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 D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
β-strand	9-13	5	9
β-strand	18-24	7	8
β-strand	29-37	9	9
β-strand	43-50	8	9
β-strand	56-58	3	8
β-strand	61-66	6	8
α-helix	67-69	3
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-93	9	9
β-strand	102-103	2	9
β-strand	107-112	6	9
β-strand	121-127	7	10
β-strand	134-139	6	10
α-helix	148-150	3
β-strand	156-165	10	10
α-helix	166-168	3
β-strand	170-178	9	10
β-strand	200	1	10

Chain E: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	11
β-strand	8-12	5	12
β-strand	17-19	3	13
β-strand	20-23	4	11
β-strand	29-35	7	12
β-strand	42-47	6	12
β-strand	54-55	2	12
β-strand	62-64	3	13
β-strand	71	1	11
β-strand	74-76	3	13
α-helix	81-83	3
β-strand	85-92	8	12
β-strand	101-102	2	12
β-strand	106-111	6	12
β-strand	118	1	14
α-helix	119-120	2
β-strand	121-126	6	10
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	10
β-strand	148	1	14
β-strand	152-158	7	15
β-strand	161-163	3	15
β-strand	167-169	3	10
β-strand	174-175	2	10
β-strand	185-194	10	10
α-helix	195-198	4
β-strand	204-211	8	15
β-strand	214	1	16
β-strand	228	1	16
β-strand	230-237	8	15

Chain F: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	17
α-helix	20	1
β-strand	21-28	8	17
β-strand	31-37	7	17
β-strand	46-47	2	17
α-helix	57-84	28
β-strand	94-103	10	17
β-strand	109-118	10	17
β-strand	121-126	6	17
β-strand	133-135	3	17
α-helix	139-149	11
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	18
α-helix	184-185	2
β-strand	186-193	8	19
β-strand	198-208	11	19
β-strand	209	1	18
β-strand	214-219	6	20
β-strand	222-223	2	20
β-strand	229-230	2	19
α-helix	231-233	3
β-strand	234-235	2	19
β-strand	241-250	10	19
β-strand	257-262	6	20
β-strand	270-272	3	20

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	21
α-helix	4-5	2
β-strand	6-11	6	22
α-helix	14-15	2
β-strand	21-30	10	22
β-strand	31	1	21
β-strand	36-41	6	23
β-strand	44-45	2	23
β-strand	50-51	2	22
β-strand	55-56	2	22
β-strand	62-70	9	22
β-strand	78-83	6	23
β-strand	91-94	4	23

Chain K: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	24
β-strand	9-13	5	25
β-strand	18-24	7	24
β-strand	29-37	9	25
β-strand	43-50	8	25
β-strand	55-58	4	24
β-strand	61-66	6	24
β-strand	71-76	6	24
α-helix	81-83	3
β-strand	85-93	9	25
β-strand	102-103	2	25
β-strand	107-112	6	25
β-strand	121-127	7	26
β-strand	134-139	6	26
α-helix	148-150	3
β-strand	156-157	2	26
α-helix	158-160	3
β-strand	161-165	5	26
α-helix	166-168	3
β-strand	170-178	9	26
α-helix	186-188	3
β-strand	200	1	26

Chain L: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	27
β-strand	8-12	5	28
β-strand	17-19	3	29
β-strand	20-23	4	27
β-strand	29-36	8	28
β-strand	40-47	8	28
β-strand	54-55	2	28
β-strand	63-64	2	29
β-strand	71	1	27
β-strand	74-76	3	29
α-helix	81-83	3
β-strand	85-92	8	28
β-strand	101-102	2	28
β-strand	106-111	6	28
α-helix	114-116	3
β-strand	118	1	30
β-strand	121-126	6	26
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	26
β-strand	148	1	30
β-strand	152-158	7	31
β-strand	161-163	3	31
β-strand	167-169	3	26
β-strand	174-175	2	26
α-helix	183-184	2
β-strand	185-194	10	26
α-helix	195-198	4
β-strand	204-211	8	31
β-strand	214	1	32
β-strand	228	1	32
β-strand	230-237	8	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen	A, F	protein	274	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Cancer/testis antigen 1B	C, H	protein	9		P78358 (AlphaFold model)
T-cell receptor alpha chain	D, K	protein	206	Homo sapiens	P01848 (AlphaFold model)
T-cell receptor beta chain	E, L	protein	241	Homo sapiens	P01850

Sequence of entity 1 (A, F), FASTA

>2F54_1 HLA class I histocompatibility antigen (chains A, F)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 2 (B, G), FASTA

>2F54_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYCTEFTPTEKDEYACRVNHVTLSQPCIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>2F54_3 Cancer/testis antigen 1B (chains C, H)
SLLMWITQC

Sequence of entity 4 (D, K), FASTA

>2F54_4 T-cell receptor alpha chain (chains D, K)
KQQVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGGKLTSLLLIQSSQREQTSG
RLNASLDKSAGSSTLYIAASQPGDSATYLCAVRPTSGGSYIPTFGRGTSLIVHPYIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPE

Sequence of entity 5 (E, L), FASTA

>2F54_5 T-cell receptor beta chain (chains E, L)
GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPN
GYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGELFFGEGSRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity. Dunn, S.M., Rizkallah, P.J., Baston, E. et al. Protein Sci (2006) 15:710-721. DOI 10.1110/ps.051936406 · 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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