2BNQ: HLA class I histocompatibility antigen

Structural and kinetic basis for heightened immunogenicity of T cell vaccines. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 May 2005.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: HOMO SAPIENS
Chains: 5
Atoms: 7,153
Mol. weight: 94.1 kDa
Released: 23 May 2005

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

Secondary structure: helices and β-sheets

2BNQ contains 24 α-helices and 74 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: 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	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	159-164	6
α-helix	165-174	10
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	222-223	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	270-273	4	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: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	30-38	9	9
β-strand	44-51	8	9
β-strand	56-59	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	103-104	2	9
β-strand	108-113	6	9
β-strand	122-127	6	10
β-strand	128	1	11
β-strand	135-140	6	10
α-helix	148-151	4
β-strand	156-158	3	10
α-helix	159-161	3
β-strand	162-166	5	10
α-helix	167-169	3
β-strand	171-180	10	10
α-helix	187-190	4
β-strand	201	1	10

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	9-13	5	13
β-strand	18-20	3	14
β-strand	21-24	4	12
β-strand	30-37	8	13
β-strand	41-50	10	13
β-strand	53-56	4	13
β-strand	64-65	2	14
β-strand	72	1	12
β-strand	75-77	3	14
α-helix	82-84	3
β-strand	86-93	8	13
β-strand	102-103	2	13
β-strand	107-112	6	13
α-helix	115-117	3
β-strand	119	1	15
β-strand	122-126	5	11
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	11
β-strand	149	1	15
β-strand	153-159	7	16
β-strand	162-164	3	16
β-strand	168-170	3	11
β-strand	175-176	2	11
β-strand	186-195	10	11
α-helix	196-199	4
β-strand	205-212	8	16
β-strand	215	1	17
α-helix	226-227	2
β-strand	229	1	17
β-strand	231-238	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen	A	protein	276	HOMO SAPIENS	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	HOMO SAPIENS	P61769 (AlphaFold model)
Synthetic peptide	C	protein	9	HOMO SAPIENS	P78358 (AlphaFold model)
T-cell receptor alpha chain V region	D	protein	203	HOMO SAPIENS	A0A0B4J279 (AlphaFold model), P01848
T-cell receptor beta chain C region	E	protein	241	HOMO SAPIENS	A0A0K0K1A5, P01850

Sequence of entity 1 (A), FASTA

>2BNQ_1 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>2BNQ_2 BETA-2-MICROGLOBULIN (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>2BNQ_3 SYNTHETIC PEPTIDE (chains C)
SLLMWITQV

Sequence of entity 4 (D), FASTA

>2BNQ_4 T-CELL RECEPTOR ALPHA CHAIN V REGION (chains D)
QEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGR
LNASLDKSSGRSTLYIAASQPGDSATYLCAVRPTSGGSYIPTFGRGTSLIVHPYIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>2BNQ_5 T-CELL RECEPTOR BETA CHAIN C REGION (chains E)
GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPN
GYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGELFFGEGSRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

Structural and Kinetic Basis for Heightened Immunogenicity of T Cell Vaccines. Chen, J.-L., Stewart-Jones, G., Bossi, G. et al. J Exp Med (2005) 201:1243. DOI 10.1084/JEM.20042323 · 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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