6BJ3: TCR55

TCR55 in complex with HIV(Pol448-456)/HLA-B35. Determined by X-ray diffraction at 1.9 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 5
Atoms: 7,022
Mol. weight: 95.65 kDa
Released: 25 Jul 2018

Explore 6BJ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BJ3 contains 32 α-helices and 71 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	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	50-54	5
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	138-150	13
α-helix	152-161	10
α-helix	163-174	12
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
α-helix	225-227	3
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: 2 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	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain D: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-14	5	9
β-strand	19-21	3	8
β-strand	24-25	2	8
β-strand	32-39	8	9
β-strand	45-52	8	9
α-helix	56-58	3
β-strand	59-60	2	8
β-strand	63-68	6	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	87-95	9	9
β-strand	102-103	2	9
β-strand	107-112	6	9
α-helix	113	1
β-strand	121-124	4	10
α-helix	125-128	4
β-strand	134-139	6	10
α-helix	148-150	3
β-strand	156-157	2	10
α-helix	158-160	3
β-strand	161-165	5	10
α-helix	166-168	3
β-strand	170-179	10	10
α-helix	186-189	4
β-strand	200	1	10

Chain H: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-14	5	12
β-strand	19-25	7	11
β-strand	31-37	7	12
β-strand	43-49	7	12
α-helix	57-59	3
α-helix	61	1
β-strand	64-68	5	11
β-strand	73-78	6	11
α-helix	83-85	3
β-strand	87-94	8	12
α-helix	102-103	2
β-strand	104-105	2	12
α-helix	106	1
β-strand	109-114	6	12
α-helix	117-119	3
β-strand	121	1	13
α-helix	122-123	2
β-strand	124-128	5	14
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	14
β-strand	151	1	13
β-strand	155-161	7	15
β-strand	164-166	3	15
β-strand	170-172	3	14
β-strand	177-178	2	14
β-strand	188-197	10	14
α-helix	198-201	4
β-strand	207-214	8	15
β-strand	217	1	16
α-helix	228-229	2
β-strand	231	1	16
β-strand	233-240	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, B-35 alpha chain	A	protein	276	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
TCR 55 alpha chain	D	protein	204	Homo sapiens	Q6IRV4 (AlphaFold model)
TCR 55 beta chain	H	protein	242	Homo sapiens	K7N5M4 (AlphaFold model)
HIV Pol B35 peptide	C	protein	9	Human immunodeficiency virus 1	P04585

Sequence of entity 1 (A), FASTA

>6BJ3_1 HLA class I histocompatibility antigen, B-35 alpha chain (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6BJ3_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>6BJ3_3 TCR 55 alpha chain (chains D)
MQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKS
GRYSVNFKKAAKSVALTISALQLEDSAKYFCALGEGGAQKLVFGQGTRLTINPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 4 (H), FASTA

>6BJ3_4 TCR 55 beta chain (chains H)
GVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPN
GYNVSRLNKREFSLRLESAAPSQTSVYFCASRTRGGTLIEQYFGPGTRLTVTEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 5 (C), FASTA

>6BJ3_5 HIV Pol B35 peptide (chains C)
IPLTEEAEL

Primary citation

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Sibener, L.V., Fernandes, R.A., Kolawole, E.M. et al. Cell (2018) 174:672-687.e27. DOI 10.1016/j.cell.2018.06.017 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

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