6CQN: F5 TCR -DR11-RQ13 peptide complex

Crystal structure of F5 TCR -DR11-RQ13 peptide complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, HIV-1 M:B_HXB2R
Chains: 5
Atoms: 6,871
Mol. weight: 96.74 kDa
Ligands: MG, NAG
Released: 6 Jun 2018

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

Secondary structure: helices and β-sheets

6CQN contains 29 α-helices and 76 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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-34	6	1
β-strand	41-43	3	1
α-helix	48-51	4
β-strand	53-54	2	2
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	4
β-strand	138	1	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
α-helix	107-108	2
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-132	5	8
β-strand	137-138	2	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	8
α-helix	183	1
β-strand	184-189	6	8

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	90-91	2	2
α-helix	92-93	2
α-helix	98-100	3

Chain D: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	9
β-strand	10-14	5	10
β-strand	19-24	6	9
β-strand	33-44	7	10
β-strand	51-56	6	10
β-strand	66-69	4	9
β-strand	72-77	6	9
β-strand	82-87	6	9
α-helix	92-94	3
β-strand	96-103	8	10
β-strand	110-112	3	10
β-strand	116-121	6	10
α-helix	122-123	2
β-strand	130-134	5	11
β-strand	135	1	12
α-helix	136	1
β-strand	143-148	6	11
β-strand	165-166	2	11
α-helix	167-169	3
β-strand	172-174	3	13
β-strand	179-181	3	13
β-strand	183-188	6	11
α-helix	195-198	4
β-strand	209	1	11

Chain E: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	14
β-strand	10-14	5	15
β-strand	19-24	6	14
β-strand	31-44	7	15
α-helix	49-50	2
β-strand	51-57	7	15
β-strand	60-68	5	15
β-strand	76-79	4	14
β-strand	87-91	5	14
α-helix	96-98	3
β-strand	100-107	8	15
α-helix	118-119	2
β-strand	120-121	2	15
α-helix	122	1
β-strand	125-130	6	15
α-helix	133-135	3
β-strand	137	1	16
α-helix	138-139	2
β-strand	140-144	5	17
β-strand	145	1	12
α-helix	146-147	2
α-helix	148-154	7
β-strand	156-166	11	17
β-strand	167	1	16
β-strand	171-177	7	18
β-strand	180-182	3	18
β-strand	186-188	3	17
β-strand	193-194	2	17
β-strand	204-213	10	17
α-helix	214-218	5
β-strand	223-230	8	18
β-strand	233	1	19
α-helix	244-245	2
β-strand	247	1	19
β-strand	249-256	8	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-11 beta chain	B	protein	190	Homo sapiens	P01911 (AlphaFold model)
Peptide from Capsid protein p24	C	protein	13	HIV-1 M:B_HXB2R	P04585 (AlphaFold model)
F5 alpha chain	D	protein	205	Homo sapiens	A0A0B4J272 (AlphaFold model)
F5 beta chain	E	protein	245	Homo sapiens	A0A0G2JMB4

Sequence of entity 1 (A), FASTA

>6CQN_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DT

Sequence of entity 2 (B), FASTA

>6CQN_2 HLA class II histocompatibility antigen, DRB1-11 beta chain (chains B)
GDTRPRFLEYSTSECHFFNGTERVRFLDRYFYNQEEYVRFDSDVGEFRAVTELGRPDEEY
WNSQKDFLEDRRAAVDTYCRHNYGVGESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C), FASTA

>6CQN_3 Peptide from Capsid protein p24 (chains C)
RFYKTLRAEQASQ

Sequence of entity 4 (D), FASTA

>6CQN_4 F5 alpha chain (chains D)
ILNVEQSPQSLHVQEGDSTNFTCSFPSSNFYALHWYRWETAKSPEALFVMTLNGDEKKKG
RISATLNTKEGYSYLYIKGSQPEDSATYLCAFKAAGNKLTFGGGTRVLVKPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6CQN_5 F5 beta chain (chains E)
EPEVTQTPSHQVTQMGQEVILRCVPISNHLYFYWYRQILGQKVEFLVSFYNNEISEKSEI
FDDQFSVERPDGSNFTLKIRSTKLEDSAMYFCASSGLAGGMDEQFFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

CD4+T cell-mediated HLA class II cross-restriction in HIV controllers. Galperin, M., Farenc, C., Mukhopadhyay, M. et al. Sci Immunol (2018) 3. DOI 10.1126/sciimmunol.aat0687 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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