6CQQ: F24 TCR -DR15-RQ13 peptide complex

Crystal structure of F24 TCR -DR15-RQ13 peptide complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, HIV-1 M:B_HXB2R
Chains: 10
Atoms: 13,785
Mol. weight: 192.36 kDa
Ligands: MG, NAG
Released: 6 Jun 2018

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

Secondary structure: helices and β-sheets

6CQQ contains 44 α-helices and 153 β-strands across 10 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: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	53-54	2	2
α-helix	57-76	20
α-helix	80-82	3
β-strand	85	1	3
β-strand	90-93	4	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-127	2	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chains B and G: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
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	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	6
β-strand	98-103	6	7
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	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
β-strand	184-189	6	8

Chains C and H: 1 helix, 1 β-strand

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

Chain D: 4 helices, 20 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
β-strand	130-134	5	11
β-strand	135-136	2	12
β-strand	143-148	6	11
β-strand	155	1	13
α-helix	157-159	3
β-strand	165-166	2	11
α-helix	167-169	3
β-strand	170-173	4	11
β-strand	180-188	9	11
α-helix	195-198	4
β-strand	203	1	13
β-strand	209	1	11

Chain E: 8 helices, 24 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	1
β-strand	50-57	8	15
β-strand	60-68	5	15
α-helix	72-75	4
β-strand	76-79	4	14
β-strand	87-91	5	14
α-helix	96-98	3
β-strand	100-107	8	15
β-strand	120-121	2	15
β-strand	125-130	6	15
α-helix	133-135	3
β-strand	137	1	16
β-strand	140-145	6	12
α-helix	146-147	2
α-helix	148-154	7
β-strand	156-166	11	12
β-strand	167	1	16
β-strand	172-177	6	17
β-strand	180-182	3	17
β-strand	186-188	3	12
β-strand	193-194	2	12
β-strand	204-213	10	12
α-helix	214-217	4
β-strand	223-230	8	17
β-strand	233	1	18
α-helix	244-245	2
β-strand	247	1	18
β-strand	249-256	8	17

Chain F: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	19
β-strand	19-26	8	19
β-strand	29-34	6	19
β-strand	41-43	3	19
α-helix	46-51	6
β-strand	53-54	2	20
α-helix	57-76	20
α-helix	80-82	3
β-strand	85	1	21
β-strand	90-93	4	22
β-strand	103-112	10	22
β-strand	113	1	21
β-strand	118-123	6	23
β-strand	126-127	2	23
β-strand	133-134	2	22
β-strand	138-139	2	22
β-strand	145-153	9	22
β-strand	161-166	6	23
β-strand	174-178	5	23

Chain I: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	27
β-strand	10-14	5	28
β-strand	19-24	6	27
β-strand	33-44	7	28
β-strand	51-56	6	28
β-strand	66-69	4	27
β-strand	72-77	6	27
β-strand	82-87	6	27
α-helix	92-94	3
β-strand	96-103	8	28
α-helix	108	1
β-strand	110-112	3	28
α-helix	113	1
β-strand	116-121	6	28
β-strand	130-134	5	29
β-strand	135	1	30
β-strand	143-148	6	29
β-strand	155	1	31
β-strand	164-166	3	29
α-helix	167-169	3
β-strand	170-173	4	29
β-strand	180-188	9	29
α-helix	195-198	4
β-strand	203	1	31
β-strand	209	1	29

Chain J: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	32
β-strand	10-14	5	33
β-strand	19-24	6	32
β-strand	31-44	7	33
β-strand	50-57	8	33
β-strand	60-68	5	33
α-helix	72-75	4
β-strand	76-79	4	32
β-strand	87-91	5	32
α-helix	96-98	3
β-strand	100-107	8	33
β-strand	120-121	2	33
β-strand	125-130	6	33
β-strand	137	1	34
β-strand	140-144	5	35
β-strand	145	1	30
α-helix	146-147	2
α-helix	148-154	7
β-strand	156-166	11	35
β-strand	167	1	34
β-strand	172-177	6	36
β-strand	180-182	3	36
β-strand	186-188	3	35
β-strand	193-194	2	35
β-strand	204-213	10	35
α-helix	214-217	4
β-strand	223-230	8	36
β-strand	233	1	37
β-strand	247	1	37
β-strand	249-256	8	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, F	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA-DRB1 protein	B, G	protein	190	Homo sapiens	P01911 (AlphaFold model)
Peptide from Capsid protein p24	C, H	protein	13	HIV-1 M:B_HXB2R	P04585 (AlphaFold model)
F24 alpha chain	D, I	protein	205	Homo sapiens	A0A0B4J272 (AlphaFold model)
F24 beta chain	E, J	protein	245	Homo sapiens	A0A5B9

Sequence of entity 1 (A, F), FASTA

>6CQQ_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, F)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DT

Sequence of entity 2 (B, G), FASTA

>6CQQ_2 HLA-DRB1 protein (chains B, G)
GDTRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEY
WNSQKDILEQARAAVDTYCRHNYGVGESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C, H), FASTA

>6CQQ_3 Peptide from Capsid protein p24 (chains C, H)
RFYKTLRAEQASQ

Sequence of entity 4 (D, I), FASTA

>6CQQ_4 F24 alpha chain (chains D, I)
ILNVEQSPQSLHVQEGDSTNFTCSFPSSNFYALHWYRWETAKSPEALFVMTLNGDEKKKG
RISATLNTKEGYSYLYIKGSQPEDSATYLCAFKAAGNKLTFGGGTRVLVKPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E, J), FASTA

>6CQQ_5 F24 beta chain (chains E, J)
EPEVTQTPSHQVTQMGQEVILRCVPISNHLYFYWYRQILGQKVEFLVSFYNNEISEKSEI
FDDQFSVERPDGSNFTLKIRSTKLEDSAMYFCASSRLAGGMDEQFFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (SO4, EDO) 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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