6CQR: F24 TCR -DR1-RQ13 peptide complex

Crystal structure of F24 TCR -DR1-RQ13 peptide complex. Determined by X-ray diffraction at 3.04 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 3.04 Å
Organisms: Homo sapiens, HIV-1 M:B_HXB2R
Chains: 10
Atoms: 13,648
Mol. weight: 191.95 kDa
Ligands: NAG
Released: 6 Jun 2018

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

Secondary structure: helices and β-sheets

6CQR contains 42 α-helices and 146 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	4-15	12	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	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
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	126-127	2	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	161-166	6	5
β-strand	174-178	5	5

Chain B: 4 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	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
β-strand	98-103	6	7
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-132	5	8
β-strand	137	1	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: 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: 4 helices, 17 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	67-69	3	9
β-strand	72-77	6	9
β-strand	82-87	6	9
α-helix	92-94	3
β-strand	97-103	7	10
β-strand	110-112	3	10
β-strand	116-121	6	10
β-strand	130-136	7	11
β-strand	143-148	6	11
α-helix	157-159	3
β-strand	164-166	3	11
α-helix	167-169	3
β-strand	170-174	5	11
β-strand	179-188	10	11
α-helix	195-197	3
β-strand	209	1	11

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	31-44	7	13
β-strand	51-57	7	13
β-strand	60-68	5	13
β-strand	76-79	4	12
β-strand	87-91	5	12
α-helix	96-98	3
β-strand	101-107	7	13
β-strand	120-121	2	13
β-strand	125-130	6	13
α-helix	133-135	3
β-strand	137	1	14
β-strand	140-145	6	11
α-helix	146-147	2
α-helix	148-153	6
β-strand	156-166	11	11
β-strand	167	1	14
β-strand	171-177	7	15
β-strand	180-182	3	15
β-strand	186-188	3	11
α-helix	192	1
β-strand	193-194	2	11
β-strand	204-213	10	11
α-helix	214-218	5
β-strand	223-230	8	15
β-strand	233	1	16
α-helix	244-245	2
β-strand	247	1	16
β-strand	249-256	8	15

Chain F: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	17
β-strand	19-26	8	17
β-strand	29-35	7	17
β-strand	40-43	4	17
α-helix	48-51	4
β-strand	53-54	2	18
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	19
β-strand	89-93	5	20
β-strand	103-112	10	20
β-strand	113	1	19
β-strand	118-123	6	21
β-strand	126-127	2	21
β-strand	133-134	2	20
β-strand	138-139	2	20
β-strand	145-153	9	20
β-strand	161-166	6	21
β-strand	174-178	5	21

Chain G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	17
β-strand	23-32	10	17
β-strand	35-41	7	17
β-strand	47-49	3	17
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	22
β-strand	98-103	6	23
β-strand	115-122	8	23
β-strand	123	1	22
β-strand	128-132	5	24
β-strand	137	1	24
β-strand	142-144	3	23
β-strand	148-149	2	23
β-strand	155-161	7	23
β-strand	170-176	7	24
β-strand	184-189	6	24

Chain I: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	25
β-strand	10-14	5	26
β-strand	19-24	6	25
β-strand	33-44	7	26
β-strand	51-56	6	26
β-strand	67-69	3	25
β-strand	72-77	6	25
β-strand	82-87	6	25
α-helix	92-94	3
β-strand	97-103	7	26
β-strand	110-112	3	26
β-strand	116-121	6	26
β-strand	130-134	5	27
β-strand	144-148	5	27
α-helix	157-159	3
β-strand	164-166	3	27
α-helix	167-169	3
β-strand	170-174	5	27
β-strand	179-188	10	27
α-helix	189-191	3
α-helix	199-201	3
β-strand	209	1	27

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

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 class II histocompatibility antigen, DRB1-1 beta chain	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

>6CQR_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, F)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DT

Sequence of entity 2 (B, G), FASTA

>6CQR_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains B, G)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C, H), FASTA

>6CQR_3 Peptide from Capsid protein p24 (chains C, H)
RFYKTLRAEQASQ

Sequence of entity 4 (D, I), FASTA

>6CQR_4 F24 alpha chain (chains D, I)
ILNVEQSPQSLHVQEGDSTNFTCSFPSSNFYALHWYRWETAKSPEALFVMTLNGDEKKKG
RISATLNTKEGYSYLYIKGSQPEDSATYLCAFKAAGNKLTFGGGTRVLVKPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E, J), FASTA

>6CQR_5 F24 beta chain (chains E, J)
EPEVTQTPSHQVTQMGQEVILRCVPISNHLYFYWYRQILGQKVEFLVSFYNNEISEKSEI
FDDQFSVERPDGSNFTLKIRSTKLEDSAMYFCASSRLAGGMDEQFFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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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