4NO0: Non-phosphorylated form of RQA_V phosphopeptide

Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1. Determined by X-ray diffraction at 2.7 Å resolution. Released 19 Nov 2014.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,732
Mol. weight: 66.81 kDa
Released: 19 Nov 2014

Explore 4NO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NO0 contains 14 α-helices and 51 β-strands across 3 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	59-84	26
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	153-158	6
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	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	228-230	3	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: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	35-41	7	8
β-strand	44-45	2	8
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-84	7	8
β-strand	87	1	9
β-strand	91-94	4	8

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	10
β-strand	15-17	3	11
β-strand	22-27	6	10
β-strand	35-39	5	12
α-helix	47-49	3
β-strand	59-62	4	10
α-helix	67-69	3
β-strand	71-77	7	12
α-helix	85-90	6
β-strand	91-93	3	12
β-strand	94-96	3	11
β-strand	99	1	9
β-strand	103-107	5	13
β-strand	111-113	3	14
β-strand	118-123	6	13
β-strand	126	1	5
β-strand	130-136	7	15
β-strand	143-147	5	15
β-strand	156-161	6	13
β-strand	171-177	7	15
β-strand	184	1	11
α-helix	187-191	5
β-strand	192-193	2	15
β-strand	195-197	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Lymphocyte-specific protein 1	C	protein	12	Homo sapiens	P33241 (AlphaFold model)
Leukocyte immunoglobulin-like receptor subfamily B member 1	D	protein	195	Homo sapiens	Q8NHL6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NO0_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>4NO0_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4NO0_3 Lymphocyte-specific protein 1 (chains C)
RQASIELPSMAV

Sequence of entity 4 (D), FASTA

>4NO0_4 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains D)
PKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQFPIP
SITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTLQCD
SQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPY
EWSLPSDLLELLVLG

Primary citation

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status. Mohammed, F., Stones, D.H., Zarling, A.L. et al. Oncotarget (2017) 8:54160-54172. DOI 10.18632/oncotarget.16952 · 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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