3FQR: PDB entry 3FQR

Phosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted antigen presentation and generates tumor specific epitopes. Determined by X-ray diffraction at 1.7 Å resolution. Released 3 Mar 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,850
Mol. weight: 45.59 kDa
Ligands: MG, CD
Released: 3 Mar 2009

Explore 3FQR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FQR contains 14 α-helices and 30 β-strands across 2 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	3-12	10	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-53	4
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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
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	222-224	3	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	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
α-helix	3-4	2
β-strand	5-10	6	6
β-strand	20-29	10	6
β-strand	30	1	5
β-strand	35-40	6	7
β-strand	43-44	2	7
α-helix	45	1
β-strand	49-50	2	6
α-helix	51-53	3
β-strand	54-55	2	6
β-strand	61-69	9	6
β-strand	77-82	6	7
β-strand	90-93	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	98	Homo sapiens	P61769 (AlphaFold model)
phospho-peptide 30-39 from beta-Catenin: YLD(Sep)GIHSGA	C	protein	10		P35222 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3FQR_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>3FQR_2 Beta-2-microglobulin (chains B)
QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWS
FYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>3FQR_3 phospho-peptide 30-39 from beta-Catenin: YLD(Sep)GIHSGA (chains C)
YLDSGIHSGA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
CD	Cadmium ion	Cd	6

Water and common crystallization additives (GOL) are not listed.

Primary citation

Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes. Petersen, J., Wurzbacher, S.J., Williamson, N.A. et al. Proc Natl Acad Sci U S A (2009) 106:2776-2781. DOI 10.1073/pnas.0812901106 · 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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