4U1M: PDB entry 4U1M

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes. Determined by X-ray diffraction at 1.18 Å resolution. Released 8 Apr 2015.

Method: X-ray diffraction
Resolution: 1.18 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,973
Mol. weight: 46.97 kDa
Released: 8 Apr 2015

Explore 4U1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U1M contains 16 α-helices and 30 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: 12 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	50-52	3
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
α-helix	182	1
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	222-223	2	4
α-helix	225-227	3
β-strand	228-230	3	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	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, B-42 alpha chain	A	protein	277	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Protein Nef	C	protein	9	Human immunodeficiency virus 1	P03407

Sequence of entity 1 (A), FASTA

>4U1M_1 HLA class I histocompatibility antigen, B-42 alpha chain (chains A)
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
DRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYDG
KDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLEGTCVEWLRRYLENGKDTLE
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPS

Sequence of entity 2 (B), FASTA

>4U1M_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4U1M_3 Protein Nef (chains C)
RPQVPLRPM

Primary citation

A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape. Klverpris, H.N., Cole, D.K., Fuller, A. et al. Retrovirology (2015) 12:20-20. DOI 10.1186/s12977-015-0149-5 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide
6P2C 1.4 Å, Structure of a nested set of N-terminally extended MHC I-peptides provides novel…

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