9BD3: MAGEA4 MHD-RAD18 R6BD Complex

Structure of the MAGEA4 MHD-RAD18 R6BD Complex. Determined by X-ray diffraction at 2.58 Å resolution. Released 5 Jun 2024.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,756
Mol. weight: 56.71 kDa
Released: 5 Jun 2024

Explore 9BD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BD3 contains 32 α-helices and 18 β-strands across 4 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: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	102-126	25
β-strand	131-132	2	1
α-helix	133-139	7
α-helix	142-147	6
α-helix	148-158	11
α-helix	159-163	5
β-strand	165-171	7	1
β-strand	176-181	6	1
α-helix	182-184	3
β-strand	191	1	2
β-strand	194	1	2
α-helix	200-213	14
β-strand	217-218	2	3
α-helix	219-228	10
β-strand	237	1	4
β-strand	241	1	4
α-helix	243-245	3
α-helix	246-250	5
α-helix	251-253	3
β-strand	257-261	5	3
α-helix	262	1
β-strand	270-274	5	3
α-helix	276-281	6
α-helix	284-296	13
α-helix	298-304	7
α-helix	305-311	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	349-365	17

Chain C: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	102-126	25
β-strand	131-132	2	5
α-helix	133-139	7
α-helix	142-147	6
α-helix	148-163	16
β-strand	165-171	7	5
β-strand	176-181	6	5
α-helix	182-184	3
α-helix	200-213	14
β-strand	217-218	2	6
α-helix	219-228	10
β-strand	237	1	7
β-strand	241	1	7
α-helix	243-245	3
α-helix	246-250	5
α-helix	251-253	3
β-strand	257-261	5	6
β-strand	270-274	5	6
α-helix	276-281	6
α-helix	284-295	12
α-helix	298-303	6
α-helix	305-311	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	349-364	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Melanoma antigen A 4	A, C	protein	220	Homo sapiens	P43358 (AlphaFold model)
E3 ubiquitin-protein ligase RAD18	B, D	protein	28	Homo sapiens	Q9NS91 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9BD3_1 Melanoma antigen A 4 (chains A, C)
SNADAESLFREALSNKVDELAHFLLRKYRAKELVTKAEMLERVIKNYKRCFPVIFGKASE
SLKMIFGIDVKEVDPTSNTYTLVTCLGLSYDGLLGNNQIFPKTGLLIIVLGTIAMEGDSA
SEEEIWEELGVMGVYDGREHTVYGEPRKLLTQDWVQENYLEYRQVPGSNPARYEFLWGPR
ALAETSYVKVLEHVVRVNARVRIAYPSLREAALLEEEEGV

Sequence of entity 2 (B, D), FASTA

>9BD3_2 E3 ubiquitin-protein ligase RAD18 (chains B, D)
HSKYRKKHKSEFQLLVDQARKGYKKIAG

Primary citation

Crystal structure of MAGEA4 MHD-RAD18 R6BD reveals a flipped binding mode compared to AlphaFold2 prediction. Forker, K., Fleming, M.C., Pearce, K.H. et al. EMBO J (2024) 43:2835-2839. DOI 10.1038/s44318-024-00140-2 · PubMed

Other PDB entries of the same protein (UniProt P43358 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRN 1.35 Å, Crystal structure of HLA A2*01-AVYDGREHTV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
33CG 2.2 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
33CI 2.2 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-58
2WA0 2.3 Å, Crystal structure of the human MAGEA4
33CH 2.4 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
6TRO 3.0 Å, Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV
8FJA 3.0 Å, CryoEM structure of HLA-A2 MAGEA4 (230-239) in complex with REGN6972 Fab
8ES9 3.25 Å, CryoEM structure of PN45428 TCR-CD3 in complex with HLA-A2 MAGEA4
7UOA 3.5 Å, MAGEA4-MTP1 linear peptide complex

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