9D72: Anti-MHC-I Fab M1/42 complex with H2-Dd

CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd. Determined by electron microscopy at 2.67 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 2.67 Å
Organisms: Mus musculus, Rattus norvegicus, synthetic construct
Chains: 5
Atoms: 6,040
Mol. weight: 91.73 kDa
Released: 4 Feb 2026

Explore 9D72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D72 contains 13 α-helices and 74 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
α-helix	20	1
β-strand	21-28	8	11
β-strand	31-35	5	11
β-strand	37	1	11
β-strand	46-47	2	11
α-helix	50-52	3
α-helix	57-84	28
β-strand	96-103	8	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	140-150	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	12
β-strand	186-189	4	13
β-strand	202-208	7	13
β-strand	209	1	12
β-strand	214-218	5	14
β-strand	228-230	3	13
β-strand	234-235	2	13
β-strand	241-247	7	13
β-strand	258-262	5	14
β-strand	270-272	3	14

Chain B: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	6-8	3	2
β-strand	11	1	2
β-strand	16	1	3
β-strand	19	1	3
β-strand	21-30	10	2
β-strand	31	1	1
β-strand	36-39	4	4
β-strand	40-41	2	5
β-strand	44-45	2	5
β-strand	51-56	6	2
β-strand	62-70	9	2
β-strand	80-83	4	4

Chain H: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	12	1	16
β-strand	16-23	8	15
β-strand	35-42	8	17
β-strand	48-54	7	17
β-strand	59-61	3	17
β-strand	69-73	5	15
β-strand	79-87	9	15
β-strand	93-100	8	17
β-strand	101-103	3	18
β-strand	106-108	3	18
β-strand	113	1	17
β-strand	117-119	3	17
β-strand	121	1	16
β-strand	130-134	5	19
β-strand	147-155	9	19
β-strand	161-164	4	20
β-strand	173-175	3	19
β-strand	179-181	3	19
β-strand	184-192	9	19
β-strand	204-209	6	20
α-helix	210-212	3
β-strand	214-219	6	20

Chain L: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	6
β-strand	10-12	3	7
β-strand	19-23	5	6
β-strand	34-38	5	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	64-67	4	6
β-strand	70-75	6	6
β-strand	85-89	5	7
β-strand	98	1	7
β-strand	102-105	4	7
β-strand	116-118	3	8
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	8
β-strand	145-146	2	9
β-strand	150	1	10
β-strand	153	1	10
β-strand	160-163	4	8
β-strand	173-182	10	8
α-helix	183-188	6
β-strand	191-197	7	9
β-strand	204-210	7	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin	B	protein	98	Mus musculus	P01887 (AlphaFold model)
Fab M1/42 Light Chain	L	protein	213	Rattus norvegicus
Surface protein gp120	P	protein	10	synthetic construct	P04582
H-2 class I histocompatibility antigen, D-D alpha chain	A	protein	273	Mus musculus	P01900 (AlphaFold model)
Fab M1/42 Heavy Chain	H	protein	222	Rattus norvegicus

Sequence of entity 1 (B), FASTA

>9D72_1 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRD

Sequence of entity 2 (L), FASTA

>9D72_2 Fab M1/42 Light Chain (chains L)
DIQMTQSPSSMSASLGDKVTINCLASEDIGNYLSWYQQRPGKSPKLMIYGVTNLEDGVPS
RFSGSRSGSDYSLTINSLGYDDEGIYHCHEYYEYPFTFGSGTKLEIKRADAAPTVSIFPP
STEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLS
LTKADYESHNLYTCEVVHKTSSSPVVKSFNRNE

Sequence of entity 3 (P), FASTA

>9D72_3 Surface protein gp120 (chains P)
RGPGRAFVTI

Sequence of entity 4 (A), FASTA

>9D72_4 H-2 class I histocompatibility antigen, D-D alpha chain (chains A)
SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE
RETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGC
DYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR
TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF
QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW

Sequence of entity 5 (H), FASTA

>9D72_5 Fab M1/42 Heavy Chain (chains H)
QVTLKESGPGMLQPSKTLSLTCSFSGFSLSTSGLVVNWIRQPSGKSLEWLAAIDWDGDEY
YNPSPKSRLTVSKDTSNTQVFLKITSVDTVDTATYYCARSRRYGRYSGAFDYWGLGVMVT
VSSAETTAPSVYPLAPGTALKSNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVL
QSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVP

Primary citation

Structural mechanism of anti-MHC-I antibody blocking of inhibitory NK cell receptors in tumor immunity. Jiang, J., Panda, A.K., Natarajan, K. et al. Res Sq (2025). DOI 10.21203/rs.3.rs-7133881/v1 · PubMed

Other PDB entries of the same protein (UniProt P01887 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LK2 1.35 Å, 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
1G7P 1.5 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
1KPU 1.5 Å, High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3G08 1.6 Å, Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d
3GMO 1.6 Å, Structure of mouse CD1d in complex with C8PhF
7LFK 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, thr mutant, refined…
7LFL 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant,…
7LFM 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant,…
6C6F 1.67 Å, Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…

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