9MCX: Immunoglobulin gamma-1 heavy chain Fc fragment

Crystal structure of human IgG1 fc fragment-fc-gamma receptor iia complex H131 variant. Determined by X-ray diffraction at 2.38 Å resolution. Released 3 Dec 2025.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,219
Mol. weight: 73.49 kDa
Ligands: NAG
Released: 3 Dec 2025

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

Secondary structure: helices and β-sheets

9MCX contains 24 α-helices and 59 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
α-helix	244-246	3
β-strand	258-266	9	1
β-strand	274-279	6	2
β-strand	282-284	3	2
β-strand	288-289	2	1
β-strand	293-294	2	1
β-strand	300-307	8	1
α-helix	310-314	5
β-strand	319-324	6	2
β-strand	332-336	5	2
α-helix	338-340	3
β-strand	344	1	3
α-helix	345-346	2
β-strand	347-351	5	4
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	4
β-strand	373	1	3
β-strand	378-383	6	5
β-strand	386-388	3	5
β-strand	391-393	3	4
α-helix	394-396	3
β-strand	397-398	2	4
β-strand	404-413	10	4
α-helix	414-419	6
β-strand	423-428	6	5
α-helix	433-435	3
β-strand	436-441	6	5

Chain B: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	6
β-strand	274-279	6	7
β-strand	282-284	3	7
β-strand	288-289	2	6
α-helix	290-292	3
β-strand	293-294	2	6
β-strand	300-307	8	6
α-helix	310-314	5
β-strand	319-324	6	7
β-strand	332-336	5	7
α-helix	338-340	3
β-strand	344	1	8
β-strand	347-351	5	9
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-388	3	10
β-strand	391-393	3	9
α-helix	394-396	3
β-strand	397-398	2	9
β-strand	404-413	10	9
α-helix	414-418	5
β-strand	423-428	6	10
α-helix	433-435	3
β-strand	436-441	6	10

Chain C: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	11
β-strand	15-17	3	12
β-strand	21-25	5	11
β-strand	39-41	3	13
β-strand	44-46	3	13
β-strand	53-57	5	11
α-helix	60-62	3
β-strand	64-68	5	13
α-helix	75-78	4
β-strand	79-81	3	13
β-strand	82-84	3	12
β-strand	88-91	4	14
β-strand	96-98	3	15
β-strand	103-109	7	14
α-helix	110-112	3
β-strand	116-122	7	16
β-strand	125-130	6	16
β-strand	135-138	4	14
α-helix	143-145	3
β-strand	147-155	9	16
β-strand	158-161	4	16
α-helix	162-164	3
β-strand	165-167	3	16
β-strand	168-170	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin gamma-1 heavy chain Fc fragment	A, B	protein	223	Homo sapiens	P0DOX5 (AlphaFold model)
Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant	C	protein	173	Homo sapiens	P12318 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9MCX_1 Immunoglobulin gamma-1 heavy chain Fc fragment (chains A, B)
TCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPR
EPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 2 (C), FASTA

>9MCX_2 Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant (chains C)
APPKAVLKLEPPWINVLQEDSVTLTCQGARSPESDSIQWFHNGNLIPTHTQPSYRFKANN
NDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIMLRCHSWKDKPLVKVTF
FQNGKSQKFSHLDPTFSIPQANHSHSGDYHCTGNIGYTLFSSKPVTITVQVPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Cross-species analysis of Fc gamma RIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque. Tolbert, W.D., Nhan, P.B., Conley, H.E. et al. Front Immunol (2025) 16:1726068-1726068. DOI 10.3389/fimmu.2025.1726068 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…

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