6EAQ: Glycosylated FCGR3B / CD16b

Glycosylated FCGR3B / CD16b in complex with afucosylated IgG1 Fc. Determined by X-ray diffraction at 2.22 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 2.22 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,189
Mol. weight: 73.6 kDa
Released: 7 Nov 2018

Explore 6EAQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EAQ contains 29 α-helices and 61 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: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-266	9	1
β-strand	274-279	6	2
β-strand	282-284	3	2
β-strand	288-289	2	1
α-helix	290-292	3
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	386-387	2	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: 11 helices, 19 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	288-294	7	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	339-340	2
β-strand	344	1	8
α-helix	345-346	2
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	386-387	2	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	414-419	6
α-helix	421-422	2
β-strand	423-428	6	10
α-helix	433-435	3
β-strand	437-441	5	10

Chain C: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7	1	11
α-helix	8	1
β-strand	9-13	5	12
β-strand	18-20	3	13
β-strand	25-30	6	12
β-strand	40-44	5	14
β-strand	47-48	2	14
β-strand	55-58	4	12
α-helix	63-65	3
β-strand	67-73	7	14
β-strand	77	1	11
α-helix	78-81	4
β-strand	82-84	3	14
β-strand	85-87	3	13
β-strand	91-94	4	15
β-strand	99-100	2	16
β-strand	106-108	3	17
β-strand	109-112	4	15
α-helix	113-115	3
β-strand	119-125	7	18
β-strand	128-135	8	18
β-strand	139-141	3	17
α-helix	146-148	3
β-strand	150-158	9	18
β-strand	161-164	4	18
α-helix	165-167	3
β-strand	168-170	3	18
β-strand	171-172	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin gamma-1 heavy chain	A, B	protein	220	Homo sapiens	P0DOX5 (AlphaFold model)
Low affinity immunoglobulin gamma Fc region receptor III-B	C	protein	175	Homo sapiens	O75015 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6EAQ_1 Immunoglobulin gamma-1 heavy chain (chains A, B)
TCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPR
EPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS

Sequence of entity 2 (C), FASTA

>6EAQ_2 Low affinity immunoglobulin gamma Fc region receptor III-B (chains C)
RTEDLPKAVVFLEPQWYSVLEKDSVTLKCQGAYSPEDQSTQWFHNESLISSQASSYFIDA
ATVQDSGEYRCQTQLSTLSDPVQLEVHIGWLLLQAPRWVFKEEDPIHLRCHSWKNTALHK
VTYLQNGKDRKYFHHNSDFHIPKATLKDSGSYFCRGLVGSKNVSSETVQITITQG

Primary citation

A single amino acid distorts the Fc gamma receptor IIIb/CD16b structure upon binding immunoglobulin G1 and reduces affinity relative to CD16a. Roberts, J.T., Barb, A.W. J Biol Chem (2018) 293:19899-19908. DOI 10.1074/jbc.RA118.005273 · 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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