7LF9: Hyperglycosylated Human IgG1 Fc

Structure of Hyperglycosylated Human IgG1 Fc (Fc329). Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,320
Mol. weight: 55.45 kDa
Ligands: NAG, FUC
Released: 27 Jan 2021

Explore 7LF9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LF9 contains 24 α-helices and 39 β-strands across 2 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, 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	273-279	7	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	319-325	7	2
β-strand	330-336	7	2
α-helix	339	1
β-strand	344	1	3
α-helix	345-346	2
β-strand	347-351	5	4
α-helix	352-354	3
α-helix	356-359	4
β-strand	362-372	11	4
β-strand	373	1	3
β-strand	378-383	6	5
β-strand	386-387	2	5
α-helix	388	1
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	414-418	5
β-strand	423-428	6	5
α-helix	433-435	3
β-strand	437-441	5	5

Chain B: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	240-243	4	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-263	6	6
β-strand	274-279	6	7
β-strand	282-284	3	7
β-strand	289-290	2	6
α-helix	291-292	2
β-strand	303-307	5	6
α-helix	310-314	5
β-strand	319-324	6	7
β-strand	333-336	4	7
α-helix	338-340	3
β-strand	344	1	8
α-helix	345-346	2
β-strand	347-351	5	9
α-helix	352-354	3
α-helix	356-359	4
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-387	2	10
α-helix	388	1
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG1 Fc (Fc329)	A, B	protein	233	Homo sapiens	Q6MZV7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7LF9_1 IgG1 Fc (Fc329) (chains A, B)
GEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVK
FNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALNSTIEK
TISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTT
PPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
FUC	alpha-L-fucopyranose	C6 H12 O5	2

Primary citation

Silent Antibodies: Generation of Hyperglycosylated FCs to Ablate Effector Functions. Fields, J.K., Sundberg, E.J. To be published.

Other PDB entries of the same protein (UniProt Q6MZV7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RHO 2.0 Å, Human IgG1 Fc fragment, hinge-free, expressed in E. coli
5NSG 2.22 Å, Fc DEDE homodimer variant
5NSC 2.3 Å, Fc DEKK heterodimer variant
6CHF 2.4 Å, Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal…
6CJX 2.44 Å, Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal…
6CJC 2.58 Å, Crystal structure of a fc fragment lala mutant (L234A, L235A) of human IgG1 (crystal…
6N9T 2.58 Å, Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc
7LF5 2.6 Å, Structure of Hyperglycosylated Human IgG1 Fc (Fc267)
7LFN 2.6 Å, Structure of Hyperglycosylated Human IgG1 Fc (Fc267_329)
8F8X 2.6 Å, Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form II
8F8W 2.71 Å, Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form I
9IUJ 2.78 Å, Integrin alpha-v beta-3 in complex with rhodostomin

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