8F8X: Nb.X0

Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form II. Determined by X-ray diffraction at 2.6 Å resolution. Released 29 Mar 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Camelidae mixed library
Chains: 4
Atoms: 5,357
Mol. weight: 79.56 kDa
Released: 29 Mar 2023

Explore 8F8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F8X contains 26 α-helices and 63 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: 10 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	311-314	4
β-strand	319-325	7	2
β-strand	332-336	5	2
α-helix	338-340	3
β-strand	344	1	3
β-strand	347-351	5	4
α-helix	352-354	3
α-helix	355-357	3
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	414-418	5
β-strand	423-428	6	5
α-helix	433-435	3
β-strand	437-441	5	5

Chain B: 9 helices, 21 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	273	1	7
β-strand	276-279	4	8
β-strand	282-284	3	8
β-strand	288-289	2	6
α-helix	290-292	3
β-strand	300-307	8	6
α-helix	311-314	4
β-strand	318-323	6	8
β-strand	325	1	7
β-strand	332-337	6	8
β-strand	344	1	9
β-strand	347-351	5	10
α-helix	352-354	3
α-helix	356-359	4
β-strand	362-372	11	10
β-strand	373	1	9
β-strand	378-383	6	11
β-strand	386-387	2	11
β-strand	391-393	3	10
α-helix	394-396	3
β-strand	397-398	2	10
β-strand	404-413	10	10
α-helix	414-418	5
β-strand	423-428	6	11
α-helix	433-435	3
β-strand	437-441	5	11

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-13	4	13
β-strand	18-23	6	12
α-helix	24-25	2
β-strand	33-39	7	13
β-strand	46-51	6	13
β-strand	57-59	3	13
β-strand	67-72	6	12
α-helix	73-75	3
β-strand	77-82	6	12
α-helix	87-89	3
β-strand	91-100	10	13
β-strand	105-110	6	13
β-strand	114-119	6	13

Chain D: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-13	4	15
β-strand	18-24	7	14
α-helix	25	1
β-strand	33-39	7	15
β-strand	45-51	7	15
β-strand	57-59	3	15
α-helix	61-63	3
β-strand	67-72	6	14
α-helix	73-75	3
β-strand	77-82	6	14
α-helix	87-89	3
β-strand	91-100	10	15
β-strand	105-110	6	15
β-strand	114-119	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein DKFZp686C11235	A, B	protein	224	Homo sapiens	Q6MZV7 (AlphaFold model)
Nb.X0	C, D	protein	120	Camelidae mixed library

Sequence of entity 1 (A, B), FASTA

>8F8X_1 Uncharacterized protein DKFZp686C11235 (chains A, B)
DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVD
GVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAK
GQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWRSNGQPENNYKTTPPVLDS
DGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS

Sequence of entity 2 (C, D), FASTA

>8F8X_2 Nb.X0 (chains C, D)
QVQLQESGGGLVQAGGSLRLSCAASPGISRYKTMGWYRQAPGKERSFVAAITWGGLTYYA
DSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCSVDGGTRADPYHYYWGQGTQVTVSS

Primary citation

Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody. Gupta, A., Kao, K.S., Yamin, R. et al. Nat Commun (2023) 14:2853-2853. DOI 10.1038/s41467-023-38453-1 · PubMed

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
7LF9 2.2 Å, Structure of Hyperglycosylated Human IgG1 Fc (Fc329)
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)
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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