6XZU: Nanobody hC3Nb1

Complex of C-terminal domain of murine complement C3b with the hC3Nb3 nanobody. Determined by X-ray diffraction at 1.5 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Lama glama, Mus musculus
Chains: 2
Atoms: 2,431
Mol. weight: 31.14 kDa
Released: 12 Aug 2020

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

Secondary structure: helices and β-sheets

6XZU contains 11 α-helices and 17 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: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
β-strand	11-14	4	2
β-strand	19-26	8	1
β-strand	35-40	6	2
α-helix	45-46	2
β-strand	47-52	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	113-118	6	2

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1520-1523	4
α-helix	1529-1535	7
β-strand	1541-1554	14	3
β-strand	1559-1570	12	3
β-strand	1581-1586	6	3
α-helix	1588-1590	3
α-helix	1591-1594	4
β-strand	1601-1607	7	3
α-helix	1608-1610	3
β-strand	1611-1612	2	3
β-strand	1619-1621	3	3
β-strand	1627-1631	5	3
α-helix	1634-1637	4
α-helix	1643-1659	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
nanobody hC3Nb1	A	protein	127	Lama glama
Complement C3	B	protein	148	Mus musculus	P01027 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XZU_1 nanobody hC3Nb1 (chains A)
MQVQLVESGGGLVQAGGSLRLSCVVSGSTFSDYAMGWYRQAAGEQRELVAAIYSTGRTNY
IDSVKGRFTISRDNAKTTVYLQMNSLKPEDTAVYYCNLLGATTMINTKWGQGTQVTVSSL
EHHHHHH

Sequence of entity 2 (B), FASTA

>6XZU_2 Complement C3 (chains B)
ANCFMQQSQEKINLNVRLDKACEPGVDYVYKTELTNIELLDDFDEYTMTIQQVIKSGSDE
VQAGQQRKFISHIKCRNALKLQKGKKYLMWGLSSDLWGEKPNTSYIIGKDTWVEHWPEAE
ECQDQKYQKQCEELGAFTESMVVYGCPN

Primary citation

A Complement C3-Specific Nanobody for Modulation of the Alternative Cascade Identifies the C-Terminal Domain of C3b as Functional in C5 Convertase Activity. Pedersen, H., Jensen, R.K., Jensen, J.M.B. et al. J Immunol (2020) 205:2287-2300. DOI 10.4049/jimmunol.2000752 · PubMed

Other PDB entries of the same protein (UniProt P01027 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9KZK 3.54 Å, Structure of mouse C3a bound mouse C3aR in complex with Go

Browse structure collections

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