9EKD: C1r Zymogen Fragment

Structure of a C1r Zymogen Fragment Bound to SALO. Determined by X-ray diffraction at 3.28 Å resolution. Released 12 Feb 2025.

Method: X-ray diffraction
Resolution: 3.28 Å
Organisms: Lutzomyia longipalpis, Homo sapiens
Chains: 4
Atoms: 7,644
Mol. weight: 117.65 kDa
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9EKD contains 41 α-helices and 71 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	25-42	18
α-helix	50-52	3
α-helix	56-66	11
α-helix	72-86	15
α-helix	94-104	11
α-helix	108-110	3

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	25-42	18
α-helix	50-52	3
α-helix	56-66	11
α-helix	72-86	15
α-helix	94-104	11
α-helix	107-110	4

Chain C: 14 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	309	1	1
α-helix	310-312	3
β-strand	319-322	4	2
β-strand	328	1	1
β-strand	333-338	6	2
β-strand	342-343	2	3
β-strand	344	1	4
β-strand	351	1	4
β-strand	354-357	4	2
β-strand	358	1	5
β-strand	364	1	5
β-strand	372-373	2	3
β-strand	375	1	6
α-helix	379-382	4
β-strand	385-389	5	7
β-strand	397	1	6
β-strand	401-406	6	7
β-strand	411-413	3	8
β-strand	426-429	4	7
β-strand	435-436	2	7
β-strand	447-449	3	8
α-helix	450	1
α-helix	457-459	3
β-strand	469	1	9
α-helix	470-471	2
β-strand	478-482	5	10
β-strand	486-492	7	10
β-strand	496-499	4	10
α-helix	501-503	3
β-strand	519-521	3	10
α-helix	526-532	7
α-helix	534	1
β-strand	535	1	10
α-helix	536	1
β-strand	537-542	6	10
β-strand	559-563	5	10
β-strand	570	1	11
β-strand	573	1	11
β-strand	577	1	9
α-helix	578-579	2
α-helix	582-585	4
β-strand	590-595	6	9
β-strand	608-614	7	9
α-helix	617-626	10
β-strand	637-640	4	9
α-helix	649-651	3
β-strand	657-662	6	9
β-strand	667-674	8	9
β-strand	685-689	5	9
α-helix	694-701	8

Chain D: 15 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	309	1	12
α-helix	310-312	3
β-strand	319-322	4	13
β-strand	328	1	12
β-strand	333-338	6	13
β-strand	342-343	2	14
β-strand	354-357	4	13
β-strand	358	1	15
β-strand	364	1	15
β-strand	372-373	2	14
α-helix	374	1
β-strand	375	1	16
α-helix	379-382	4
β-strand	385-389	5	17
β-strand	397	1	16
β-strand	401-406	6	17
β-strand	411-413	3	18
β-strand	426-429	4	17
β-strand	435-436	2	17
β-strand	447-449	3	18
α-helix	450	1
α-helix	457-459	3
β-strand	469	1	19
β-strand	479-482	4	20
β-strand	486-487	2	20
β-strand	490-492	3	21
β-strand	496-499	4	21
α-helix	501-503	3
β-strand	519-521	3	20
α-helix	526-532	7
α-helix	534	1
β-strand	535	1	20
α-helix	536	1
β-strand	537-542	6	21
β-strand	559-563	5	21
β-strand	570	1	22
β-strand	573	1	22
β-strand	577	1	19
α-helix	578-579	2
α-helix	582-585	4
β-strand	590-595	6	19
β-strand	608-614	7	19
α-helix	617-626	10
β-strand	637-640	4	19
α-helix	649-651	3
β-strand	657-662	6	19
β-strand	667-674	8	19
β-strand	685-689	5	19
α-helix	690-693	4
α-helix	694-701	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Salivary anti-complement protein	A, B	protein	104	Lutzomyia longipalpis	Q5WPZ4 (AlphaFold model)
Complement C1r subcomponent	C, D	protein	409	Homo sapiens	P00736 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9EKD_1 Salivary anti-complement protein (chains A, B)
SEDCENIFHDNAYLLKLDCEAGRVDPVEYDDISDEEIYEITVDVGVSSEDQEKVAKIIRE
CIAQVSTQDCTKFSEIYDCYMKKKICNYYPENMGSGHHHHHHHH

Sequence of entity 2 (C, D), FASTA

>9EKD_2 Complement C1r subcomponent (chains C, D)
KCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRA
MPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVY
TCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQRIIGGQKAKMGNFPWQVFTNIHGRG
GGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYR
QDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDL
RFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDAGGVFAVRDPNTDR
WVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEEEDGSGHHHHHHHH

Primary citation

Blocking activation of the C1r zymogen defines a novel mode of complement inhibition. Duan, H., Wu, W., Li, P. et al. J Biol Chem (2025) 301:108301-108301. DOI 10.1016/j.jbc.2025.108301 · PubMed

Other PDB entries of the same protein (UniProt Q5WPZ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KX4 1.94 Å, Structure of SALO
9EKE 3.1 Å, Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant

Browse structure collections

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