9EKE: C1r Zymogen Fragment

Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant. Determined by X-ray diffraction at 3.1 Å resolution. Released 12 Feb 2025.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Lutzomyia longipalpis, Homo sapiens
Chains: 4
Atoms: 7,515
Mol. weight: 117.45 kDa
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9EKE contains 37 α-helices and 78 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	25-43	19
α-helix	48-51	4
α-helix	56-66	11
α-helix	73-86	14
α-helix	94-104	11

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	70-72	3
α-helix	73-86	14
α-helix	94-104	11

Chain C: 13 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	309	1	1
α-helix	310-312	3
β-strand	319-321	3	2
β-strand	328	1	1
β-strand	333-338	6	2
β-strand	342-344	3	3
β-strand	351	1	3
β-strand	354-357	4	2
β-strand	358	1	4
β-strand	364	1	4
β-strand	371-373	3	3
α-helix	374	1
β-strand	375	1	5
α-helix	379-382	4
β-strand	385-389	5	6
β-strand	397	1	5
β-strand	401-406	6	6
β-strand	411-413	3	7
α-helix	423-425	3
β-strand	426-429	4	6
β-strand	435-436	2	6
β-strand	447-449	3	7
α-helix	457-459	3
β-strand	469	1	8
β-strand	479-482	4	9
β-strand	486-489	4	9
β-strand	490-492	3	10
β-strand	496-499	4	10
α-helix	501-503	3
β-strand	519-521	3	9
β-strand	525	1	11
α-helix	526-531	6
β-strand	537-542	6	10
β-strand	559-563	5	10
β-strand	570	1	12
β-strand	573	1	12
β-strand	577	1	8
α-helix	578-579	2
α-helix	582-585	4
β-strand	590-595	6	8
β-strand	606	1	11
β-strand	608-613	6	8
β-strand	614	1	13
α-helix	615-616	2
α-helix	617-627	11
β-strand	637-640	4	13
β-strand	657-662	6	8
β-strand	667-673	7	8
β-strand	674	1	13
β-strand	685-688	4	13
α-helix	691-693	3
α-helix	694-702	9

Chain D: 13 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	309	1	14
α-helix	310-312	3
β-strand	319-321	3	15
β-strand	328	1	14
β-strand	333-335	3	16
β-strand	336-338	3	15
α-helix	339	1
β-strand	342-344	3	17
β-strand	351	1	17
β-strand	355-357	3	16
β-strand	358	1	18
β-strand	364	1	18
β-strand	371-373	3	17
α-helix	374	1
β-strand	375	1	19
α-helix	379-381	3
β-strand	385-389	5	20
β-strand	397	1	19
β-strand	401-406	6	20
β-strand	411-413	3	21
α-helix	414-415	2
β-strand	426-429	4	20
β-strand	435-436	2	20
β-strand	447-449	3	21
α-helix	457-459	3
β-strand	469	1	22
α-helix	470-471	2
β-strand	478-481	4	23
β-strand	487-492	6	23
β-strand	496-499	4	23
β-strand	519-521	3	23
β-strand	525	1	24
α-helix	526-531	6
β-strand	537-542	6	23
β-strand	559-563	5	23
β-strand	570	1	25
β-strand	573	1	25
β-strand	577	1	22
α-helix	582-585	4
β-strand	590-595	6	22
β-strand	606	1	24
β-strand	608-613	6	22
β-strand	614	1	26
α-helix	617-626	10
β-strand	637-641	5	26
α-helix	653	1
β-strand	657-662	6	22
β-strand	667-673	7	22
β-strand	674-676	3	26
β-strand	684-688	5	26
α-helix	690-693	4
α-helix	694-702	9

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

>9EKE_1 Salivary anti-complement protein (chains A, B)
SEDCENIFHDNAYLLKLDCEAGRVDPVEFDDISDEEIYEITVDVGVSSEDQEKVAKIIRE
CIAQVSTQDCTKFSEIYDCYMKKKICNYYPENMGSGHHHHHHHH

Sequence of entity 2 (C, D), FASTA

>9EKE_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
9EKD 3.28 Å, Structure of a C1r Zymogen Fragment Bound to SALO

Browse structure collections

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