4J1Y: Human complement protease C1s zymogen

The X-ray crystal structure of human complement protease C1s zymogen. Determined by X-ray diffraction at 2.66 Å resolution. Released 24 Apr 2013.

Method: X-ray diffraction
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,661
Mol. weight: 87.53 kDa
Released: 24 Apr 2013

Explore 4J1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4J1Y contains 30 α-helices and 82 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: 15 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	293-294	2	1
α-helix	295	1
β-strand	302-305	4	2
β-strand	311-312	2	1
β-strand	316-321	6	2
α-helix	322	1
β-strand	325-326	2	3
β-strand	327-329	3	4
β-strand	332-334	3	4
β-strand	336-340	5	2
β-strand	341	1	5
β-strand	347	1	5
β-strand	355-356	2	3
β-strand	358	1	6
α-helix	362-364	3
β-strand	368-370	3	7
β-strand	377	1	6
β-strand	381-383	3	8
β-strand	384-386	3	7
β-strand	391-393	3	9
β-strand	400-403	4	8
β-strand	409-410	2	8
β-strand	411	1	10
β-strand	415	1	10
α-helix	417-420	4
β-strand	421-423	3	9
α-helix	424-425	2
β-strand	442-443	2	11
α-helix	446-448	3
β-strand	452-456	5	12
β-strand	459-464	6	12
β-strand	469-472	4	12
α-helix	474-477	4
β-strand	485-486	2	12
β-strand	491-492	2	13
α-helix	494-499	6
β-strand	502-503	2	12
β-strand	505-510	6	12
α-helix	520-522	3
β-strand	531-535	5	12
α-helix	538-541	4
β-strand	542	1	14
β-strand	545	1	14
β-strand	549	1	11
α-helix	550-551	2
α-helix	555-557	3
β-strand	564-569	6	11
β-strand	580-581	2	13
β-strand	583-590	8	11
β-strand	616-620	5	11
α-helix	627-629	3
β-strand	635-639	5	11
β-strand	647-653	7	11
β-strand	662-667	6	11
α-helix	668-671	4
α-helix	672-681	10

Chain B: 15 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	293-294	2	15
α-helix	295	1
β-strand	302-305	4	16
β-strand	311-312	2	15
β-strand	316-321	6	16
α-helix	322	1
β-strand	325-326	2	17
β-strand	327-329	3	18
β-strand	332-334	3	18
β-strand	336-340	5	16
β-strand	341	1	19
β-strand	347	1	19
β-strand	355-356	2	17
β-strand	358	1	20
α-helix	362-364	3
β-strand	368-370	3	21
β-strand	377	1	20
β-strand	381-383	3	22
β-strand	384-386	3	21
β-strand	391-393	3	23
β-strand	400-403	4	22
β-strand	409-410	2	22
β-strand	411	1	24
β-strand	415	1	24
α-helix	417-420	4
β-strand	421-423	3	23
α-helix	424-425	2
β-strand	443	1	25
α-helix	446-448	3
β-strand	452-456	5	26
β-strand	459-464	6	26
β-strand	469-472	4	26
α-helix	474-477	4
β-strand	485-487	3	26
β-strand	491-492	2	27
β-strand	501-503	3	26
β-strand	505-510	6	26
α-helix	520-522	3
β-strand	531-535	5	26
α-helix	538-541	4
β-strand	542	1	28
β-strand	545	1	28
β-strand	549	1	25
α-helix	550-551	2
α-helix	555-557	3
β-strand	564-569	6	25
β-strand	580-581	2	27
β-strand	583-590	8	25
α-helix	592-594	3
β-strand	616-620	5	25
α-helix	627-629	3
β-strand	635-639	5	25
β-strand	647-653	7	25
β-strand	662-667	6	25
α-helix	668-671	4
α-helix	672-680	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C1s subcomponent	A, B	protein	397	Homo sapiens	P09871 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4J1Y_1 Complement C1s subcomponent (chains A, B)
MPCPKEDTPNSVWEPAKAKYVFRDVVQITCLDGFEVVEGRVGATSFYSTCQSNGKWSNSK
LKCQPVDCGIPESIENGKVEDPESTLFGSVIRYTCEEPYYYMENGGGGEYHCAGNGSWVN
EVLGPELPKCVPVCGVPREPFEEKARAIGGSDADIKNFPWQVFFDNPWAGGALINEYWVL
TAAHVVEGNREPTMYVGSTSVQTSRLAKSKMLTPEHVFIHPGWKLLEVPEGRTNFDNDIA
LVRLKDPVKMGPTVSPICLPGTSSDYNLMDGDLGLISGWGRTEKRDRAVRLKAARLPVAP
LRKCKEVKVEKPTADAEAYVFTPNMICAGGEKGMDSCKGDSGGAFAVQDPNDKTKFYAAG
LVSWGPQCGTYGLYTRVKNYVDWIMKTMQENSTPRED

Primary citation

A Molecular Switch Governs the Interaction between the Human Complement Protease C1s and Its Substrate, Complement C4. Perry, A.J., Wijeyewickrema, L.C., Wilmann, P.G. et al. J Biol Chem (2013) 288:15821-15829. DOI 10.1074/jbc.M113.464545 · PubMed

Other PDB entries of the same protein (UniProt P09871 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NZI 1.5 Å, Crystal Structure of the CUB1-EGF Interaction Domain of Complement Protease C1s
1ELV 1.7 Å, Crystal structure of the catalytic domain of human complement C1S protease
8TYP 1.8 Å, Complement Protease C1s Inhibited by 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide
4LOS 2.0 Å, C1s CUB2-CCP1
4LOR 2.5 Å, C1s CUB1-EGF-CUB2 in complex with a collagen-like peptide from C1q
5UBM 2.5 Å, Crystal structure of human C1s in complex with inhibitor gigastasin
8GMN 2.6 Å, Crystal structure of human C1s in complex with inhibitor
9X1H 2.6 Å, Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121
4LOT 2.92 Å, C1s CUB2-CCP1-CCP2
4LMF 2.92 Å, C1s CUB1-egf-CUB2
8W18 3.94 Å, The crystal structure of the Michaelis-Menten complex of a C1s/C1-INH at 3.94 Angstroms
6F1C 4.2 Å, C1rC1s complex

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