5UBM: Human C1s

Crystal structure of human C1s in complex with inhibitor gigastasin. Determined by X-ray diffraction at 2.5 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Haementeria ghilianii
Chains: 3
Atoms: 3,936
Mol. weight: 61.25 kDa
Released: 8 Nov 2017

Explore 5UBM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UBM contains 22 α-helices and 56 β-strands across 3 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	439	1	1
β-strand	442-443	2	2
α-helix	446-448	3
β-strand	452-456	5	3
β-strand	459	1	4
β-strand	460-466	7	3
β-strand	469-472	4	3
α-helix	474-477	4
β-strand	484-487	4	3
β-strand	491	1	5
α-helix	494-497	4
β-strand	501-503	3	3
β-strand	505-510	6	3
β-strand	524	1	6
β-strand	531-535	5	3
α-helix	538-541	4
β-strand	542	1	7
β-strand	545	1	7
α-helix	547-548	2
β-strand	549	1	2
α-helix	550-551	2
α-helix	555-557	3
β-strand	564-569	6	2
β-strand	581	1	5
β-strand	583-590	8	2
α-helix	592-594	3
β-strand	610	1	6
β-strand	616-620	5	2
β-strand	626	1	1
β-strand	635-640	6	2
β-strand	643-656	14	2
β-strand	662-667	6	2
α-helix	668-671	4
α-helix	672-681	10

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	291-292	2
β-strand	293-294	2	8
α-helix	295	1
β-strand	302-305	4	9
β-strand	311-312	2	8
β-strand	316-321	6	9
α-helix	322	1
β-strand	325-326	2	10
β-strand	327-328	2	11
β-strand	333-334	2	11
β-strand	336-340	5	9
β-strand	341	1	12
β-strand	347	1	12
β-strand	355-356	2	10
β-strand	358	1	13
α-helix	362-364	3
β-strand	368-370	3	14
α-helix	371-373	3
β-strand	377	1	13
β-strand	381-383	3	15
β-strand	384-386	3	14
β-strand	391-393	3	16
β-strand	400-403	4	15
β-strand	409-410	2	15
β-strand	411	1	17
β-strand	415	1	17
α-helix	417-419	3
β-strand	421-423	3	16

Chain I: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	11-14	4
β-strand	19-20	2	18
β-strand	29-30	2	18
α-helix	33-35	3
β-strand	44-46	3	19
α-helix	51	1
β-strand	52-56	5	19
β-strand	63-64	2	2
β-strand	67	1	4
β-strand	72-74	3	20
α-helix	79	1
β-strand	80-85	6	20
α-helix	86-87	2
β-strand	102-104	3	21
β-strand	109-111	3	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C1s subcomponent	A	protein	252	Homo sapiens	P09871 (AlphaFold model)
Complement C1s subcomponent	B	protein	152	Homo sapiens	P09871 (AlphaFold model)
Gigastasin	I	protein	137	Haementeria ghilianii

Sequence of entity 1 (A), FASTA

>5UBM_1 Complement C1s subcomponent (chains A)
RIIGGSDADIKNFPWQVFFDNPWAGGALINEYWVLTAAHVVEGNREPTMYVGSTSVQTSR
LAKSKMLTPEHVFIHPGWKLLEVPEGRTNFDNDIALVRLKDPVKMGPTVSPICLPGTSSD
YNLMDGDLGLISGWGRTEKRDRAVRLKAARLPVAPLRKCKEVKVEKPTADAEAYVFTPNM
ICAGGEKGMDSCKGDSGGAFAVQDPNDKTKFYAAGLVSWGPQCGTYGLYTRVKNYVDWIM
KTMQENSTPRED

Sequence of entity 2 (B), FASTA

>5UBM_2 Complement C1s subcomponent (chains B)
LRYHGDPMPCPKEDTPNSVWEPAKAKYVFRDVVQITCLDGFEVVEGRVGATSFYSTCQSN
GKWSNSKLKCQPVDCGIPESIENGKVEDPESTLFGSVIRYTCEEPYYYMENGGGGEYHCA
GNGSWVNEVLGPELPKCVPVCGVPREPFEEKQ

Sequence of entity 3 (I), FASTA

>5UBM_3 Gigastasin (chains I)
AHHHHHHTSGDDDDKAKKKLPKCQKQEDCGSWDLKCNNVTKKCECRNQVCGRGCPKERYQ
RDKYGCRKCLCKGCDGFKCRLGCTYGFKTDKKGCEAFCTCNTKETACVNIWCTDPYKCNP
ESGRCEDPNEEYEYDYE

Primary citation

The Structural Basis for Complement Inhibition by Gigastasin, a Protease Inhibitor from the Giant Amazon Leech. Pang, S.S., Wijeyewickrema, L.C., Hor, L. et al. J Immunol (2017) 199:3883-3891. DOI 10.4049/jimmunol.1700158 · 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
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
4J1Y 2.66 Å, The X-ray crystal structure of human complement protease C1s zymogen
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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