9X1H: Human complement C1s CUB domain

Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121. Determined by electron microscopy at 2.6 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,888
Mol. weight: 161.43 kDa
Ligands: CA
Released: 19 Nov 2025

Explore 9X1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9X1H contains 16 α-helices and 75 β-strands across 6 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	16
α-helix	16-18	3
β-strand	21-28	8	17
β-strand	33-43	11	16
α-helix	48-50	3
β-strand	54-59	6	17
β-strand	62-67	6	17
β-strand	70-71	2	16
β-strand	82-86	5	16
β-strand	90-97	8	17
β-strand	107-116	10	16
α-helix	117	1
β-strand	131-135	5	18
β-strand	138-142	5	18
β-strand	148-149	2	19
β-strand	156-157	2	19

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	9
α-helix	16-18	3
β-strand	21-28	8	10
β-strand	33-43	11	9
α-helix	48-50	3
β-strand	54-59	6	10
β-strand	62-67	6	10
β-strand	70-71	2	9
β-strand	82-86	5	9
β-strand	90-97	8	10
β-strand	107-116	10	9
β-strand	131-135	5	11
β-strand	138-142	5	11
β-strand	147-149	3	12
β-strand	156-158	3	12

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11	1	14
β-strand	18-25	8	13
β-strand	34-39	6	15
β-strand	46-51	6	15
β-strand	57-59	3	15
α-helix	61-63	3
β-strand	67-71	5	13
β-strand	78-82	5	13
β-strand	91-98	8	15
β-strand	107-110	4	15
β-strand	114-116	3	15
β-strand	117	1	14

Chain I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-11	2	8
β-strand	18-24	7	7
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-71	5	7
β-strand	78-82	5	7
α-helix	87-89	3
β-strand	91-98	8	8
β-strand	107-110	4	8
β-strand	114-117	4	8

Chain L: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-12	3	2
β-strand	19-24	6	1
α-helix	28	1
β-strand	29	1	3
α-helix	30-32	3
β-strand	35-40	6	2
β-strand	47-51	5	2
β-strand	55-56	2	2
α-helix	57	1
β-strand	64-68	5	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	87-93	7	2
β-strand	94	1	3
β-strand	102-104	3	2
β-strand	108-111	4	2

Chain M: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-12	3	5
β-strand	19-25	7	4
α-helix	28	1
β-strand	29	1	6
α-helix	30-32	3
β-strand	35-40	6	5
β-strand	47-51	5	5
β-strand	55-56	2	5
α-helix	57	1
β-strand	64-67	4	4
β-strand	72-77	6	4
α-helix	82-84	3
β-strand	87-93	7	5
β-strand	94	1	6
β-strand	102-104	3	5
β-strand	108-111	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RAY121 Fab Light chain	L, M	protein	220	Homo sapiens
RAY121 Fab Heavy chain	H, I	protein	225	Homo sapiens
Complement C1s subcomponent heavy chain	A, B	protein	290	Homo sapiens	P09871 (AlphaFold model)

Sequence of entity 1 (L, M), FASTA

>9X1H_1 RAY121 Fab Light chain (chains L, M)
DIQMTQSPSSLSASVGDRVTITCQAHEILHDKKNLAWYQQKPGQPPKLLIYSASILESGV
PSRFSGSGSGTDFTLTISSLQPEDFATYYCHGEFSHGSGDLNHFGQGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H, I), FASTA

>9X1H_2 RAY121 Fab Heavy chain (chains H, I)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSAYAMNWIRQPPGKGLEWIGLIYGSGHEFYA
SWAEERVTISVDTSKNQFSLKLSSVTAADTAVYYCARGRSKNYNSDFHLWGQGTLVTVSS
ASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 3 (A, B), FASTA

>9X1H_3 Complement C1s subcomponent heavy chain (chains A, B)
EPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHLYFTHLDIELSENCAYDSVQIISG
DTEEGRLCGQRSSNNPHSPIVEEFQVPYNKLQVIFKSDFSNEERFTGFAAYYVATDINEC
TDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKP
YPENSRCEYQIRLEKGFQVVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGF
PGPLNIETKSNALDIIFQTDLTGQKKGWKLRYHGDPMGGGGSDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Primary citation

Long lasting complement neutralisation by RAY121, an engineered anti-C1s antibody with C1q displacement function. Ho, A.W.S., Fukuzawa, T., Koga, H. et al. EBioMedicine (2025) 122:106009-106009. DOI 10.1016/j.ebiom.2025.106009 · 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
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

Browse structure collections

About this viewer

MolViewer shows 9X1H directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.