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9x1h

Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121

Method: ELECTRON MICROSCOPY D_max: 106.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x1h
deposition_date	2025-10-02
last_revision	2025-11-19
title	Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121
keywords	PH-DEPENDENT, RECYCLING ANTIBODY, IMMUNE SYSTEM, COMPLEMENT C1s, FAB, COMPLEX, CUB DOMAIN, EGF-LIKE DOMAIN; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.50 Å
rg_electron	31.98 Å
i0	115037000.00
molecular_weight	83577.0 kDa
excluded_volume	103490 Å³
envelope_volume	134000 Å³
shell_volume	35369 Å³
envelope_diameter	110.7 Å
shell_rg	38.56 Å
envelope_rg	31.33 Å
shape_rg	31.96 Å
total_rg	32.59 Å
total_atoms	5888
n_residues	754
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	106.0 Å
rg_real	32.52 Å
rg_real_error	0.79 Å
i0_real	1.1500e+08
i0_real_error	1.7880e+06
rg_reciprocal	32.52 Å
i0_reciprocal	115000000.0000
total_estimate	0.8943
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.6 Å
skewness	0.292
kurtosis	-0.487
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	14310000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.853

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	RAY121 Fab Light chain
formula_weight	24034.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,M
atom_count	5888

DIQMTQSPSSLSASVGDRVTITCQAHEILHDKKNLAWYQQKPGQPPKLLIYSASILESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCHGEFSHGSGDLNHFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	RAY121 Fab Heavy chain
formula_weight	24044.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,H

QVQLVESGGGVVQPGRSLRLSCAASGFTFSAYAMNWIRQPPGKGLEWIGLIYGSGHEFYASWAEERVTISVDTSKNQFSLKLSSVTAADTAVYYCARGRSKNYNSDFHLWGQGTLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Complement C1s subcomponent heavy chain
formula_weight	32556.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A

EPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHLYFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKLQVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKPYPENSRCEYQIRLEKGFQVVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGFPGPLNIETKSNALDIIFQTDLTGQKKGWKLRYHGDPMGGGGSDYKDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.60 Å
resolution_method	—
num_particles	1101481

fit	/app/data/saxs_computation/x1/9x1h/9x1h.fit
pddf	/app/data/pr_computation/x1/9x1h/9x1h.pr.out
profile	/app/data/saxs_computation/x1/9x1h/9x1h.dat

Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)