SAXSdb — 9rjc

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1. Structure Basics

entry_id	9rjc
deposition_date	2025-06-12
title	Apo Structure of the Human Signal Peptidase
keywords	Signal Peptidase Complex, protein biogenesis, secretory pathway, membrane thinning, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	34.66 Å
rg_electron	34.29 Å
i0	51510600.00
molecular_weight	60858.0 kDa
excluded_volume	77925 Å³
envelope_volume	112710 Å³
shell_volume	29410 Å³
envelope_diameter	119.5 Å
shell_rg	38.03 Å
envelope_rg	33.60 Å
shape_rg	34.30 Å
total_rg	34.58 Å
total_atoms	4299
n_residues	534
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	121.8 Å
rg_real	34.97 Å
rg_real_error	1.46 Å
i0_real	5.1510e+07
i0_real_error	7.9900e+05
rg_reciprocal	34.78 Å
i0_reciprocal	51500000.0000
total_estimate	0.8419
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.4 Å
skewness	0.494
kurtosis	-0.442
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	4623000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.761; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.728; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Signal peptidase complex catalytic subunit SEC11A
formula_weight	20395.0 kDa
ec_number	3.4.21.89
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4299

SLDFLDDVRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGAMEPAFHRGDLLFLTNRVEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVVGRARGFVPYIGIVTILMNDYPKFKYAVLFLLGLFVLVHRE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Signal peptidase complex subunit 1
formula_weight	7386.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIYRRHPLKWLP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Signal peptidase complex subunit 2
formula_weight	20338.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

DPVKIDKWDGSAVKNSLDDSAKKVLLEKYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVISYFVMMGILTIYTSYKEKSIFLVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAYEPEISRLHDSLA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Signal peptidase complex subunit 3
formula_weight	19611.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MNTVLSRANSLFAFSLSVMAALTFGCFITTAFKDRSVPVRLHVSRIMLKNVEDFTGPRERSDLGFITFDITADLENIFDWNVKQLFLYLSAEYSTKNNALNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNRNVTLTLSWNVVPNAGILPLVTGSGHVSVPFPDTY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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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	—

resolution	4.20 Å
resolution_method	—
num_particles	516615

fit	/app/data/saxs_computation/rj/9rjc/9rjc.fit
pddf	/app/data/pr_computation/rj/9rjc/9rjc.pr.out
profile	/app/data/saxs_computation/rj/9rjc/9rjc.dat

Apo Structure of the Human Signal Peptidase

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 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)