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9shp

Cryo-EM structure of the endogeneous MIWI in complex with pachytene piRNA at 3.3A

Method: ELECTRON MICROSCOPY D_max: 106.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9shp
deposition_date	2025-08-27
title	Cryo-EM structure of the endogeneous MIWI in complex with pachytene piRNA at 3.3A
keywords	MIWI, PIWIL1, piRNA, slicer, pachytene piRNA, RNA BINDING PROTEIN; RNA BINDING 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	30.85 Å
rg_electron	30.43 Å
i0	100271000.00
molecular_weight	79079.0 kDa
excluded_volume	99127 Å³
envelope_volume	133410 Å³
shell_volume	37798 Å³
envelope_diameter	109.6 Å
shell_rg	36.42 Å
envelope_rg	30.16 Å
shape_rg	30.44 Å
total_rg	30.98 Å
total_atoms	5554
n_residues	696
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	106.9 Å
rg_real	30.95 Å
rg_real_error	0.96 Å
i0_real	1.0030e+08
i0_real_error	1.6400e+06
rg_reciprocal	30.91 Å
i0_reciprocal	100300000.0000
total_estimate	0.6447
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.6 Å
skewness	0.494
kurtosis	-0.031
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	32750000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.924; Smooth: 0.789

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Piwi-like protein 1
formula_weight	99751.2 kDa
ec_number	3.1.26.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	5554

MTGRARARARGRARGQETVQHVGAAASQQPGYIPPRPQQSPTEGDLVGRGRQWSHPQFEKRGMVVGATSKSQELQISAGFQELSLAERGGRRRDFHDLGVNTRQNLDHVKESKTGSSGIIVKLSTNHFRLTSRPQWALYQYHIDYNPLMEARRLRSALLFQHEDLIGRCHAFDGTILFLPKRLQHKVTEVFSQTRNGEHVRITITLTNELPPTSPTCLQFYNIIFRRLLKIMNLQQIGRNYYNPSDPIDIPNHRLVIWPGFTTSILQYENNIMLCTDVSHKVLRSETVLDFMFNLYQQTEEHKFQEQVSKELIGLIVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLTGLTDKMRNDFNVMKDLAVHTRLTPEQRQREVGRLIDYIHKDDNVQRELRDWGLSFDSNLLSFSGRILQSEKIHQGGKTFDYNPQFADWSKETRGAPLISVKPLDNWLLIYTRRNYEAANSLIQNLFKVTPAMGIQMKKAIMIEVDDRTEAYLRALQQKVTSDTQIVVCLLSSNRKDKYDAIKKYLCTDCPTPSQCVVARTLGKQQTVMAIATKIALQMNCKMGGELWRVDMPLKLAMIVGIDCYHDTTAGRRSIAGFVASINEGMTRWFSRCVFQDRGQELVDGLKVCLQAALRAWSGCNEYMPSRVIVYRDGVGDGQLKTLVNYEVPQFLDCLKSVGRGYNPRLTVIVVKKRVNARFFAQSGGRLQNPLPGTVIDVEVTRPEWYDFFIVSQAVRSGSVSPTHYNVIYDSSGLKPDHIQRLTYKLCHVYYNWPGVIRVPAPCQYAHKLAFLVGQSIHREPNLSLSNRLYYL

Entity 2 polymer

description	;RNA (5'-R(PUPUPAPCPCPA)-3') ;
formula_weight	1836.1 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

UUACCA

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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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	3.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.70 Å
resolution_method	—
num_particles	444624

fit	/app/data/saxs_computation/sh/9shp/9shp.fit
pddf	/app/data/pr_computation/sh/9shp/9shp.pr.out
profile	/app/data/saxs_computation/sh/9shp/9shp.dat

Cryo-EM structure of the endogeneous MIWI in complex with pachytene piRNA at 3.3A

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

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)