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9s53

Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain

Method: ELECTRON MICROSCOPY D_max: 142.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s53
deposition_date	2025-07-29
title	Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain
keywords	Kinetochore, chromosome segregation, mitosis, cell cycle; CELL CYCLE
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	36.44 Å
rg_electron	37.05 Å
i0	82008900.00
molecular_weight	71018.0 kDa
excluded_volume	88622 Å³
envelope_volume	120710 Å³
shell_volume	31642 Å³
envelope_diameter	152.9 Å
shell_rg	36.85 Å
envelope_rg	37.28 Å
shape_rg	37.02 Å
total_rg	37.15 Å
total_atoms	8379
n_residues	613
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	142.6 Å
rg_real	37.14 Å
rg_real_error	1.68 Å
i0_real	8.2010e+07
i0_real_error	1.4910e+06
rg_reciprocal	36.71 Å
i0_reciprocal	81970000.0000
total_estimate	0.5311
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	139.3 Å
skewness	0.754
kurtosis	0.156
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	9397000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.429; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.202; Smooth: 0.936

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Kinetochore-associated protein DSN1
formula_weight	65777.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Ds
atom_count	8379

MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFENKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSGDATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSSLQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKSIGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRSLHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAIDWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSERRKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSFSSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIETMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 2 polymer

description	Kinetochore-associated protein MTW1
formula_weight	33291.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Mt

MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEEIKSGVAKLESLLENSVDKNFDKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENELKKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRGFKQKLNELLKCKDDVQLQKILESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIRTNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 3 polymer

description	Kinetochore-associated protein NNF1
formula_weight	23668.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Nn

MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEFWTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVECHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQPANVLLVQSLNDMVLELKENY

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 4 polymer

description	Kinetochore-associated protein NSL1
formula_weight	25448.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Ns

MSQGQSKKLDVTVEQLRSIYHQFHDILEEKTDLHLPKKEYDDDAVRREVQIQLQEFLLSAMTMASKSLEVVNADTVGKTVKQLIMESQEKYMEPFDLDLNEQVRKMYQEWEDETVKVAQLRQTGPAKINEVYNNSKDEYLAQLDGRIGVLQARMMQQQSADHDDSTDDADDHINWEHIKQDYVASLNELYQTQQDLPKVRYNVEKVKRLMDFLEED

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

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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	6.50 Å
resolution_method	—
num_particles	18160

fit	/app/data/saxs_computation/s5/9s53/9s53.fit
pddf	/app/data/pr_computation/s5/9s53/9s53.pr.out
profile	/app/data/saxs_computation/s5/9s53/9s53.dat

Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain

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)