SAXSdb — 9s4q

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1. Structure Basics

entry_id	9s4q
deposition_date	2025-07-28
title	Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking 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	65.40 Å
rg_electron	67.88 Å
i0	270280000.00
molecular_weight	137790.0 kDa
excluded_volume	173170 Å³
envelope_volume	290790 Å³
shell_volume	42703 Å³
envelope_diameter	230.9 Å
shell_rg	50.58 Å
envelope_rg	66.54 Å
shape_rg	67.85 Å
total_rg	67.46 Å
total_atoms	19471
n_residues	1193
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	211.1 Å
rg_real	67.33 Å
rg_real_error	2.33 Å
i0_real	2.7020e+08
i0_real_error	5.3600e+06
rg_reciprocal	63.58 Å
i0_reciprocal	268500000.0000
total_estimate	0.3827
solution_quality	SUSPICIOUS a SUSPICIOUS solution
n_peaks	2
r_peak_primary	35.2 Å
skewness	0.547
kurtosis	-0.846
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0001
highest_alpha	10330000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.256; Stabil: 0.999; Sysdev: 0.013; Positv: 1.000; Valcen: 0.164; Smooth: 0.004

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	Nn
atom_count	19471

MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEFWTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVECHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQPANVLLVQSLNDMVLELKENY

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	Outer kinetochore KNL1 complex subunit KRE28
formula_weight	48468.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Zw

MDTGSASIKDYETVLTDIEDSIAVSSEEVLNNQELRLKNTLHEITSSILAINEENKFVNPLRNDESLDVEGKEVFVNPKILSAKIKEFNKLMELLKLTYLEQETLDYFFRFTLSSTKPLQLDSEKDPQFVKLNERVNDLKEEISNVQESKIEQIKAEIQETGHNFAERQDLINELYLEATGDIENCWDSLNELKNLTNKEDKNMMGEKDTILNSSDSDDFVEETYTNWQKLLFLQKQNQRLTKELKEMHEVKNQIIRKGEQSKKEDSGHLMANESELCQSINLLTKFWEKHFLLKGSKTTILNFEIFTQLGKVQFEIKDMQYIIAISLSDLKRPMIKDITILQKAGGNIVTDIEASSKFNNKYRNNTKVQIFEVMDDIISELTNEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 4 polymer

description	Outer kinetochore KNL1 complex subunit SPC105
formula_weight	55581.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Kl

MSGIALPTQDYTLREFINEVGVGFLDTKLIDDLDKKVNFPLNSFNFVENQRIDNVFSAFYIDIPILEVEAFRCKELWRSINESKDKFKDFEAQIDKSHPPLLLQEYFSSDEKMKQLMRDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENLNTLKREYEKLNEEVEKVNSIRGKIRKLNEAIKEEIRSLKNLPSDSYKPTLMNRIKIEAFKQELMEHSISLSSSNDFTQEMRSLKLAIAKKSNDILTLRSEVASIDKKIEKRKLFTRFDLPKLRDTLKILESLTGVRFLKFSKATLSIAFLQLDDLRVDINLANFKNNPLSSMKVMNDSNNDDMSYHLFTMLLKNVEAEHQDSMLSNLFFAMKKWRPLLKYIKLLKLLFPVKITQTEEEEALLQFKDYDRRNKTAFFYVISLVSFAQGVFSENGQIPMKVHISTQQDYSPSREVLSDRITHKISGVLPSFTKSRIHLEFT

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 5 polymer

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

Polymer

type	polypeptide(L)
strand_id	Ds

MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFENKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSGDATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSSLQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKSIGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRSLHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAIDWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSERRKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSFSSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIETMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 6 polymer

description	Kinetochore protein SPC24
formula_weight	24639.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	24

MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESNKKLNAERINVAKLEGDLEYTNEESNEFGSKDELVKLLKDLDGLERNIVSLRSELDEKMKLYLKDSEIISTPNGSKIKAKVIEPELEEQSAVTPEANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 7 polymer

description	Kinetochore protein SPC25
formula_weight	25280.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	25

MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQLHNQHQHLIDELQRLATQRTALQQQIHAAQQATNTTREQWRSYHERESELSRRQSTLAAQSRELDSLLQQRGKECVQLRARWAAQSGNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 8 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	4.90 Å
resolution_method	—
num_particles	113688

fit	/app/data/saxs_computation/s4/9s4q/9s4q.fit
pddf	/app/data/pr_computation/s4/9s4q/9s4q.pr.out
profile	/app/data/saxs_computation/s4/9s4q/9s4q.dat

Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking 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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)