SAXSdb — 9s53

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Kinetochore-associated protein DSN1

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore-associated protein MTW1 × 1 （P39731） Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein NSL1 × 1 （Q12143）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSN1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Ds； PDBConstruct 1–576； UniProt 1–576

Kinetochore-associated protein MTW1

Saccharomyces cerevisiae S288C

UniProt P39731

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein NSL1 × 1 （Q12143）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTW1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Mt； PDBConstruct 1–289； UniProt 1–289

Kinetochore-associated protein NNF1

Saccharomyces cerevisiae S288C

UniProt P47149

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore-associated protein MTW1 × 1 （P39731） Kinetochore-associated protein NSL1 × 1 （Q12143）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NNF1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Nn； PDBConstruct 1–201； UniProt 1–201

Kinetochore-associated protein NSL1

Saccharomyces cerevisiae S288C

UniProt Q12143

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore-associated protein MTW1 × 1 （P39731） Kinetochore-associated protein NNF1 × 1 （P47149）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NSL1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain Ns； PDBConstruct 1–216； UniProt 1–216

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9s53
Deposition date deposition_date	2025-07-29
Structure title title	Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain
Keywords keywords	Kinetochore, chromosome segregation, mitosis, cell cycle; CELL CYCLE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9s53__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9s53__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9s53__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	36.44 Å
Rg (electron density)	37.05 Å
Total Rg	37.15 Å
Atom count	8379
Residues	613
Excluded volume	88622 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9s53__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Kinetochore-associated protein DSN1
Molecular weight formula_weight	65777.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ds
Atom count atom_count	8379

MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFENKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSGDATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSSLQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKSIGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRSLHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAIDWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSERRKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSFSSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIETMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Kinetochore-associated protein MTW1
Molecular weight formula_weight	33291.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Mt

MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEEIKSGVAKLESLLENSVDKNFDKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENELKKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRGFKQKLNELLKCKDDVQLQKILESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIRTNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Kinetochore-associated protein NNF1
Molecular weight formula_weight	23668.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Nn

MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEFWTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVECHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQPANVLLVQSLNDMVLELKENY

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Kinetochore-associated protein NSL1
Molecular weight formula_weight	25448.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ns

MSQGQSKKLDVTVEQLRSIYHQFHDILEEKTDLHLPKKEYDDDAVRREVQIQLQEFLLSAMTMASKSLEVVNADTVGKTVKQLIMESQEKYMEPFDLDLNEQVRKMYQEWEDETVKVAQLRQTGPAKINEVYNNSKDEYLAQLDGRIGVLQARMMQQQSADHDDSTDDADDHINWEHIKQDYVASLNELYQTQQDLPKVRYNVEKVKRLMDFLEED

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	6.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	18160

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Kinetochore-associated protein DSN1

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore-associated protein MTW1

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore-associated protein NNF1

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore-associated protein NSL1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9s53__assembly_1__model_1

9s53__assembly_1__model_1 | I(q)

9s53__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Kinetochore-associated protein DSN1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore-associated protein MTW1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore-associated protein NNF1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Kinetochore-associated protein NSL1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9s53__assembly_1__model_1

9s53__assembly_1__model_1 | I(q)

9s53__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)