9s5n

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

Method: ELECTRON MICROSCOPY

▼

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

Kinetochore-associated protein NNF1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） 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	1
Chains and sequence ranges	Author chain Nn； PDBConstruct 1–201； UniProt 1–201

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 8	Kinetochore-associated protein NNF1 × 1 （P47149） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） 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

Outer kinetochore KNL1 complex subunit KRE28

Saccharomyces cerevisiae S288C

UniProt Q04431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） 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	ZWINT_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Zw； PDBConstruct 1–385； UniProt 1–385

Outer kinetochore KNL1 complex subunit SPC105

Saccharomyces cerevisiae S288C

UniProt P53148

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） 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	KNL1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain Kl； PDBConstruct 2–474； UniProt 445–917

Kinetochore-associated protein DSN1

Saccharomyces cerevisiae S288C

UniProt P40568

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014） 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	5
Chains and sequence ranges	Author chain Ds； PDBConstruct 1–576； UniProt 1–576

Kinetochore protein SPC24

Saccharomyces cerevisiae S288C

UniProt Q04477

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC25 × 1 （P40014） 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	SPC24_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain 24； PDBConstruct 1–213； UniProt 1–213

Kinetochore protein SPC25

Saccharomyces cerevisiae S288C

UniProt P40014

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC24 × 1 （Q04477） 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	SPC25_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain 25； PDBConstruct 1–221； UniProt 1–221

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 8	Kinetochore-associated protein NNF1 × 1 （P47149） Kinetochore-associated protein MTW1 × 1 （P39731） Outer kinetochore KNL1 complex subunit KRE28 × 1 （Q04431） Outer kinetochore KNL1 complex subunit SPC105 × 1 （P53148） Kinetochore-associated protein DSN1 × 1 （P40568） Kinetochore protein SPC24 × 1 （Q04477） Kinetochore protein SPC25 × 1 （P40014）	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	8
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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9s5n
Deposition date deposition_date	2025-07-29
Structure title title	Cryo-EM structure 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

▼

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.

9s5n__assembly_1__model_1

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

Download this curve (.dat)

9s5n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9s5n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	75.42 Å
Rg (electron density)	77.17 Å
Total Rg	76.73 Å
Atom count	20996
Residues	1386
Excluded volume	200900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9s5n__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 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
Atom count atom_count	20996

MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEFWTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVECHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQPANVLLVQSLNDMVLELKENY

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
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	Outer kinetochore KNL1 complex subunit KRE28
Molecular weight formula_weight	48468.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Zw

MDTGSASIKDYETVLTDIEDSIAVSSEEVLNNQELRLKNTLHEITSSILAINEENKFVNPLRNDESLDVEGKEVFVNPKILSAKIKEFNKLMELLKLTYLEQETLDYFFRFTLSSTKPLQLDSEKDPQFVKLNERVNDLKEEISNVQESKIEQIKAEIQETGHNFAERQDLINELYLEATGDIENCWDSLNELKNLTNKEDKNMMGEKDTILNSSDSDDFVEETYTNWQKLLFLQKQNQRLTKELKEMHEVKNQIIRKGEQSKKEDSGHLMANESELCQSINLLTKFWEKHFLLKGSKTTILNFEIFTQLGKVQFEIKDMQYIIAISLSDLKRPMIKDITILQKAGGNIVTDIEASSKFNNKYRNNTKVQIFEVMDDIISELTNEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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	Outer kinetochore KNL1 complex subunit SPC105
Molecular weight formula_weight	55581.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Kl

MSGIALPTQDYTLREFINEVGVGFLDTKLIDDLDKKVNFPLNSFNFVENQRIDNVFSAFYIDIPILEVEAFRCKELWRSINESKDKFKDFEAQIDKSHPPLLLQEYFSSDEKMKQLMRDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENLNTLKREYEKLNEEVEKVNSIRGKIRKLNEAIKEEIRSLKNLPSDSYKPTLMNRIKIEAFKQELMEHSISLSSSNDFTQEMRSLKLAIAKKSNDILTLRSEVASIDKKIEKRKLFTRFDLPKLRDTLKILESLTGVRFLKFSKATLSIAFLQLDDLRVDINLANFKNNPLSSMKVMNDSNNDDMSYHLFTMLLKNVEAEHQDSMLSNLFFAMKKWRPLLKYIKLLKLLFPVKITQTEEEEALLQFKDYDRRNKTAFFYVISLVSFAQGVFSENGQIPMKVHISTQQDYSPSREVLSDRITHKISGVLPSFTKSRIHLEFT

Source Source

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

Entity 5 Entity 5 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

MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFENKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSGDATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSSLQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKSIGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRSLHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAIDWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSERRKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSFSSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIETMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL

Source Source

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

Entity 6 Entity 6 polymer

Description description	Kinetochore protein SPC24
Molecular weight formula_weight	24639.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	24

MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESNKKLNAERINVAKLEGDLEYTNEESNEFGSKDELVKLLKDLDGLERNIVSLRSELDEKMKLYLKDSEIISTPNGSKIKAKVIEPELEEQSAVTPEANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Source Source

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

Entity 7 Entity 7 polymer

Description description	Kinetochore protein SPC25
Molecular weight formula_weight	25280.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	25

MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQLHNQHQHLIDELQRLATQRTALQQQIHAAQQATNTTREQWRSYHERESELSRRQSTLAAQSRELDSLLQQRGKECVQLRARWAAQSGNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Source Source

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

Entity 8 Entity 8 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

▶

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	7.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	18160

Cryo-EM structure 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 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 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

Outer kinetochore KNL1 complex subunit KRE28

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Outer kinetochore KNL1 complex subunit SPC105

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 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 protein SPC24

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 protein SPC25

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

9s5n__assembly_1__model_1

9s5n__assembly_1__model_1 | I(q)

9s5n__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer