8q5h

Human KMN network (outer kinetochore)

Method: ELECTRON MICROSCOPY Dmax: 225.6 Å Quality: REASONABLE

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

Kinetochore protein Spc24

Homo sapiens

UniProt Q8NBT2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain 4; UniProt 110–197 Not recorded Kinetochore protein Spc25 × 1 (Q9HBM1) Protein MIS12 homolog × 1 (Q9H081) Polyamine-modulated factor 1 × 1 (Q6P1K2) Kinetochore-associated protein DSN1 homolog × 1 (Q9H410) Kinetochore scaffold 1 × 1 (Q8NG31) Kinetochore-associated protein NSL1 homolog × 1 (Q96IY1) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPC24_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain 4; PDBConstruct 2–89; UniProt 110–197

Kinetochore protein Spc25

Homo sapiens

UniProt Q9HBM1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain 5; UniProt 93–224 Not recorded Kinetochore protein Spc24 × 1 (Q8NBT2) Protein MIS12 homolog × 1 (Q9H081) Polyamine-modulated factor 1 × 1 (Q6P1K2) Kinetochore-associated protein DSN1 homolog × 1 (Q9H410) Kinetochore scaffold 1 × 1 (Q8NG31) Kinetochore-associated protein NSL1 homolog × 1 (Q96IY1) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPC25_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain 5; PDBConstruct 2–133; UniProt 93–224

Protein MIS12 homolog

Homo sapiens

UniProt Q9H081

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 1–205 Not recorded Kinetochore protein Spc24 × 1 (Q8NBT2) Kinetochore protein Spc25 × 1 (Q9HBM1) Polyamine-modulated factor 1 × 1 (Q6P1K2) Kinetochore-associated protein DSN1 homolog × 1 (Q9H410) Kinetochore scaffold 1 × 1 (Q8NG31) Kinetochore-associated protein NSL1 homolog × 1 (Q96IY1) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MIS12_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–205; UniProt 1–205

Polyamine-modulated factor 1

Homo sapiens

UniProt Q6P1K2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain B; UniProt 1–205 Not recorded Kinetochore protein Spc24 × 1 (Q8NBT2) Kinetochore protein Spc25 × 1 (Q9HBM1) Protein MIS12 homolog × 1 (Q9H081) Kinetochore-associated protein DSN1 homolog × 1 (Q9H410) Kinetochore scaffold 1 × 1 (Q8NG31) Kinetochore-associated protein NSL1 homolog × 1 (Q96IY1) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PMF1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain B; PDBConstruct 1–205; UniProt 1–205

Kinetochore-associated protein DSN1 homolog

Homo sapiens

UniProt Q9H410

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain D; UniProt 1–356 Not recorded Kinetochore protein Spc24 × 1 (Q8NBT2) Kinetochore protein Spc25 × 1 (Q9HBM1) Protein MIS12 homolog × 1 (Q9H081) Polyamine-modulated factor 1 × 1 (Q6P1K2) Kinetochore scaffold 1 × 1 (Q8NG31) Kinetochore-associated protein NSL1 homolog × 1 (Q96IY1) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DSN1_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain D; PDBConstruct 1–356; UniProt 1–356

Kinetochore scaffold 1

Homo sapiens

UniProt Q8NG31

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain K; UniProt 2021–2342 Not recorded Kinetochore protein Spc24 × 1 (Q8NBT2) Kinetochore protein Spc25 × 1 (Q9HBM1) Protein MIS12 homolog × 1 (Q9H081) Polyamine-modulated factor 1 × 1 (Q6P1K2) Kinetochore-associated protein DSN1 homolog × 1 (Q9H410) Kinetochore-associated protein NSL1 homolog × 1 (Q96IY1) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KNL1_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain K; PDBConstruct 8–329; UniProt 2021–2342

Kinetochore-associated protein NSL1 homolog

Homo sapiens

UniProt Q96IY1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain N; UniProt 1–281 Not recorded Kinetochore protein Spc24 × 1 (Q8NBT2) Kinetochore protein Spc25 × 1 (Q9HBM1) Protein MIS12 homolog × 1 (Q9H081) Polyamine-modulated factor 1 × 1 (Q6P1K2) Kinetochore-associated protein DSN1 homolog × 1 (Q9H410) Kinetochore scaffold 1 × 1 (Q8NG31) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NSL1_HUMAN
Isoform
PDB entities 7
Chains and sequence ranges Author chain N; PDBConstruct 1–281; UniProt 1–281

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8q5h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8q5h
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8q5h
Deposition date deposition_date2023-08-09
Structure title titleHuman KMN network (outer kinetochore)
Keywords keywordsOUTER KINETOCHORE, KMN, COMPLEX, CELL CYCLE; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier74.59
Radius of gyration Rg (electron density) rg_electron76.36
Forward intensity I(0) i0259392000.00
Molecular weight molecular_weight136010.0 kDa
Excluded volume excluded_volume170760 ų
Envelope volume envelope_volume314380 ų
Hydration-shell volume shell_volume39245 ų
Envelope diameter envelope_diameter254.7
Shell Rg shell_rg54.24
Envelope Rg envelope_rg75.46
Shape Rg shape_rg76.36
Total Rg total_rg75.84
Total atoms total_atoms9574
Residues n_residues1173
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax225.6
Rg (real space) rg_real75.52
Rg uncertainty (real space) rg_real_error2.50
I(0) (real space) i0_real2.5920e+08
I(0) uncertainty (real space) i0_real_error6.2070e+06
Rg (reciprocal space) rg_reciprocal70.39
I(0) (reciprocal space) i0_reciprocal256600000.0000
Solution quality estimate total_estimate0.6200
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.0
Skewness Skewness skewness0.443
Kurtosis Kurtosis kurtosis-1.000
Angular range angular_range— – 0.1050 −1
Current regularization parameter α current_alpha0.0015
Highest regularization parameter α highest_alpha7645000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.291; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.186; Smooth: 0.001

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)