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4nf9

Structure of the Knl1/Nsl1 complex

Method: X-RAY DIFFRACTION Dmax: 100.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein CASC5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2117–2337 Fragment：Knl1 C-terminal domain, UNP residues 2117-2337 Non-standard monomer：Yes (specific site not provided by mmCIF) Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；16-20 % (v/v) PEG 3350, 220 mM sodium citrate and 100 mM MES (pH 6 or 6.5) and 100 mM Hepes (pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 2117–2337 Fragment：Knl1 C-terminal domain, UNP residues 2117-2337 Non-standard monomer：Yes (specific site not provided by mmCIF) Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；16-20 % (v/v) PEG 3350, 220 mM sodium citrate and 100 mM MES (pH 6 or 6.5) and 100 mM Hepes (pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.265

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.

Other PDB Difference from Current Entry 4NF9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3SI5 Kinetochore-BUBR1 kinase complex Deposited 2011-06-17 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 234–252（19 aa） Fragment：UNP residues 234-252
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；15% PEG 6000, 0.1M Magnesium Acetate, 0.1M Sodium Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.20 Å R-free 0.247
3SI5 Kinetochore-BUBR1 kinase complex Deposited 2011-06-17 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 234–252（19 aa） Fragment：UNP residues 234-252
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；15% PEG 6000, 0.1M Magnesium Acetate, 0.1M Sodium Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.20 Å R-free 0.247
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 150–200（51 aa） Fragment：KI MOTIF, RESIDUES 150-200
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 150–200（51 aa） Fragment：KI MOTIF, RESIDUES 150-200
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 150–200（51 aa） Fragment：KI MOTIF, RESIDUES 150-200
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 150–200（51 aa） Fragment：KI MOTIF, RESIDUES 150-200
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4NFA Structure of the C-terminal doamin of Knl1 Deposited 2013-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2117–2323（207 aa） Fragment：Knl1 C-terminal domain, UNP residues 2131-2337
Not recorded CL CHLORIDE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；120-300 KSCN, 100 mM BisTris Propane (pH 8.6-9.2), 17 % (v/v) PEG 3350 and 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.242
8PPR Structure of the human outer kinetochore KMN network complex Deposited 2023-07-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 1–2342（2342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8Q5H Human KMN network (outer kinetochore) Deposited 2023-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain K 2021–2342（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CASC5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–221； UniProt 2117–2337 Author chain B； PDBConstruct 1–221； UniProt 2117–2337

Kinetochore-associated protein NSL1 homolog

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 256–281 Fragment：Nsl1 C-terminal tail, UNP residues 256-281 Protein CASC5 × 1 （Q8NG31） CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；16-20 % (v/v) PEG 3350, 220 mM sodium citrate and 100 mM MES (pH 6 or 6.5) and 100 mM Hepes (pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 256–281 Fragment：Nsl1 C-terminal tail, UNP residues 256-281 Protein CASC5 × 1 （Q8NG31） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；16-20 % (v/v) PEG 3350, 220 mM sodium citrate and 100 mM MES (pH 6 or 6.5) and 100 mM Hepes (pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.265

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.

Other PDB Difference from Current Entry 4NF9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LSI CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAIN CONTAINING DSN1 AND NSL1 FRAGMENTS Deposited 2016-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 29–99（71 aa） Fragment：UNP residues 29-99
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；293 K；2M ammonium sulfate, 0.2M potassium sodium phosphate, 0.1M sodium citrate pH 5.6
Resolution 2.00 Å R-free 0.246
5LSJ CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX Deposited 2016-09-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain N 92–206（115 aa） Fragment：UNP residues 92-206
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；20% PEG3350, 0.2M potassium sodium tartrate
Resolution 3.25 Å R-free 0.297
5LSJ CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX Deposited 2016-09-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 92–206（115 aa） Fragment：UNP residues 92-206
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；20% PEG3350, 0.2M potassium sodium tartrate
Resolution 3.25 Å R-free 0.297
5LSK CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C COMPLEX Deposited 2016-09-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain N 1–206（206 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；6-12% PEG6000
Resolution 3.50 Å R-free 0.298
8PPR Structure of the human outer kinetochore KMN network complex Deposited 2023-07-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–281（281 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8Q5H Human KMN network (outer kinetochore) Deposited 2023-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–281（281 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NSL1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–26； UniProt 256–281 Author chain D； PDBConstruct 1–26； UniProt 256–281

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 4nf9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4nf9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4nf9
Deposition date deposition_date2013-10-31
Structure title titleStructure of the Knl1/Nsl1 complex
Keywords keywordsRWD domain, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.31 Å
Radius of gyration Rg (electron density) rg_electron29.70 Å
Forward intensity I(0) i041189000.00
Molecular weight molecular_weight52027.0 kDa
Excluded volume excluded_volume65715 ų
Envelope volume envelope_volume85049 ų
Hydration-shell volume shell_volume25347 ų
Envelope diameter envelope_diameter109.2 Å
Shell Rg shell_rg34.80 Å
Envelope Rg envelope_rg29.39 Å
Shape Rg shape_rg29.68 Å
Total Rg total_rg30.26 Å
Total atoms total_atoms3670
Residues n_residues437
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.7 Å
Rg (real space) rg_real30.46 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real4.1190e+07
I(0) uncertainty (real space) i0_real_error5.8480e+05
Rg (reciprocal space) rg_reciprocal30.40 Å
I(0) (reciprocal space) i0_reciprocal41190000.0000
Solution quality estimate total_estimate0.8708
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.2 Å
Skewness Skewness skewness0.378
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha10410000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.882
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)