← Back to search
3si5

Kinetochore-BUBR1 kinase complex

Method: X-RAY DIFFRACTION Dmax: 81.1 Å Quality: EXCELLENT
▼

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

Mitotic checkpoint serine/threonine-protein kinase BUB1 beta

Homo sapiens

UniProt O60566

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 67–230 Fragment：UNP residues 67-220 Protein CASC5 × 1 （Q8NG31） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 67–230 Fragment：UNP residues 67-220 Protein CASC5 × 1 （Q8NG31） 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

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 3SI5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2WVI Crystal Structure of the N-terminal Domain of BubR1 Deposited 2009-10-16 Different construct 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 57–220（164 aa） Fragment：N-TERMINAL TPR DOMAIN, RESIDUES 57-220
Not recorded PR PRASEODYMIUM ION × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；22.5% (W/V) PEG 8000, 0.17 M TRIS PH 8.0, 0.01 M PRASEODYMIUM(III) ACETATE
Resolution 1.80 Å R-free 0.260
4GGD Structural analysis of human Cdc20 supports multisite degron recognition by APC/C. Deposited 2012-08-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–42（23 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions sitting-drop vapor diffusion；pH 9.3；293 K；50 mM CAPSO, 5% (w/v) PEG 6000, and 15.5 % MPD, pH 9.3, sitting-drop vapor diffusion, temperature 293K
Resolution 2.44 Å R-free 0.201
4GGD Structural analysis of human Cdc20 supports multisite degron recognition by APC/C. Deposited 2012-08-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 20–42（23 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions sitting-drop vapor diffusion；pH 9.3；293 K；50 mM CAPSO, 5% (w/v) PEG 6000, and 15.5 % MPD, pH 9.3, sitting-drop vapor diffusion, temperature 293K
Resolution 2.44 Å R-free 0.201
5JJA Crystal structure of a PP2A B56gamma/BubR1 complex Deposited 2016-04-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 661–734（74 aa）
Mutation：S670D, S676D, T680D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.5 and 20% PEG 3350
Resolution 2.35 Å R-free 0.204
5JJA Crystal structure of a PP2A B56gamma/BubR1 complex Deposited 2016-04-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 661–734（74 aa）
Mutation：S670D, S676D, T680D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.5 and 20% PEG 3350
Resolution 2.35 Å R-free 0.204
5KHU Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex with the Mitotic checkpoint complex (APC/C-CDC20-MCC) based on cryo EM data at 4.8 Angstrom resolution Deposited 2016-06-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain Q 1–1050（1050 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
5LCW Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 4.2 angstrom resolution Deposited 2016-06-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain S 1–310（310 aa）
Chain S 529–560（32 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6TLJ Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 3.8 angstrom resolution Deposited 2019-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain S 1–1050（1050 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BUB1B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 13–176； UniProt 67–230 Author chain B； PDBConstruct 13–176； UniProt 67–230

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 X； UniProt 234–252 Fragment：UNP residues 234-252 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta × 1 （O60566） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain Y； UniProt 234–252 Fragment：UNP residues 234-252 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta × 1 （O60566） 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

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 3SI5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 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 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
4NF9 Structure of the Knl1/Nsl1 complex Deposited 2013-10-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2117–2337（221 aa） Fragment：Knl1 C-terminal domain, UNP residues 2117-2337
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
4NF9 Structure of the Knl1/Nsl1 complex Deposited 2013-10-31 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2117–2337（221 aa） Fragment：Knl1 C-terminal domain, UNP residues 2117-2337
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule 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
4NFA Structure of the C-terminal doamin of Knl1 Deposited 2013-10-31 Different construct 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 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 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 2
Chains and sequence ranges Author chain X； PDBConstruct 6–24； UniProt 234–252 Author chain Y； PDBConstruct 6–24； UniProt 234–252

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 3si5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3si5
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3si5
Deposition date deposition_date2011-06-17
Structure title titleKinetochore-BUBR1 kinase complex
Keywords keywordsBUBR1-Blinkin complex, mitotic checkpoint, BUBR1, Blinkin/KNL1, chromosome segregation, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier25.96 Å
Radius of gyration Rg (electron density) rg_electron25.30 Å
Forward intensity I(0) i026740200.00
Molecular weight molecular_weight38898.0 kDa
Excluded volume excluded_volume48284 ų
Envelope volume envelope_volume62482 ų
Hydration-shell volume shell_volume21552 ų
Envelope diameter envelope_diameter83.5 Å
Shell Rg shell_rg30.92 Å
Envelope Rg envelope_rg25.29 Å
Shape Rg shape_rg25.31 Å
Total Rg total_rg25.96 Å
Total atoms total_atoms2756
Residues n_residues332
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
▼

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

Maximum dimension Dmax dmax81.1 Å
Rg (real space) rg_real26.01 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real2.6740e+07
I(0) uncertainty (real space) i0_real_error3.6080e+05
Rg (reciprocal space) rg_reciprocal26.00 Å
I(0) (reciprocal space) i0_reciprocal26740000.0000
Solution quality estimate total_estimate0.9073
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.3 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.541
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3634000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.941
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3si5A00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily430 —
Domain ID domain_id3si5B00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily430 —
▶

8. Citations (1)

▶

9. Files and Curves (10)