SAXSdb — 2wvi

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

MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA

HOMO SAPIENS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 57–220	Fragment：N-TERMINAL TPR DOMAIN, RESIDUES 57-220	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

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 2WVI	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 67–230（164 aa） Fragment：UNP residues 67-220	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 67–230（164 aa） Fragment：UNP residues 67-220	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
4GGD Structural analysis of human Cdc20 supports multisite degron recognition by APC/C. Deposited 2012-08-06	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 9 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 1–164； UniProt 57–220

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	2wvi
Deposition date deposition_date	2009-10-16
Structure title title	Crystal Structure of the N-terminal Domain of BubR1
Keywords keywords	;TUMOR SUPPRESSOR, MITOTIC CHECKPOINT, TPR, KINASE, APOPTOSIS, SERINE/THREONINE-PROTEIN KINASE, CELL DIVISION, CELL CYCLE, KINETOCHORE, TRANSFERASE, CYTOSKELETON ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.74 Å
Radius of gyration Rg (electron density) rg_electron	21.03 Å
Forward intensity I(0) i0	7653450.00
Molecular weight molecular_weight	19644.0 kDa
Excluded volume excluded_volume	24143 Å³
Envelope volume envelope_volume	30833 Å³
Hydration-shell volume shell_volume	13916 Å³
Envelope diameter envelope_diameter	87.2 Å
Shell Rg shell_rg	24.79 Å
Envelope Rg envelope_rg	22.01 Å
Shape Rg shape_rg	20.77 Å
Total Rg total_rg	22.32 Å
Total atoms total_atoms	1372
Residues n_residues	160
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	83.6 Å
Rg (real space) rg_real	22.12 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	7.6530e+06
I(0) uncertainty (real space) i0_real_error	1.1740e+05
Rg (reciprocal space) rg_reciprocal	22.05 Å
I(0) (reciprocal space) i0_reciprocal	7653000.0000
Solution quality estimate total_estimate	0.6803
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.704
Kurtosis Kurtosis kurtosis	0.138
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1055000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.527; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.259; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA
Molecular weight formula_weight	19597.7 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1489

QQKRAFEYEIRFYTGNDPLDVWDRYISWTEQNYPQGGKESNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLCNEPLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPLERLQSQHRQFQARVSRQTLLALEKEEEEEVFESS

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PRASEODYMIUM ION
Molecular weight formula_weight	140.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2wviA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	430 —

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8. Citations (1)

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Unit-cell length a length_a	62.796 Å
Unit-cell length b length_b	62.796 Å
Unit-cell length c length_c	90.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	54.390 Å
R factor r_factor	0.2237
R_work r_work	0.2219
R_free r_free	0.2599

fit	/app/data/saxs_computation/wv/2wvi/2wvi.fit
pddf	/app/data/pr_computation/wv/2wvi/2wvi.pr.out
profile	/app/data/saxs_computation/wv/2wvi/2wvi.dat

Crystal Structure of the N-terminal Domain of BubR1

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

MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction