SAXSdb — 2kdd

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

Borealin

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 207–280 Chain B； UniProt 207–280	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.2；299 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.6 mM Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition：0.8 mM [U-100% 15N] Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.7 mM [U-100% 13C; U-100% 15N] Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.7 mM [U-100% 13C; U-100% 15N] Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition：0.8 mM 50% [U-100% 13C; U-100% 15N], 50% natural abundance Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided

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 2KDD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QFA Crystal structure of a Survivin-Borealin-INCENP core complex Deposited 2007-06-27	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 × 3 PDB declaration: trimeric	Chain B 15–76（62 aa） Fragment：UNP residues 15-76	Not recorded	ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；50mM MES pH6, 10% PEG3350, VAPOR DIFFUSION, temperature 293K	Resolution 1.40 Å R-free 0.202
2RAW Crystal structure of the Borealin-Survivin complex Deposited 2007-09-17	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 × 2 PDB declaration: dimeric	Chain B 20–78（59 aa） Fragment：N-terminal region (residues 20-78)	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein and 0.5 ul well solution (0.1 M Na HEPES, pH 7.5; 0.2 M CaCl2; 28% (w/v) PEG 400), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.298
2RAX Crystal structure of Borealin (20-78) bound to Survivin (1-120) Deposited 2007-09-17	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 × 2 PDB declaration: dimeric	Chain B 20–78（59 aa） Fragment：N-terminal fragment, residues 20-78	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.284
2RAX Crystal structure of Borealin (20-78) bound to Survivin (1-120) Deposited 2007-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 20–78（59 aa） Fragment：N-terminal fragment, residues 20-78	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.284
2RAX Crystal structure of Borealin (20-78) bound to Survivin (1-120) Deposited 2007-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 20–78（59 aa） Fragment：N-terminal fragment, residues 20-78	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.284
6YIE Structure of a Borealin-INCENP-Survivin complex Deposited 2020-04-01	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 × 3 PDB declaration: trimeric	Chain B 10–109（100 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；5 % (w/v) PEG 3,350, 50 mM MES pH 6.0	Resolution 3.49 Å R-free 0.324
6YIE Structure of a Borealin-INCENP-Survivin complex Deposited 2020-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 10–109（100 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；5 % (w/v) PEG 3,350, 50 mM MES pH 6.0	Resolution 3.49 Å R-free 0.324
6YIF Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 1.8 A. Deposited 2020-04-01	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 × 4 PDB declaration: tetrameric	Chain B 10–76（67 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；20 % (w/v) PEG 4,000, 200 mM Lithium sulphate, 50 mM MES pH 6.5	Resolution 1.81 Å R-free 0.223
6YIH Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 2.6 A. Deposited 2020-04-01	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 × 4 PDB declaration: tetrameric	Chain B 10–76（67 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；20 % (w/v) PEG 4,000, 100 mM HEPES pH 7.0, 150 mM ammonium sulphate	Resolution 2.55 Å R-free 0.259
7U5V Crystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and Borealin peptide Deposited 2022-03-02	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 × 2 PDB declaration: dimeric	Chain C 137–145（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；60% Tacsimate pH 7.0	Resolution 2.59 Å R-free 0.304
8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain L 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.	Resolution 2.42 Å
8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain L 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.	Resolution 2.29 Å
9D41 Crystal structure of N-terminal domain of Borealin (20-88) in complex with synthetic antibody fragment Deposited 2024-08-12	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 × 3 PDB declaration: trimeric	Chain A 20–88（69 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；292 K；0.1 M CAPS, 40 % v/v MPD	Resolution 1.84 Å R-free 0.197
9SI3 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Deposited 2025-08-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain L 1–280（280 aa） Chain O 1–280（280 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
9SI9 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Deposited 2025-08-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain L 1–280（280 aa） Chain O 1–280（280 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9SJ5 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Deposited 2025-08-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain L 1–280（280 aa） Chain O 1–280（280 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
9SLJ Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Deposited 2025-09-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric	Chain L 1–280（280 aa） Chain O 1–280（280 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

14 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BOREA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–76； UniProt 207–280 Author chain B； PDBConstruct 3–76； UniProt 207–280

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	2kdd
Deposition date deposition_date	2009-01-06
Structure title title	Solution structure of the conserved C-terminal dimerization domain of Borealin
Keywords keywords	;protein dimer, Cell cycle, Cell division, Centromere, Chromosomal protein, Cytoplasm, Mitosis, Nucleus, Phosphoprotein, Polymorphism ;; CELL CYCLE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.17 Å
Radius of gyration Rg (electron density) rg_electron	14.40 Å
Forward intensity I(0) i0	221709000.00
Molecular weight molecular_weight	124280.0 kDa
Excluded volume excluded_volume	156300 Å³
Envelope volume envelope_volume	28380 Å³
Hydration-shell volume shell_volume	14872 Å³
Envelope diameter envelope_diameter	58.7 Å
Shell Rg shell_rg	22.15 Å
Envelope Rg envelope_rg	16.94 Å
Shape Rg shape_rg	14.41 Å
Total Rg total_rg	14.65 Å
Total atoms total_atoms	17980
Residues n_residues	1140
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	52.0 Å
Rg (real space) rg_real	15.12 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.2170e+08
I(0) uncertainty (real space) i0_real_error	2.4280e+06
Rg (reciprocal space) rg_reciprocal	15.13 Å
I(0) (reciprocal space) i0_reciprocal	221700000.0000
Solution quality estimate total_estimate	0.7551
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.286
Kurtosis Kurtosis kurtosis	-0.014
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	450100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2kddA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	560 —

Domain ID domain_id	2kddB00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	560 —

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8. Citations (1)

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Description description	Borealin
Molecular weight formula_weight	8082.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	17980

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

fit	/app/data/saxs_computation/kd/2kdd/2kdd.fit
pddf	/app/data/pr_computation/kd/2kdd/2kdd.pr.out
profile	/app/data/saxs_computation/kd/2kdd/2kdd.dat

Solution structure of the conserved C-terminal dimerization domain of Borealin

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

Borealin

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)