SAXSdb — 5lsi

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

Kinetochore-associated protein DSN1 homolog

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 68–200	Fragment：head2 domain, UNP residues 68-200	Kinetochore-associated protein NSL1 homolog × 1 （Q96IY1） 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

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 5LSI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LSJ CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX Deposited 2016-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 186–356（171 aa） Fragment：UNP residues 186-356	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 186–356（171 aa） Fragment：UNP residues 186-356	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 68–356（289 aa） Fragment：UNP residues 68-356	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–356（356 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–356（356 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

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	1
Chains and sequence ranges	Author chain D； PDBConstruct 2–134； UniProt 68–200

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 29–99	Fragment：UNP residues 29-99	Kinetochore-associated protein DSN1 homolog × 1 （Q9H410） 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

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 5LSI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NF9 Structure of the Knl1/Nsl1 complex Deposited 2013-10-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 256–281（26 aa） Fragment：Nsl1 C-terminal tail, UNP residues 256-281	Not recorded	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 256–281（26 aa） Fragment：Nsl1 C-terminal tail, UNP residues 256-281	Not recorded	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
5LSJ CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX Deposited 2016-09-02	Different construct Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 7 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 E； PDBConstruct 6–76； UniProt 29–99

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	5lsi
Deposition date deposition_date	2016-09-02
Structure title title	CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAIN CONTAINING DSN1 AND NSL1 FRAGMENTS
Keywords keywords	ALPHA-HELICAL, cell cycle; CELL CYCLE
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	18.69 Å
Radius of gyration Rg (electron density) rg_electron	17.64 Å
Forward intensity I(0) i0	6399180.00
Molecular weight molecular_weight	17598.0 kDa
Excluded volume excluded_volume	21757 Å³
Envelope volume envelope_volume	27460 Å³
Hydration-shell volume shell_volume	13967 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	22.86 Å
Envelope Rg envelope_rg	18.81 Å
Shape Rg shape_rg	17.61 Å
Total Rg total_rg	18.63 Å
Total atoms total_atoms	1235
Residues n_residues	158
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	48.1 Å
Rg (real space) rg_real	17.40 Å
Rg uncertainty (real space) rg_real_error	0.06 Å
I(0) (real space) i0_real	6.0540e+06
I(0) uncertainty (real space) i0_real_error	5.7410e+04
Rg (reciprocal space) rg_reciprocal	18.82 Å
I(0) (reciprocal space) i0_reciprocal	6399000.0000
Solution quality estimate total_estimate	0.6867
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	3.1010
Highest regularization parameter α highest_alpha	1036000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.005; Oscil: 0.995; Stabil: 0.981; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Kinetochore-associated protein DSN1 homolog
Molecular weight formula_weight	15313.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	1288

MSHQERLQSKSLHLSPQEQSASYQDRRQSWRRASMKETNRRKSLHPIHQGITELSRSISVDLAESKRLGCLLLSSFQFSIQKLEPFLRDTKGFSLESFRAKASSLSEELKHFADGLETDGTLQKCFEDSNGKAS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Kinetochore-associated protein NSL1 homolog
Molecular weight formula_weight	8487.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPLGSSATPREDFRVRCTSKRAVTEMLQLCGRFVQKLGDALPEEIREPALRDAQWTFESAVQENISINGQAWQEAS

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 BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

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8. Citations (1)

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Unit-cell length a length_a	59.640 Å
Unit-cell length b length_b	59.640 Å
Unit-cell length c length_c	82.340 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	2.002 Å
Low-resolution limit resolution_low	43.754 Å
R factor r_factor	0.2173
R_work r_work	0.2158
R_free r_free	0.2458

fit	/app/data/saxs_computation/ls/5lsi/5lsi.fit
pddf	/app/data/pr_computation/ls/5lsi/5lsi.pr.out
profile	/app/data/saxs_computation/ls/5lsi/5lsi.dat

CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAIN CONTAINING DSN1 AND NSL1 FRAGMENTS

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

Kinetochore-associated protein DSN1 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore-associated protein NSL1 homolog

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)