SAXSdb — 8g0p

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

Kinetochore protein NDC80 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 A； UniProt 370–509	Not recorded	Kinetochore protein Nuf2 × 1 （Q9BZD4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) polyethylene glycol 4000, 0.1 M TRIS pH 8.6, and 0.2 M magnesium chloride	Resolution 2.00 Å R-free 0.297

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 8G0P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IGP Crystal Structure of Hec1 CH domain Deposited 2006-09-22	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 81–196（116 aa）	Not recorded	BME BETA-MERCAPTOETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1 M cacodylate, pH 6.5, 22-30% PEG 8K, 0.2 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.231
2VE7 Crystal structure of a bonsai version of the human Ndc80 complex Deposited 2007-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–286（207 aa） Fragment：CHIMERA OF NDC80 RESIDUES 80-286 WITH SPC25 RESIDUES 118-224	Not recorded	GOL GLYCEROL × 1 IPH PHENOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；4.5-6.5 PEG 6000, 1.5-2 MPD, 0.1 M NAHEPES PH 7.5, 16 MM TCEP, 15 MM PHENOL	Resolution 2.88 Å R-free 0.261
2VE7 Crystal structure of a bonsai version of the human Ndc80 complex Deposited 2007-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 80–286（207 aa） Fragment：CHIMERA OF NDC80 RESIDUES 80-286 WITH SPC25 RESIDUES 118-224	Not recorded	GOL GLYCEROL × 1 IPH PHENOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；4.5-6.5 PEG 6000, 1.5-2 MPD, 0.1 M NAHEPES PH 7.5, 16 MM TCEP, 15 MM PHENOL	Resolution 2.88 Å R-free 0.261
9N9G Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule Deposited 2025-02-10	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 × 9 PDB declaration: nonameric	Chain 1 1–642（642 aa） Chain N 1–642（642 aa） Chain n 1–642（642 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NDC80_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–142； UniProt 370–509

Kinetochore protein Nuf2

Homo sapiens

UniProt Q9BZD4

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 B； UniProt 252–347	Not recorded	Kinetochore protein NDC80 homolog × 1 （O14777）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) polyethylene glycol 4000, 0.1 M TRIS pH 8.6, and 0.2 M magnesium chloride	Resolution 2.00 Å R-free 0.297

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 8G0P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VE7 Crystal structure of a bonsai version of the human Ndc80 complex Deposited 2007-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–169（169 aa） Fragment：CHIMERA OF NUF2 RESIDUES 1-169 WITH SPC24 RESIDUES 122-197	Mutation：YES	GOL GLYCEROL × 1 IPH PHENOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；4.5-6.5 PEG 6000, 1.5-2 MPD, 0.1 M NAHEPES PH 7.5, 16 MM TCEP, 15 MM PHENOL	Resolution 2.88 Å R-free 0.261
2VE7 Crystal structure of a bonsai version of the human Ndc80 complex Deposited 2007-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–169（169 aa） Fragment：CHIMERA OF NUF2 RESIDUES 1-169 WITH SPC24 RESIDUES 122-197	Mutation：YES	GOL GLYCEROL × 1 IPH PHENOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；4.5-6.5 PEG 6000, 1.5-2 MPD, 0.1 M NAHEPES PH 7.5, 16 MM TCEP, 15 MM PHENOL	Resolution 2.88 Å R-free 0.261
9N9G Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule Deposited 2025-02-10	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 × 9 PDB declaration: nonameric	Chain F 1–464（464 aa） Chain f 1–464（464 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–97； UniProt 252–347

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	8g0p
Deposition date deposition_date	2023-02-01
Structure title title	Crystal structure of the human Ndc80:Nuf2 loop region
Keywords keywords	Cell division, chromosome segregation, kinetochore, Ndc80 complex, Ndc80, Nuf2, loop, hinge, human, 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	38.28 Å
Radius of gyration Rg (electron density) rg_electron	40.04 Å
Forward intensity I(0) i0	13453700.00
Molecular weight molecular_weight	28155.0 kDa
Excluded volume excluded_volume	35217 Å³
Envelope volume envelope_volume	49722 Å³
Hydration-shell volume shell_volume	14963 Å³
Envelope diameter envelope_diameter	153.0 Å
Shell Rg shell_rg	30.55 Å
Envelope Rg envelope_rg	41.79 Å
Shape Rg shape_rg	39.85 Å
Total Rg total_rg	39.82 Å
Total atoms total_atoms	3985
Residues n_residues	241
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	147.0 Å
Rg (real space) rg_real	39.86 Å
Rg uncertainty (real space) rg_real_error	2.58 Å
I(0) (real space) i0_real	1.3450e+07
I(0) uncertainty (real space) i0_real_error	2.8520e+05
Rg (reciprocal space) rg_reciprocal	38.87 Å
I(0) (reciprocal space) i0_reciprocal	13440000.0000
Solution quality estimate total_estimate	0.5939
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.776
Kurtosis Kurtosis kurtosis	-0.048
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	471900.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.046; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.010; Smooth: 0.568

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Kinetochore protein NDC80 homolog
Molecular weight formula_weight	16652.0 kDa
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	4010

SCNHERNELQQTINKLTKDLEAEQQKLWNEELKYARGKEAIETQLAEYHKLARKLKLIPKGAENSKGYDFEIKFNPEAGANCLVKYRAQVYVPLKELLNETEEEINKALNKKMGLEDTLEQLNAMITESKRSVRTLKEEVQKC

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 polymer

Description description	Kinetochore protein Nuf2
Molecular weight formula_weight	11567.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

CKNYKEKMKDTVQKLKNARQEVVEKYEIYGDSVDCLPSCQLEVQLYQKKIQDLSDNREKLASILKESLNLEDQIESDESELKKLKTEENSFKRLMIVC

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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8. Citations (1)

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Unit-cell length a length_a	49.903 Å
Unit-cell length b length_b	72.259 Å
Unit-cell length c length_c	80.065 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	40.750 Å
R factor r_factor	0.2620
R_work r_work	0.2600
R_free r_free	0.2968

fit	/app/data/saxs_computation/g0/8g0p/8g0p.fit
pddf	/app/data/pr_computation/g0/8g0p/8g0p.pr.out
profile	/app/data/saxs_computation/g0/8g0p/8g0p.dat

Crystal structure of the human Ndc80:Nuf2 loop region

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

Kinetochore protein NDC80 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Kinetochore protein Nuf2

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)