5nd2

Microtubule-bound MKLP2 motor domain in the presence of ADP

Method: ELECTRON MICROSCOPY Dmax: 102.4 Å Quality: REASONABLE

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

Kinesin-like protein KIF20A

Mus musculus

UniProt P97329

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 21–521 Not recorded Tubulin alpha chain × 1 (F2Z4C1) Tubulin beta-2B chain × 1 (Q6B856) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.80 Å

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KI20A_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 1–501; UniProt 21–521

Tubulin alpha chain

OrganismNot specified

UniProt F2Z4C1

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–451 Not recorded Kinesin-like protein KIF20A × 1 (P97329) Tubulin beta-2B chain × 1 (Q6B856) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.80 Å

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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2Z4C1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451

Tubulin beta-2B chain

OrganismNot specified

UniProt Q6B856

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–445 Not recorded Kinesin-like protein KIF20A × 1 (P97329) Tubulin alpha chain × 1 (F2Z4C1) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 5.80 Å

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.

273 other PDB entries and 275 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB2B_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 1–445; UniProt 1–445

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 5nd2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nd2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nd2
Deposition date deposition_date2017-03-07
Structure title titleMicrotubule-bound MKLP2 motor domain in the presence of ADP
Keywords keywordsKinesin Mitosis Microtubules, Motor protein; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier32.52
Radius of gyration Rg (electron density) rg_electron32.45
Forward intensity I(0) i05874880000.00
Molecular weight molecular_weight638750.0 kDa
Excluded volume excluded_volume793940 ų
Envelope volume envelope_volume198580 ų
Hydration-shell volume shell_volume49615 ų
Envelope diameter envelope_diameter110.9
Shell Rg shell_rg40.53
Envelope Rg envelope_rg32.52
Shape Rg shape_rg32.45
Total Rg total_rg32.57
Total atoms total_atoms44865
Residues n_residues5590
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax102.4
Rg (real space) rg_real32.40
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real5.8750e+09
I(0) uncertainty (real space) i0_real_error8.7380e+07
Rg (reciprocal space) rg_reciprocal32.46
I(0) (reciprocal space) i0_reciprocal5875000000.0000
Solution quality estimate total_estimate0.6954
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6
Skewness Skewness skewness0.227
Kurtosis Kurtosis kurtosis-0.524
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58810000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.999; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)