7nba

Plasmodium falciparum kinesin-5 motor domain bound to AMPPNP, complexed with 14 protofilament microtubule.

Method: ELECTRON MICROSCOPY Dmax: 110.1 Å Quality: REASONABLE

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

Tubulin alpha-1B chain

OrganismNot specified

UniProt Q2XVP4

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 Tubulin beta chain × 1 (P02554) Kinesin motor domain-containing protein,Kinesin motor domain-containing protein × 1 (W7K044) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE;5 uM microtubules were applied to the grid and incubated for 30 seconds. The grid was blotted, then 40 uM kinesin motor domain added, incubated for 30 seconds, then blotted. 40 uM Kinesin motor domain was again added, incubated for 40 seconds, blotted, then plunge frozen. Resolution 4.00 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.

230 other PDB entries and 243 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_PIG
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451

Tubulin beta chain

OrganismNot specified

UniProt P02554

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 Tubulin alpha-1B chain × 1 (Q2XVP4) Kinesin motor domain-containing protein,Kinesin motor domain-containing protein × 1 (W7K044) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE;5 uM microtubules were applied to the grid and incubated for 30 seconds. The grid was blotted, then 40 uM kinesin motor domain added, incubated for 30 seconds, then blotted. 40 uM Kinesin motor domain was again added, incubated for 40 seconds, blotted, then plunge frozen. Resolution 4.00 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.

137 other PDB entries and 159 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB_PIG
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–445; UniProt 1–445

Kinesin motor domain-containing protein,Kinesin motor domain-containing protein

Plasmodium falciparum (isolate NF54)

UniProt W7K044

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 K; UniProt 1–174 Chain K; UniProt 269–493 Not recorded Tubulin alpha-1B chain × 1 (Q2XVP4) Tubulin beta chain × 1 (P02554) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE;5 uM microtubules were applied to the grid and incubated for 30 seconds. The grid was blotted, then 40 uM kinesin motor domain added, incubated for 30 seconds, then blotted. 40 uM Kinesin motor domain was again added, incubated for 40 seconds, blotted, then plunge frozen. Resolution 4.00 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name W7K044_PLAFO
Isoform
PDB entities 3
Chains and sequence ranges Author chain K; PDBConstruct 7–180; UniProt 1–174 Author chain K; PDBConstruct 181–405; UniProt 269–493

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 7nba

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7nba
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7nba
Deposition date deposition_date2021-01-25
Structure title titlePlasmodium falciparum kinesin-5 motor domain bound to AMPPNP, complexed with 14 protofilament microtubule.
Keywords keywordsCytoskeleton, motor protein, mitotic; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.63
Radius of gyration Rg (electron density) rg_electron33.13
Forward intensity I(0) i0293583000.00
Molecular weight molecular_weight135280.0 kDa
Excluded volume excluded_volume168130 ų
Envelope volume envelope_volume207680 ų
Hydration-shell volume shell_volume51001 ų
Envelope diameter envelope_diameter122.0
Shell Rg shell_rg40.90
Envelope Rg envelope_rg33.37
Shape Rg shape_rg33.13
Total Rg total_rg33.67
Total atoms total_atoms18742
Residues n_residues1185
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 dmax110.1
Rg (real space) rg_real33.56
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real2.9360e+08
I(0) uncertainty (real space) i0_real_error4.4190e+06
Rg (reciprocal space) rg_reciprocal33.60
I(0) (reciprocal space) i0_reciprocal293600000.0000
Solution quality estimate total_estimate0.6800
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.5
Skewness Skewness skewness0.283
Kurtosis Kurtosis kurtosis-0.389
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha77210000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.998; Smooth: 0.962

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id7nbaA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id7nbaA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id7nbaB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id7nbaB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id7nbaB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin

8. Citations (1)

9. Files and Curves (10)