9m1m

Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx

Method: ELECTRON MICROSCOPY Dmax: 190.5 Å Quality: GOOD

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

Tubulin-specific chaperone C

Homo sapiens

UniProt Q15814

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–346 Not recorded Tubulin-specific chaperone D × 1 (Q9BTW9) Tubulin-specific chaperone E × 1 (Q15813) ADP-ribosylation factor-like protein 2 × 1 (P36404) Tubulin alpha-1B chain × 1 (Q2XVP4) Tubulin beta chain × 1 (Q767L7) GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.21 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.

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

View Construct and Data Evidence
UniProt name TBCC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 1–346; UniProt 1–346

Tubulin-specific chaperone D

Homo sapiens

UniProt Q9BTW9

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–1192 Not recorded Tubulin-specific chaperone C × 1 (Q15814) Tubulin-specific chaperone E × 1 (Q15813) ADP-ribosylation factor-like protein 2 × 1 (P36404) Tubulin alpha-1B chain × 1 (Q2XVP4) Tubulin beta chain × 1 (Q767L7) GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.21 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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBCD_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–1192; UniProt 1–1192

Tubulin-specific chaperone E

Homo sapiens

UniProt Q15813

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 1–527 Not recorded Tubulin-specific chaperone C × 1 (Q15814) Tubulin-specific chaperone D × 1 (Q9BTW9) ADP-ribosylation factor-like protein 2 × 1 (P36404) Tubulin alpha-1B chain × 1 (Q2XVP4) Tubulin beta chain × 1 (Q767L7) GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.21 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.

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBCE_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–527; UniProt 1–527

ADP-ribosylation factor-like protein 2

Homo sapiens

UniProt P36404

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–184 Not recorded Tubulin-specific chaperone C × 1 (Q15814) Tubulin-specific chaperone D × 1 (Q9BTW9) Tubulin-specific chaperone E × 1 (Q15813) Tubulin alpha-1B chain × 1 (Q2XVP4) Tubulin beta chain × 1 (Q767L7) GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.21 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 ARL2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–184; UniProt 1–184

Tubulin alpha-1B chain

Sus scrofa

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain a; UniProt 1–451 Not recorded Tubulin-specific chaperone C × 1 (Q15814) Tubulin-specific chaperone D × 1 (Q9BTW9) Tubulin-specific chaperone E × 1 (Q15813) ADP-ribosylation factor-like protein 2 × 1 (P36404) Tubulin beta chain × 1 (Q767L7) GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.21 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 5
Chains and sequence ranges Author chain a; PDBConstruct 1–451; UniProt 1–451

Tubulin beta chain

Sus scrofa

UniProt Q767L7

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain b; UniProt 1–444 Not recorded Tubulin-specific chaperone C × 1 (Q15814) Tubulin-specific chaperone D × 1 (Q9BTW9) Tubulin-specific chaperone E × 1 (Q15813) ADP-ribosylation factor-like protein 2 × 1 (P36404) Tubulin alpha-1B chain × 1 (Q2XVP4) GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.21 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 TBB5_PIG
Isoform
PDB entities 6
Chains and sequence ranges Author chain b; PDBConstruct 1–444; UniProt 1–444

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 9m1m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9m1m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9m1m
Deposition date deposition_date2025-02-26
Structure title titleCryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
Keywords keywordschaperone, complex; CHAPERONE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier51.54
Radius of gyration Rg (electron density) rg_electron51.60
Forward intensity I(0) i01496670000.00
Molecular weight molecular_weight321090.0 kDa
Excluded volume excluded_volume401490 ų
Envelope volume envelope_volume552980 ų
Hydration-shell volume shell_volume91214 ų
Envelope diameter envelope_diameter201.2
Shell Rg shell_rg53.47
Envelope Rg envelope_rg51.51
Shape Rg shape_rg51.60
Total Rg total_rg51.64
Total atoms total_atoms22547
Residues n_residues2854
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 dmax190.5
Rg (real space) rg_real51.68
Rg uncertainty (real space) rg_real_error2.11
I(0) (real space) i0_real1.4970e+09
I(0) uncertainty (real space) i0_real_error2.9390e+07
Rg (reciprocal space) rg_reciprocal51.42
I(0) (reciprocal space) i0_reciprocal1496000000.0000
Solution quality estimate total_estimate0.8398
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.3
Skewness Skewness skewness0.489
Kurtosis Kurtosis kurtosis0.005
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha176800000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.915

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

8. Citations (2)

9. Files and Curves (10)