9g3z

Structure of the Open gamma-Tubulin Ring Complex from Pig Brain

Method: ELECTRON MICROSCOPY Dmax: 378.0 Å Quality: GOOD

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

Mitotic spindle organizing protein 1

Sus scrofa

UniProt A0A4X1VBW8

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain O; UniProt 1–79 Chain P; UniProt 1–79 Chain Q; UniProt 1–79 Not recorded Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

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

View Construct and Data Evidence
UniProt name A0A4X1VBW8_PIG
Isoform
PDB entities 1
Chains and sequence ranges Author chain O; PDBConstruct 1–79; UniProt 1–79 Author chain P; PDBConstruct 1–79; UniProt 1–79 Author chain Q; PDBConstruct 1–79; UniProt 1–79

Mitotic-spindle organizing protein 2A isoform X4

Sus scrofa

UniProt F1RK97

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain Y; UniProt 1–155 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

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

View Construct and Data Evidence
UniProt name F1RK97_PIG
Isoform
PDB entities 2
Chains and sequence ranges Author chain Y; PDBConstruct 1–155; UniProt 1–155

Tubulin gamma chain

Sus scrofa

UniProt A0A287BRH5

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain a; UniProt 1–451 Chain b; UniProt 1–451 Chain c; UniProt 1–451 Chain d; UniProt 1–451 Chain e; UniProt 1–451 Chain f; UniProt 1–451 Chain g; UniProt 1–451 Chain h; UniProt 1–451 Chain i; UniProt 1–451 Chain j; UniProt 1–451 Chain k; UniProt 1–451 Chain l; UniProt 1–451 Chain m; UniProt 1–451 Chain n; UniProt 1–451 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

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

View Construct and Data Evidence
UniProt name A0A287BRH5_PIG
Isoform
PDB entities 3
Chains and sequence ranges Author chain a; PDBConstruct 1–451; UniProt 1–451 Author chain b; PDBConstruct 1–451; UniProt 1–451 Author chain c; PDBConstruct 1–451; UniProt 1–451 Author chain d; PDBConstruct 1–451; UniProt 1–451 Author chain e; PDBConstruct 1–451; UniProt 1–451 Author chain f; PDBConstruct 1–451; UniProt 1–451 Author chain g; PDBConstruct 1–451; UniProt 1–451 Author chain h; PDBConstruct 1–451; UniProt 1–451 Author chain i; PDBConstruct 1–451; UniProt 1–451 Author chain j; PDBConstruct 1–451; UniProt 1–451 Author chain k; PDBConstruct 1–451; UniProt 1–451 Author chain l; PDBConstruct 1–451; UniProt 1–451 Author chain m; PDBConstruct 1–451; UniProt 1–451 Author chain n; PDBConstruct 1–451; UniProt 1–451

CDK5 regulatory subunit-associated protein 2

Homo sapiens

UniProt A0A0A0MRG9

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain w; UniProt 1–1663 Chain x; UniProt 1–1663 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

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

View Construct and Data Evidence
UniProt name A0A0A0MRG9_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain w; PDBConstruct 1–1663; UniProt 1–1663 Author chain x; PDBConstruct 1–1663; UniProt 1–1663

Gamma-tubulin complex component 3

Sus scrofa

UniProt F1RN46

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain B; UniProt 1–910 Chain D; UniProt 1–910 Chain F; UniProt 1–910 Chain H; UniProt 1–910 Chain N; UniProt 1–910 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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 F1RN46_PIG
Isoform
PDB entities 5
Chains and sequence ranges Author chain B; PDBConstruct 1–910; UniProt 1–910 Author chain D; PDBConstruct 1–910; UniProt 1–910 Author chain F; PDBConstruct 1–910; UniProt 1–910 Author chain H; PDBConstruct 1–910; UniProt 1–910 Author chain N; PDBConstruct 1–910; UniProt 1–910

Gamma-tubulin complex component

Sus scrofa

UniProt A0A8D1IGH3

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain A; UniProt 1–905 Chain C; UniProt 1–905 Chain E; UniProt 1–905 Chain G; UniProt 1–905 Chain M; UniProt 1–905 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

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

View Construct and Data Evidence
UniProt name A0A8D1IGH3_PIG
Isoform
PDB entities 6
Chains and sequence ranges Author chain A; PDBConstruct 1–905; UniProt 1–905 Author chain C; PDBConstruct 1–905; UniProt 1–905 Author chain E; PDBConstruct 1–905; UniProt 1–905 Author chain G; PDBConstruct 1–905; UniProt 1–905 Author chain M; PDBConstruct 1–905; UniProt 1–905

Tubulin gamma complex associated protein 6

Sus scrofa

UniProt A0A8W4FDV6

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain L; UniProt 1–1715 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Gamma-tubulin complex component × 2 (A0A8D1V2H0) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8W4FDV6_PIG
Isoform
PDB entities 7
Chains and sequence ranges Author chain L; PDBConstruct 1–1715; UniProt 1–1715

Gamma-tubulin complex component

Sus scrofa

UniProt A0A8D1V2H0

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain I; UniProt 1–667 Chain K; UniProt 1–667 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 1 (A0A287B1K1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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.

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

View Construct and Data Evidence
UniProt name A0A8D1V2H0_PIG
Isoform
PDB entities 8
Chains and sequence ranges Author chain I; PDBConstruct 1–667; UniProt 1–667 Author chain K; PDBConstruct 1–667; UniProt 1–667

Gamma-tubulin complex component

Sus scrofa

UniProt A0A287B1K1

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 × 34 PDB declaration: 34-meric(34) Consistent with protein copy count Chain J; UniProt 1–1042 Not recorded Mitotic spindle organizing protein 1 × 3 (A0A4X1VBW8) Mitotic-spindle organizing protein 2A isoform X4 × 1 (F1RK97) Tubulin gamma chain × 14 (A0A287BRH5) CDK5 regulatory subunit-associated protein 2 × 2 (A0A0A0MRG9) Gamma-tubulin complex component 3 × 5 (F1RN46) Gamma-tubulin complex component × 5 (A0A8D1IGH3) Tubulin gamma complex associated protein 6 × 1 (A0A8W4FDV6) Gamma-tubulin complex component × 2 (A0A8D1V2H0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 4.30 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 A0A287B1K1_PIG
Isoform
PDB entities 9
Chains and sequence ranges Author chain J; PDBConstruct 1–1042; UniProt 1–1042

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 9g3z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9g3z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9g3z
Deposition date deposition_date2024-07-12
Structure title titleStructure of the Open gamma-Tubulin Ring Complex from Pig Brain
Keywords keywordsTubulin Complex, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier
Radius of gyration Rg (electron density) rg_electron112.80
Forward intensity I(0) i024542200000.00
Molecular weight molecular_weight1096300.0 kDa
Excluded volume excluded_volume1263000 ų
Envelope volume envelope_volume3874000 ų
Hydration-shell volume shell_volume294250 ų
Envelope diameter envelope_diameter327.2
Shell Rg shell_rg112.90
Envelope Rg envelope_rg100.10
Shape Rg shape_rg112.80
Total Rg total_rg112.80
Total atoms total_atoms113079
Residues n_residues15819
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 dmax378.0
Rg (real space) rg_real116.80
Rg uncertainty (real space) rg_real_error2.21
I(0) (real space) i0_real2.4540e+10
I(0) uncertainty (real space) i0_real_error5.4780e+08
Rg (reciprocal space) rg_reciprocal115.80
I(0) (reciprocal space) i0_reciprocal24710000000.0000
Solution quality estimate total_estimate0.8672
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary135.0
Skewness Skewness skewness0.146
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.0700 −1
Current regularization parameter α current_alpha1.0290
Highest regularization parameter α highest_alpha710800000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 0.894; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.001

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)