8rgh

Structure of dynein-2 intermediate chain DYNC2I1 (WDR60) in complex with the dynein-2 heavy chain DYNC2H1.

Method: ELECTRON MICROSCOPY Dmax: 125.8 Å Quality: GOOD

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

Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1

Homo sapiens

UniProt P16455

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–184 Not recorded Cytoplasmic dynein 2 intermediate chain 1 × 1 (Q8WVS4) Cytoplasmic dynein 2 intermediate chain 2 × 1 (Q96EX3) Cytoplasmic dynein 2 light intermediate chain 1 × 1 (Q8TCX1) Dynein light chain roadblock-type 1 × 2 (Q9NP97) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.90 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.

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MGMT_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–184; UniProt 2–184

Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1

Homo sapiens

UniProt Q8NCM8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–4307 Not recorded Cytoplasmic dynein 2 intermediate chain 1 × 1 (Q8WVS4) Cytoplasmic dynein 2 intermediate chain 2 × 1 (Q96EX3) Cytoplasmic dynein 2 light intermediate chain 1 × 1 (Q8TCX1) Dynein light chain roadblock-type 1 × 2 (Q9NP97) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.90 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 DYHC2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 208–4513; UniProt 2–4307

Cytoplasmic dynein 2 intermediate chain 1

Homo sapiens

UniProt Q8WVS4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–1066 Not recorded Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 × 1 (P16455,Q8NCM8) Cytoplasmic dynein 2 intermediate chain 2 × 1 (Q96EX3) Cytoplasmic dynein 2 light intermediate chain 1 × 1 (Q8TCX1) Dynein light chain roadblock-type 1 × 2 (Q9NP97) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.90 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 DC2I1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1066; UniProt 1–1066

Cytoplasmic dynein 2 intermediate chain 2

Homo sapiens

UniProt Q96EX3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–536 Not recorded Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 × 1 (P16455,Q8NCM8) Cytoplasmic dynein 2 intermediate chain 1 × 1 (Q8WVS4) Cytoplasmic dynein 2 light intermediate chain 1 × 1 (Q8TCX1) Dynein light chain roadblock-type 1 × 2 (Q9NP97) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.90 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 DC2I2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–536; UniProt 1–536

Cytoplasmic dynein 2 light intermediate chain 1

Homo sapiens

UniProt Q8TCX1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 1–351 Not recorded Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 × 1 (P16455,Q8NCM8) Cytoplasmic dynein 2 intermediate chain 1 × 1 (Q8WVS4) Cytoplasmic dynein 2 intermediate chain 2 × 1 (Q96EX3) Dynein light chain roadblock-type 1 × 2 (Q9NP97) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.90 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 DC2L1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–351; UniProt 1–351

Dynein light chain roadblock-type 1

Homo sapiens

UniProt Q9NP97

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–96 Chain H; UniProt 1–96 Not recorded Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 × 1 (P16455,Q8NCM8) Cytoplasmic dynein 2 intermediate chain 1 × 1 (Q8WVS4) Cytoplasmic dynein 2 intermediate chain 2 × 1 (Q96EX3) Cytoplasmic dynein 2 light intermediate chain 1 × 1 (Q8TCX1) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.90 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.

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DLRB1_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–96; UniProt 1–96 Author chain H; PDBConstruct 1–96; UniProt 1–96

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 8rgh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8rgh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8rgh
Deposition date deposition_date2023-12-13
Structure title titleStructure of dynein-2 intermediate chain DYNC2I1 (WDR60) in complex with the dynein-2 heavy chain DYNC2H1.
Keywords keywordsdynein, cilia, intraflagellar transport, complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.88
Radius of gyration Rg (electron density) rg_electron37.27
Forward intensity I(0) i0294571000.00
Molecular weight molecular_weight137100.0 kDa
Excluded volume excluded_volume170740 ų
Envelope volume envelope_volume239540 ų
Hydration-shell volume shell_volume53951 ų
Envelope diameter envelope_diameter130.2
Shell Rg shell_rg42.97
Envelope Rg envelope_rg37.15
Shape Rg shape_rg37.29
Total Rg total_rg37.58
Total atoms total_atoms9682
Residues n_residues1287
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 dmax125.8
Rg (real space) rg_real37.89
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real2.9460e+08
I(0) uncertainty (real space) i0_real_error4.8590e+06
Rg (reciprocal space) rg_reciprocal37.89
I(0) (reciprocal space) i0_reciprocal294600000.0000
Solution quality estimate total_estimate0.8832
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.9
Skewness Skewness skewness0.355
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36900000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.872

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)