6f1z

Roadblock-1 region of the dynein tail/dynactin/BICDR1 complex

Method: ELECTRON MICROSCOPY Dmax: 74.9 Å Quality: GOOD

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

Cytoplasmic dynein 1 intermediate chain 2

Homo sapiens

UniProt Q13409

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain o; UniProt 1–612 Chain p; UniProt 1–612 Not recorded Dynein light chain roadblock-type 1 × 2 (Q9NP97) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 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.

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DC1I2_HUMAN
Isoform Q13409-3
PDB entities 1
Chains and sequence ranges Author chain o; PDBConstruct 1–612; UniProt 1–612 Author chain p; PDBConstruct 1–612; UniProt 1–612

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 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain s; UniProt 1–96 Chain t; UniProt 1–96 Not recorded Cytoplasmic dynein 1 intermediate chain 2 × 2 (Q13409) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 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 2
Chains and sequence ranges Author chain s; PDBConstruct 1–96; UniProt 1–96 Author chain t; 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 6f1z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6f1z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6f1z
Deposition date deposition_date2017-11-23
Structure title titleRoadblock-1 region of the dynein tail/dynactin/BICDR1 complex
Keywords keywordsCryo-EM, Complex, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier21.07
Radius of gyration Rg (electron density) rg_electron19.97
Forward intensity I(0) i016255900.00
Molecular weight molecular_weight30372.0 kDa
Excluded volume excluded_volume38194 ų
Envelope volume envelope_volume48696 ų
Hydration-shell volume shell_volume20756 ų
Envelope diameter envelope_diameter75.6
Shell Rg shell_rg26.35
Envelope Rg envelope_rg20.32
Shape Rg shape_rg19.99
Total Rg total_rg20.91
Total atoms total_atoms2138
Residues n_residues265
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 dmax74.9
Rg (real space) rg_real21.07
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real1.6260e+07
I(0) uncertainty (real space) i0_real_error1.9400e+05
Rg (reciprocal space) rg_reciprocal21.07
I(0) (reciprocal space) i0_reciprocal16260000.0000
Solution quality estimate total_estimate0.8344
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2
Skewness Skewness skewness0.466
Kurtosis Kurtosis kurtosis0.115
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4924000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.626; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.993

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6f1zs00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily30 — Dynein light chain 2a, cytoplasmic
Domain ID domain_id6f1zt00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily30 — Dynein light chain 2a, cytoplasmic

8. Citations (1)

9. Files and Curves (10)