5nw4

Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2

Method: ELECTRON MICROSCOPY Dmax: 298.9 Å Quality: EXCELLENT

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

Arp1

OrganismNot specified

UniProt F2Z5G5

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain G; UniProt 1–376 Chain H; UniProt 1–376 Chain O; UniProt 1–376 Chain P; UniProt 1–376 Chain Q; UniProt 1–376 Chain T; UniProt 1–376 Chain U; UniProt 1–376 Chain W; UniProt 1–376 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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.

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2Z5G5_PIG
Isoform
PDB entities 10
Chains and sequence ranges Author chain G; PDBConstruct 1–376; UniProt 1–376 Author chain H; PDBConstruct 1–376; UniProt 1–376 Author chain O; PDBConstruct 1–376; UniProt 1–376 Author chain P; PDBConstruct 1–376; UniProt 1–376 Author chain Q; PDBConstruct 1–376; UniProt 1–376 Author chain T; PDBConstruct 1–376; UniProt 1–376 Author chain U; PDBConstruct 1–376; UniProt 1–376 Author chain W; PDBConstruct 1–376; UniProt 1–376

beta-actin

OrganismNot specified

UniProt I3LVD5

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain V; UniProt 3–375 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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 I3LVD5_PIG
Isoform
PDB entities 11
Chains and sequence ranges Author chain V; PDBConstruct 24–396; UniProt 3–375

Arp11

OrganismNot specified

UniProt I3LHK5

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain X; UniProt 1–417 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name I3LHK5_PIG
Isoform
PDB entities 12
Chains and sequence ranges Author chain X; PDBConstruct 1–417; UniProt 1–417

Capping protein (Actin filament) muscle Z-line, alpha 1

OrganismNot specified

UniProt A0PFK5

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain Y; UniProt 1–286 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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.

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0PFK5_PIG
Isoform
PDB entities 13
Chains and sequence ranges Author chain Y; PDBConstruct 1–286; UniProt 1–286

F-actin capping protein beta subunit variant II

OrganismNot specified

UniProt D2JYW4

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain Z; UniProt 2–277 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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 D2JYW4_PIG
Isoform
PDB entities 14
Chains and sequence ranges Author chain Z; PDBConstruct 18–293; UniProt 2–277

Dynactin 6

OrganismNot specified

UniProt D0G6S1

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain g; UniProt 1–190 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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.

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name D0G6S1_PIG
Isoform
PDB entities 19
Chains and sequence ranges Author chain g; PDBConstruct 1–190; UniProt 1–190

Dynactin

OrganismNot specified

UniProt A0A0J9X292

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain k; UniProt 1–48 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X293) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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 A0A0J9X292_PIG
Isoform
PDB entities 23
Chains and sequence ranges Author chain k; PDBConstruct 1–48; UniProt 1–48

Dynactin

OrganismNot specified

UniProt A0A0J9X293

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain l; UniProt 1–71 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X299) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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 A0A0J9X293_PIG
Isoform
PDB entities 24
Chains and sequence ranges Author chain l; PDBConstruct 1–71; UniProt 1–71

Dynactin

OrganismNot specified

UniProt A0A0J9X299

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 × 39 PDB declaration: 39-meric(39) Consistent with protein copy count Chain m; UniProt 1–31 Not recorded dynein heavy chain × 1 dynein intermediate chain × 1 dynein intermediate chain × 1 dynein heavy chain × 1 dynein N-terminal dimerization domain × 1 dynein N-terminal dimerization domain × 1 Robl × 2 dynein light intermediate chain × 1 dynein light intermediate chain × 1 Arp1 × 8 (F2Z5G5) beta-actin × 1 (I3LVD5) Arp11 × 1 (I3LHK5) Capping protein (Actin filament) muscle Z-line, alpha 1 × 1 (A0PFK5) F-actin capping protein beta subunit variant II × 1 (D2JYW4) dynactin shoulder complex × 1 dynactin shoulder complex × 1 dynactin shoulder complex × 2 dynactin shoulder complex × 2 Dynactin 6 × 1 (D0G6S1) Dynactin subunit 5 × 1 dynactin pointed end p62 × 1 p150 × 1 Dynactin × 1 (A0A0J9X292) Dynactin × 1 (A0A0J9X293) Dynactin × 1 dynactin p150 × 1 BICD2N × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.70 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 A0A0J9X299_PIG
Isoform
PDB entities 25
Chains and sequence ranges Author chain m; PDBConstruct 1–31; UniProt 1–31

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 5nw4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nw4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nw4
Deposition date deposition_date2017-05-05
Structure title titleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Keywords keywordsMotor protein, dynein, dynactin, BICD; MOTOR 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_electron109.40
Forward intensity I(0) i014255300000.00
Molecular weight molecular_weight934540.0 kDa
Excluded volume excluded_volume1132700 ų
Envelope volume envelope_volume2718700 ų
Hydration-shell volume shell_volume227530 ų
Envelope diameter envelope_diameter452.1
Shell Rg shell_rg86.78
Envelope Rg envelope_rg111.70
Shape Rg shape_rg109.60
Total Rg total_rg108.70
Total atoms total_atoms66272
Residues n_residues10707
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 dmax298.9
Rg (real space) rg_real101.60
Rg uncertainty (real space) rg_real_error1.43
I(0) (real space) i0_real1.3620e+10
I(0) uncertainty (real space) i0_real_error2.9630e+08
Rg (reciprocal space) rg_reciprocal99.83
I(0) (reciprocal space) i0_reciprocal13840000000.0000
Solution quality estimate total_estimate0.9174
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary106.8
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.528
Angular range angular_range— – 0.0700 −1
Current regularization parameter α current_alpha0.7134
Highest regularization parameter α highest_alpha480600000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.022; Oscil: 0.998; Stabil: 0.980; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.003

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (28)

8. Citations (1)

9. Files and Curves (10)