SAXSdb — 3e2u

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

Dynactin subunit 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CAP-Gly domain-containing linker protein 1 × 1 （P30622） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CAP-Gly domain-containing linker protein 1 × 1 （P30622） ZINC ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CAP-Gly domain-containing linker protein 1 × 1 （P30622） ZINC ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	CAP-Gly domain-containing linker protein 1 × 1 （P30622） ZINC ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	CAP-Gly domain-containing linker protein 1 × 4 （P30622） ZINC ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCTN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–97； UniProt 18–111 Author chain B； PDBConstruct 4–97； UniProt 18–111 Author chain C； PDBConstruct 4–97； UniProt 18–111 Author chain D； PDBConstruct 4–97； UniProt 18–111

CAP-Gly domain-containing linker protein 1

Homo sapiens

UniProt P30622

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Dynactin subunit 1 × 1 （Q14203） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Dynactin subunit 1 × 1 （Q14203） ZINC ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Dynactin subunit 1 × 1 （Q14203） ZINC ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Dynactin subunit 1 × 1 （Q14203） ZINC ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	Dynactin subunit 1 × 4 （Q14203） ZINC ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLIP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 3–42； UniProt 1388–1427 Author chain F； PDBConstruct 3–42； UniProt 1388–1427 Author chain G； PDBConstruct 3–42； UniProt 1388–1427 Author chain H； PDBConstruct 3–42； UniProt 1388–1427

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3e2u
Deposition date deposition_date	2008-08-06
Structure title title	Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED)
Keywords keywords	;STRUCTURAL PROTEIN MICROTUBULE BINDING, DYNACTIN, CYTOSKELETON ASSOCIATED PROTEIN, P150GLUED, CLIP-170/RESTIN, +TIP PROTEIN COMPLEX STRUCTURE, ZINC-KNUCKLE, AUTOINHIBITION, PROTEIN BINDING, Cytoskeleton, Dynein, Microtubule, Motor protein, Phosphoprotein ;; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3e2u__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3e2u__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e2u__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	14.40 Å
Rg (electron density)	13.27 Å
Total Rg	14.36 Å
Atom count	754
Residues	96
Excluded volume	13277 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e2u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e2u__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3e2u__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3e2u__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3e2u__assembly_5__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Dynactin subunit 1
Molecular weight formula_weight	10309.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3085

GSHMSAEASARPLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVFEDGADTTSPETPDS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CAP-Gly domain-containing linker protein 1
Molecular weight formula_weight	4804.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GSMSEDPPHSTHHGSRGEERPYCEICEMFGHWATNCNDDETF

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3e2ua_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.10 — Cap-Gly domain
Family Family family	b.34.10.1 — Cap-Gly domain

Domain ID domain_id	d3e2ub_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.10 — Cap-Gly domain
Family Family family	b.34.10.1 — Cap-Gly domain

Domain ID domain_id	d3e2uc_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.10 — Cap-Gly domain
Family Family family	b.34.10.1 — Cap-Gly domain

Domain ID domain_id	d3e2ud_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.10 — Cap-Gly domain
Family Family family	b.34.10.1 — Cap-Gly domain

CATH v4.4 (4 domains)

Domain ID domain_id	3e2uA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	190 — CAP Gly-rich-like domain

Domain ID domain_id	3e2uB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	190 — CAP Gly-rich-like domain

Domain ID domain_id	3e2uC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	190 — CAP Gly-rich-like domain

Domain ID domain_id	3e2uD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	190 — CAP Gly-rich-like domain

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Unit-cell length a length_a	116.220 Å
Unit-cell length b length_b	116.310 Å
Unit-cell length c length_c	79.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	47.015 Å
R factor r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2380

Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED)

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

Dynactin subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

CAP-Gly domain-containing linker protein 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3e2u__assembly_3__model_1

3e2u__assembly_3__model_1 | I(q)

3e2u__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED)

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

Dynactin subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CAP-Gly domain-containing linker protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3e2u__assembly_3__model_1

3e2u__assembly_3__model_1 | I(q)

3e2u__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)