SAXSdb — 2aka

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

myosin II heavy chain

Dictyostelium discoideum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	LINKER × 1 Dynamin-1 × 1 （P21575） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MYS2_DICDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–776； UniProt 2–765

Dynamin-1

Rattus norvegicus

UniProt P21575

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	myosin II heavy chain × 1 （P08799） LINKER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DYN1_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–299； UniProt 6–304

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	2aka
Deposition date deposition_date	2005-08-03
Structure title title	Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus
Keywords keywords	fusion protein, GTPase domain, dynamin, myosin, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN
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.

2aka__assembly_1__model_1

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

Download this curve (.dat)

2aka__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2aka__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.73 Å
Rg (electron density)	42.19 Å
Total Rg	42.33 Å
Atom count	8519
Residues	1069
Excluded volume	151720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2aka__assembly_1__model_1`	trimeric （3）	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	myosin II heavy chain
Molecular weight formula_weight	88594.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9377

MHHHHHHHDGTENPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRISEI

Source Source

Source organism organism	Dictyostelium discoideum
NCBI taxonomy ID ncbi_taxonomy_id	44689
Host organism host_organism	Dictyostelium discoideum

Entity 2 Entity 2 polymer

Description description	LINKER
Molecular weight formula_weight	1442.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

TRLVPRGSELALE

Entity 3 Entity 3 polymer

Description description	Dynamin-1
Molecular weight formula_weight	33217.1 kDa
EC 编号 ec_number	3.6.5.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEDLIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLVNSTTEYAEFLHCKGKKFTDFEEVRLEIEAETDRVTGTNKGISPVPINLRVYSPHVLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKIAKEVDPQGQRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAALAAERKFFLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQL

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Dictyostelium discoideum

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	754

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2akab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (3 domains)

Domain ID domain_id	2akaA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	530 —

Domain ID domain_id	2akaA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2akaB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	57.420 Å
Unit-cell length b length_b	126.990 Å
Unit-cell length c length_c	160.810 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2240

Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus

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

myosin II heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Dynamin-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

2aka__assembly_1__model_1

2aka__assembly_1__model_1 | I(q)

2aka__assembly_1__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

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus

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

myosin II heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Dynamin-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

2aka__assembly_1__model_1

2aka__assembly_1__model_1 | I(q)

2aka__assembly_1__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

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (2)