SAXSdb — 4kp3

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

Unconventional myosin-Va

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	RILP-like protein 2 × 2 （Q99LE1） Melanophilin × 2 （Q91V27） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MYO5A_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–404； UniProt 1469–1853 Author chain B； PDBConstruct 20–404； UniProt 1469–1853

RILP-like protein 2

Mus musculus

UniProt Q99LE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Unconventional myosin-Va × 2 （Q99104） Melanophilin × 2 （Q91V27） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIPL2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 7–103； UniProt 1–97 Author chain D； PDBConstruct 7–103； UniProt 1–97

Melanophilin

Mus musculus

UniProt Q91V27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Unconventional myosin-Va × 2 （Q99104） RILP-like protein 2 × 2 （Q99LE1） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MELPH_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 5–43； UniProt 170–208 Author chain F； PDBConstruct 5–43； UniProt 170–208

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	4kp3
Deposition date deposition_date	2013-05-13
Structure title title	Crystal Structure of MyoVa-GTD in Complex with Two Cargos
Keywords keywords	Helix bundle, MOTOR PROTEIN-PROTEIN TRANSPORT complex; MOTOR PROTEIN/PROTEIN TRANSPORT
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.

4kp3__assembly_1__model_1

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

Download this curve (.dat)

4kp3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4kp3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.17 Å
Rg (electron density)	39.18 Å
Total Rg	39.40 Å
Atom count	7286
Residues	907
Excluded volume	130850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4kp3__assembly_1__model_1`	hexameric （6）	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	Unconventional myosin-Va
Molecular weight formula_weight	46106.3 kDa
Mutation mutation	C1674S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7359

HHHHHHSSGLGVLFQGPGSKDFQGMLEYKREDEQKLVKNLILELKPRGVAVNLIPGLPAYILFMCVRHADYLNDDQKVRSLLTSTINSIKKVLKKRGDDFETVSFWLSNTCRFLHCLKQYSGEEGFMKHNTSRQNEHCLTNFDLAEYRQVLSDLAIQIYQQLVRVLENILQPMIVSGMLEHETIQGVSGVKPTGLRKRTSSIADEGTYTLDSILRQLNSFHSVMSQHGMDPELIKQVVKQMFYIVGAITLNNLLLRKDMCSWSKGMQIRYNVSQLEEWLRDKNLMNSGAKETLEPLIQAAQLLQVKKKTDDDAEAICSMCNALTTAQIVKVLNLYTPVNEFEERVSVSFIRTIQMRLRDRKDSPQLLMDAKHIFPVTFPFNPSSLALETIQIPASLGLGFIARV

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RILP-like protein 2
Molecular weight formula_weight	11608.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GPGSEFMEDHPVREEEDGEEDEGALAKSPLQLTTDDVYDISYVVGRELMALGSDPRVTRLQFKIVRVMEMLETLVNEGSLAVEELRMERDNLKQEVEGLRKAG

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Melanophilin
Molecular weight formula_weight	4882.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPGSDLDTEARDQPLNSKKKKRLLSFRDVDFEEDSDHLVQPCS

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4kp3a_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d4kp3b_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

CATH v4.4 (2 domains)

Domain ID domain_id	4kp3C00
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	1770 —

Domain ID domain_id	4kp3D00
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	1770 —

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Unit-cell length a length_a	81.850 Å
Unit-cell length b length_b	107.933 Å
Unit-cell length c length_c	83.510 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.405 Å
Low-resolution limit resolution_low	38.694 Å
R factor r_factor	0.1945
R_work r_work	0.1920
R_free r_free	0.2411

Crystal Structure of MyoVa-GTD in Complex with Two Cargos

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

Unconventional myosin-Va

State in the Current Structure

Other States of the Same Protein in the Database

RILP-like protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Melanophilin

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

4kp3__assembly_1__model_1

4kp3__assembly_1__model_1 | I(q)

4kp3__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of MyoVa-GTD in Complex with Two Cargos

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

Unconventional myosin-Va

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RILP-like protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Melanophilin

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

4kp3__assembly_1__model_1

4kp3__assembly_1__model_1 | I(q)

4kp3__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)