5x6v

Crystal structure of human heteroheptameric complex

Method: X-RAY DIFFRACTION

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

Ragulator complex protein LAMTOR3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR5 × 1 （O43504） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q99K70） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–127； UniProt 2–124

Ragulator complex protein LAMTOR2

Homo sapiens

UniProt Q9Y2Q5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR5 × 1 （O43504） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q99K70） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–125； UniProt 1–125

Ragulator complex protein LAMTOR5

Homo sapiens

UniProt O43504

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q99K70） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–91； UniProt 1–91

Ragulator complex protein LAMTOR4

Homo sapiens

UniProt Q0VGL1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR5 × 1 （O43504） Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q99K70） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–99； UniProt 1–99

Ragulator complex protein LAMTOR1

Homo sapiens

UniProt Q6IAA8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR5 × 1 （O43504） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q99K70） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTOR1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 4–123； UniProt 42–161

Ras-related GTP-binding protein A

Homo sapiens

UniProt Q7L523

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR5 × 1 （O43504） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ras-related GTP-binding protein C × 1 （Q99K70） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRAGA_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 5–135； UniProt 183–313

Ras-related GTP-binding protein C

Mus musculus

UniProt Q99K70

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR5 × 1 （O43504） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ras-related GTP-binding protein A × 1 （Q7L523） SODIUM ION × 1 ACETATE ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRAGC_MOUSE
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 2–139； UniProt 238–375

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	5x6v
Deposition date deposition_date	2017-02-23
Structure title title	Crystal structure of human heteroheptameric complex
Keywords keywords	Ragulator Rag GTPase complex, scaffold, roadblock, lysosome, mTOR signaling, cell growth, PROTEIN BINDING; 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.

5x6v__assembly_1__model_1

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

Download this curve (.dat)

5x6v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5x6v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.77 Å
Rg (electron density)	32.45 Å
Total Rg	32.90 Å
Atom count	6050
Residues	780
Excluded volume	108450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5x6v__assembly_1__model_1`	heptameric （7）	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 (10)

Entity 1 Entity 1 polymer

Description description	Ragulator complex protein LAMTOR3
Molecular weight formula_weight	13868.9 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	6417

MGSSADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQVVEVS

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	Ragulator complex protein LAMTOR2
Molecular weight formula_weight	13517.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVAAS

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 polymer

Description description	Ragulator complex protein LAMTOR5
Molecular weight formula_weight	9622.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

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 4 Entity 4 polymer

Description description	Ragulator complex protein LAMTOR4
Molecular weight formula_weight	10753.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMNVPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

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 5 Entity 5 polymer

Description description	Ragulator complex protein LAMTOR1
Molecular weight formula_weight	13405.1 kDa
Mutation mutation	S98E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GAASLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSDLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

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 6 Entity 6 polymer

Description description	Ras-related GTP-binding protein A
Molecular weight formula_weight	15661.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MADLNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKHSLLMR

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 7 Entity 7 polymer

Description description	Ras-related GTP-binding protein C
Molecular weight formula_weight	15764.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRKAIHEVFEVGVTSHRS

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 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	348

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5x6va_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d5x6vb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

CATH v4.4 (5 domains)

Domain ID domain_id	5x6vA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5x6vB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5x6vC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	5x6vF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	190 —

Domain ID domain_id	5x6vG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	190 —

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Unit-cell length a length_a	74.099 Å
Unit-cell length b length_b	93.476 Å
Unit-cell length c length_c	125.452 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	2.020 Å
Low-resolution limit resolution_low	20.360 Å
R factor r_factor	0.1950
R_work r_work	0.1930
R_free r_free	0.2430

Crystal structure of human heteroheptameric complex

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

Ragulator complex protein LAMTOR3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ragulator complex protein LAMTOR1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related GTP-binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related GTP-binding protein C

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

5x6v__assembly_1__model_1

5x6v__assembly_1__model_1 | I(q)

5x6v__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 (10)

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 polymer

Polymer Polymer