6wj2

CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state

Method: ELECTRON MICROSCOPY

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

Ragulator complex protein LAMTOR1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q9HB90） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–166； UniProt 1–161

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 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q9HB90） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	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 3–127； UniProt 1–125

Ragulator complex protein LAMTOR3

Homo sapiens

UniProt Q9UHA4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q9HB90） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–124； UniProt 1–124

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 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q9HB90） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	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 LAMTOR5

Homo sapiens

UniProt A0A0C4DGV4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q9HB90） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0C4DGV4_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–173； UniProt 1–173

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 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein C × 1 （Q9HB90） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	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 24–336； UniProt 1–313

Ras-related GTP-binding protein C

Homo sapiens

UniProt Q9HB90

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein A × 1 （Q7L523） Sodium-coupled neutral amino acid transporter 9 × 1 （Q8NBW4） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRAGC_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 6–404； UniProt 1–399

Sodium-coupled neutral amino acid transporter 9

Homo sapiens

UniProt Q8NBW4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Ragulator complex protein LAMTOR1 × 1 （Q6IAA8） Ragulator complex protein LAMTOR2 × 1 （Q9Y2Q5） Ragulator complex protein LAMTOR3 × 1 （Q9UHA4） Ragulator complex protein LAMTOR4 × 1 （Q0VGL1） Ragulator complex protein LAMTOR5 × 1 （A0A0C4DGV4） Ras-related GTP-binding protein A × 1 （Q7L523） Ras-related GTP-binding protein C × 1 （Q9HB90） GUANOSINE-5'-DIPHOSPHATE × 1 ;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ; × 1 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S38A9_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 4–122； UniProt 1–119

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	6wj2
Deposition date deposition_date	2020-04-11
Structure title title	CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state
Keywords keywords	small GTPase, mTORC1 activation, amino acid signaling, lysosome, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6wj2__assembly_1__model_1

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

Download this curve (.dat)

6wj2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wj2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.49 Å
Rg (electron density)	42.38 Å
Total Rg	42.36 Å
Atom count	8909
Residues	1167
Excluded volume	158740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wj2__assembly_1__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 (11)

Entity 1 Entity 1 polymer

Description description	Ragulator complex protein LAMTOR1
Molecular weight formula_weight	18325.3 kDa
Mutation mutation	G2A
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	8909

SNAEFMACCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Ragulator complex protein LAMTOR2
Molecular weight formula_weight	13645.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GAMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVAAS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Ragulator complex protein LAMTOR3
Molecular weight formula_weight	13637.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQVVEVS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

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	Spodoptera frugiperda

Entity 5 Entity 5 polymer

Description description	Ragulator complex protein LAMTOR5
Molecular weight formula_weight	18178.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MEPGAGHLDGHRAGSPSLRQALCDGSAVMFSSKERGRCTVINFVPLEAPLRSTPRSRQVTEACGGEGRAVPLGSEPEWSVGGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 6 Entity 6 polymer

Description description	Ras-related GTP-binding protein A
Molecular weight formula_weight	39362.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSWSHPQFEKGGFDIDYKDDDDKMPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKHSLLMR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 7 Entity 7 polymer

Description description	Ras-related GTP-binding protein C
Molecular weight formula_weight	44758.3 kDa
Mutation mutation	D181N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GADSRMSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSSKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKVNGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRKAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 8 Entity 8 polymer

Description description	Sodium-coupled neutral amino acid transporter 9
Molecular weight formula_weight	13610.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GGTMANMNSDSRHLGTSEVDHERDPGPMNIQFEPSDLRSKRPFCIEPTNIVNVNHVIQRVSDHASAMNKRIHYYSRLTTPADKALIAPDHVVPAPEECYVYSPLGSAYKLQSYTEGYGKNTS

Source Source

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

Entity 9 Entity 9 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	;9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione ;
Molecular weight formula_weight	540.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	129553

CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state

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

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

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 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 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 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

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

Sodium-coupled neutral amino acid transporter 9

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

6wj2__assembly_1__model_1

6wj2__assembly_1__model_1 | I(q)

6wj2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer