9lvj

Cryo-EM structure of Sestrin2 bound human GATOR2 complex

Method: ELECTRON MICROSCOPY

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

GATOR2 complex protein MIOS

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	GATOR2 complex protein WDR24 × 2 （Q96S15） GATOR2 complex protein WDR59 × 2 （Q6PJI9） Isoform B of Nucleoporin SEH1 × 6 （Q96EE3） Protein SEC13 homolog × 2 （P55735） Sestrin-2 × 2 （P58004） ZINC ION × 32	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MIOS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–875； UniProt 1–875 Author chain B； PDBConstruct 1–875； UniProt 1–875 Author chain K； PDBConstruct 1–875； UniProt 1–875 Author chain L； PDBConstruct 1–875； UniProt 1–875

GATOR2 complex protein WDR24

Homo sapiens

UniProt Q96S15

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	GATOR2 complex protein MIOS × 4 （Q9NXC5） GATOR2 complex protein WDR59 × 2 （Q6PJI9） Isoform B of Nucleoporin SEH1 × 6 （Q96EE3） Protein SEC13 homolog × 2 （P55735） Sestrin-2 × 2 （P58004） ZINC ION × 32	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WDR24_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–790； UniProt 1–790 Author chain M； PDBConstruct 1–790； UniProt 1–790

GATOR2 complex protein WDR59

Homo sapiens

UniProt Q6PJI9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	GATOR2 complex protein MIOS × 4 （Q9NXC5） GATOR2 complex protein WDR24 × 2 （Q96S15） Isoform B of Nucleoporin SEH1 × 6 （Q96EE3） Protein SEC13 homolog × 2 （P55735） Sestrin-2 × 2 （P58004） ZINC ION × 32	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WDR59_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–974； UniProt 1–974 Author chain N； PDBConstruct 1–974； UniProt 1–974

Isoform B of Nucleoporin SEH1

Homo sapiens

UniProt Q96EE3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	GATOR2 complex protein MIOS × 4 （Q9NXC5） GATOR2 complex protein WDR24 × 2 （Q96S15） GATOR2 complex protein WDR59 × 2 （Q6PJI9） Protein SEC13 homolog × 2 （P55735） Sestrin-2 × 2 （P58004） ZINC ION × 32	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEH1_HUMAN
Isoform	Q96EE3-1
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–421； UniProt 1–421 Author chain F； PDBConstruct 1–421； UniProt 1–421 Author chain G； PDBConstruct 1–421； UniProt 1–421 Author chain O； PDBConstruct 1–421； UniProt 1–421 Author chain P； PDBConstruct 1–421； UniProt 1–421 Author chain Q； PDBConstruct 1–421； UniProt 1–421

Protein SEC13 homolog

Homo sapiens

UniProt P55735

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	GATOR2 complex protein MIOS × 4 （Q9NXC5） GATOR2 complex protein WDR24 × 2 （Q96S15） GATOR2 complex protein WDR59 × 2 （Q6PJI9） Isoform B of Nucleoporin SEH1 × 6 （Q96EE3） Sestrin-2 × 2 （P58004） ZINC ION × 32	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC13_HUMAN
Isoform	P55735-3
PDB entities	5
Chains and sequence ranges	Author chain H； PDBConstruct 1–368； UniProt 1–368 Author chain R； PDBConstruct 1–368； UniProt 1–368

Sestrin-2

Homo sapiens

UniProt P58004

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	GATOR2 complex protein MIOS × 4 （Q9NXC5） GATOR2 complex protein WDR24 × 2 （Q96S15） GATOR2 complex protein WDR59 × 2 （Q6PJI9） Isoform B of Nucleoporin SEH1 × 6 （Q96EE3） Protein SEC13 homolog × 2 （P55735） ZINC ION × 32	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SESN2_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain U； PDBConstruct 1–480； UniProt 1–480 Author chain V； PDBConstruct 1–480； UniProt 1–480

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	9lvj
Deposition date deposition_date	2025-02-12
Last revision last_revision	2025-08-13
Structure title title	Cryo-EM structure of Sestrin2 bound human GATOR2 complex
Keywords keywords	Amino acid sensor, 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.

9lvj__assembly_1__model_1

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

Download this curve (.dat)

9lvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9lvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	96.25 Å
Rg (electron density)	97.52 Å
Total Rg	97.71 Å
Atom count	47837
Residues	7630
Excluded volume	817680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9lvj__assembly_1__model_1`	octadecameric （18）	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 (7)

Entity 1 Entity 1 polymer

Description description	GATOR2 complex protein MIOS
Molecular weight formula_weight	98700.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,K,L
Atom count atom_count	47837

MSGTKPDILWAPHHVDRFVVCDSELSLYHVESTVNSELKAGSLRLSEDSAATLLSINSDTPYMKCVAWYLNYDPECLLAVGQANGRVVLTSLGQDHNSKFKDLIGKEFVPKHARQCNTLAWNPLDSNWLAAGLDKHRADFSVLIWDICSKYTPDIVPMEKVKLSAGETETTLLVTKPLYELGQNDACLSLCWLPRDQKLLLAGMHRNLAIFDLRNTSQKMFVNTKAVQGVTVDPYFHDRVASFYEGQVAIWDLRKFEKPVLTLTEQPKPLTKVAWCPTRTGLLATLTRDSNIIRLYDMQHTPTPIGDETEPTIIERSVQPCDNYIASFAWHPTSQNRMIVVTPNRTMSDFTVFERISLAWSPITSLMWACGRHLYECTEEENDNSLEKDIATKMRLRALSRYGLDTEQVWRNHILAGNEDPQLKSLWYTLHFMKQYTEDMDQKSPGNKGSLVYAGIKSIVKSSLGMVESSRHNWSGLDKQSDIQNLNEERILALQLCGWIKKGTDVDVGPFLNSLVQEGEWERAAAVALFNLDIRRAIQILNEGASSEKGDLNLNVVAMALSGYTDEKNSLWREMCSTLRLQLNNPYLCVMFAFLTSETGSYDGVLYENKVAVRDRVAFACKFLSDTQLNRYIEKLTNEMKEAGNLEGILLTGLTKDGVDLMESYVDRTGDVQTASYCMLQGSPLDVLKDERVQYWIENYRNLLDAWRFWHKRAEFDIHRSKLDPSSKPLAQVFVSCNFCGKSISYSCSAVPHQGRGFSQYGVSGSPTKSKVTSCPGCRKPLPRCALCLINMGTPVSSCPGGTKSDEKVDLSKDKKLAQFNNWFTWCHNCRHGGHAGHMLSWFRDHAECPVSACTCKCMQLDTTGNLVPAETVQP

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 2 Entity 2 polymer

Description description	GATOR2 complex protein WDR24
Molecular weight formula_weight	88327.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEKMSRVTTALGGSVLTGRTMHCHLDAPANAISVCRDAAQVVVAGRSIFKIYAIEEEQFVEKLNLRVGRKPSLNLSCADVVWHQMDENLLATAATNGVVVTWNLGRPSRNKQDQLFTEHKRTVNKVCFHPTEAHVLLSGSQDGFMKCFDLRRKDSVSTFSGQSESVRDVQFSIRDYFTFASTFENGNVQLWDIRRPDRCERMFTAHNGPVFCCDWHPEDRGWLATGGRDKMVKVWDMTTHRAKEMHCVQTIASVARVKWRPECRHHLATCSMMVDHNIYVWDVRRPFVPAAMFEEHRDVTTGIAWRHPHDPSFLLSGSKDSSLCQHLFRDASQPVERANPEGLCYGLFGDLAFAAKESLVAAESGRKPYTGDRRHPIFFKRKLDPAEPFAGLASSALSVFETEPGGGGMRWFVDTAERYALAGRPLAELCDHNAKVARELGRNQVAQTWTMLRIIYCSPGLVPTANLNHSVGKGGSCGLPLMNSFNLKDMAPGLGSETRLDRSKGDARSDTVLLDSSATLITNEDNEETEGSDVPADYLLGDVEGEEDELYLLDPEHAHPEDPECVLPQEAFPLRHEIVDTPPGPEHLQDKADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSRLPPDFFGVLVRDMLHFYAEQGDVQMAVSVLIVLGERVRKDIDEQTQEHWYTSYIDLLQRFRLWNVSNEVVKLSTSRAVSCLNQASTTLHVNCSHCKRPMSSRGWVCDRCHRCASMCAVCHHVVKGLFVWCQGCSHGGHLQHIMKWLEGSSHCPAGCGHLCEYS

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 3 Entity 3 polymer

Description description	GATOR2 complex protein WDR59
Molecular weight formula_weight	109938.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAARWSSENVVVEFRDSQATAMSVDCLGQHAVLSGRRFLYIVNLDAPFEGHRKISRQSKWDIGAVQWNPHDSFAHYFAASSNQRVDLYKWKDGSGEVGTTLQGHTRVISDLDWAVFEPDLLVTSSVDTYIYIWDIKDTRKPTVALSAVAGASQVKWNKKNANCLATSHDGDVRIWDKRKPSTAVEYLAAHLSKIHGLDWHPDSEHILATSSQDNSVKFWDYRQPRKYLNILPCQVPVWKARYTPFSNGLVTVMVPQLRRENSLLLWNVFDLNTPVHTFVGHDDVVLEFQWRKQKEGSKDYQLVTWSRDQTLRMWRVDSQMQRLCANDILDGVDEFIESISLLPEPEKTLHTEDTDHQHTASHGEEEALKEDPPRNLLEERKSDQLGLPQTLQQEFSLINVQIRNVNVEMDAADRSCTVSVHCSNHRVKMLVKFPAQYPNNAAPSFQFINPTTITSTMKAKLLKILKDTALQKVKRGQSCLEPCLRQLVSCLESFVNQEDSASSNPFALPNSVTPPLPTFARVTTAYGSYQDANIPFPRTSGARFCGAGYLVYFTRPMTMHRAVSPTEPTPRSLSALSAYHTGLIAPMKIRTEAPGNLRLYSGSPTRSEKEQVSISSFYYKERKSRRWKSKREGSDSGNRQIKAAGKVIIQDIACLLPVHKSLGELYILNVNDIQETCQKNAASALLVGRKDLVQVWSLATVATDLCLGPKSDPDLETPWARHPFGRQLLESLLAHYCRLRDVQTLAMLCSVFEAQSRPQGLPNPFGPFPNRSSNLVVSHSRYPSFTSSGSCSSMSDPGLNTGGWNIAGREAEHLSSPWGESSPEELRFGSLTYSDPRERERDQHDKNKRLLDPANTQQFDDFKKCYGEILYRWGLREKRAEVLKFVSCPPDPHKGIEFGVYCSHCRSEVRGTQCAICKGFTFQCAICHVAVRGSSNFCLTCGHGGHTSHMMEWFRTQEVCPTGCGCHCLLESTF

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 4 Entity 4 polymer

Description description	Isoform B of Nucleoporin SEH1
Molecular weight formula_weight	46636.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,O,P,Q

MFVARSIAADHKDLIHDVSFDFHGRRMATCSSDQSVKVWDKSESGDWHCTASWKTHSGSVWRVTWAHPEFGQVLASCSFDRTAAVWEEIVGESNDKLRGQSHWVKRTTLVDSRTSVTDVKFAPKHMGLMLATCSADGIVRIYEAPDVMNLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMIAVGSDDSSPNAMAKVQIFEYNENTRKYAKAETLMTVTDPVHDIAFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHIVAQFDNHNSQVWRVSWNITGTVLASSGDDGCVRLWKANYMDNWKCTGILKGNGSPVNGSSQQGTSNPSLGSTIPSLQNSLNGSSAGRYFFTPLDSPRAGSRWSSYAQLLPPPPPPLVEHSCDADTANLQYPHPRRRYLSRPLNPLPENEGI

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 5 Entity 5 polymer

Description description	Protein SEC13 homolog
Molecular weight formula_weight	40791.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,R

MREPVLTWCVPLELLCSHPLPLSAFLKSQVKLYTYRACAGKDEMGKMVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMYGNILASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSASVTEGQQNEQ

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 6 Entity 6 polymer

Description description	Sestrin-2
Molecular weight formula_weight	54560.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V

MIVADSECRAELKDYLRFAPGGVGDSGPGEEQRESRARRGPRGPSAFIPVEEVLREGAESLEQHLGLEALMSSGRVDNLAVVMGLHPDYFTSFWRLHYLLLHTDGPLASSWRHYIAIMAAARHQCSYLVGSHMAEFLQTGGDPEWLLGLHRAPEKLRKLSEINKLLAHRPWLITKEHIQALLKTGEHTWSLAELIQALVLLTHCHSLSSFVFGCGILPEGDADGSPAPQAPTPPSEQSSPPSRDPLNNSGGFESARDVEALMERMQQLQESLLRDEGTSQEEMESRFELEKSESLLVTPSADILEPSPHPDMLCFVEDPTFGYEDFTRRGAQAPPTFRAQDYTWEDHGYSLIQRLYPEGGQLLDEKFQAAYSLTYNTIAMHSGVDTSVLRRAIWNYIHCVFGIRYDDYDYGEVNQLLERNLKVYIKTVACYPEKTTRRMYNLFWRHFRHSEKVHVNLLLLEARMQAALLYALRAITRYMT

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 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	32

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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	3.820 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.82 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	190375

Cryo-EM structure of Sestrin2 bound human GATOR2 complex

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

GATOR2 complex protein MIOS

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GATOR2 complex protein WDR24

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GATOR2 complex protein WDR59

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Isoform B of Nucleoporin SEH1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein SEC13 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sestrin-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9lvj__assembly_1__model_1

9lvj__assembly_1__model_1 | I(q)

9lvj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer