2qlv

Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1

Method: X-RAY DIFFRACTION

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

Carbon catabolite derepressing protein kinase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein SIP2 × 1 （P34164） Nuclear protein SNF4 × 1 （P12904） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Protein SIP2 × 1 （P34164） Nuclear protein SNF4 × 1 （P12904） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNF1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 460–630 Author chain D； PDBConstruct 1–171； UniProt 460–630

Protein SIP2

Saccharomyces cerevisiae

UniProt P34164

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Carbon catabolite derepressing protein kinase × 1 （P06782） Nuclear protein SNF4 × 1 （P12904） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Carbon catabolite derepressing protein kinase × 1 （P06782） Nuclear protein SNF4 × 1 （P12904） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIP2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–252； UniProt 161–412 Author chain E； PDBConstruct 1–252； UniProt 161–412

Nuclear protein SNF4

Saccharomyces cerevisiae

UniProt P12904

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Carbon catabolite derepressing protein kinase × 1 （P06782） Protein SIP2 × 1 （P34164） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Carbon catabolite derepressing protein kinase × 1 （P06782） Protein SIP2 × 1 （P34164） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNF4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–315； UniProt 7–321 Author chain F； PDBConstruct 1–315； UniProt 7–321

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	2qlv
Deposition date deposition_date	2007-07-13
Structure title title	Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1
Keywords keywords	;heterotrimer, ATP-binding, Carbohydrate metabolism, Kinase, Membrane, Nucleotide-binding, Nucleus, Phosphorylation, Serine/threonine-protein kinase, Transferase, Lipoprotein, Myristate, CBS domain, Transcription, Transcription regulation, Transferase-Protein binding COMPLEX ;; Transferase/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.

2qlv__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2qlv__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qlv__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.40 Å
Rg (electron density)	27.38 Å
Total Rg	28.18 Å
Atom count	4668
Residues	583
Excluded volume	84318 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qlv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qlv__assembly_2__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	Carbon catabolite derepressing protein kinase
Molecular weight formula_weight	19596.3 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	9579

YKEEDSTVSILPTSLPQIHRANMLAQGSPAASKISPLVTKKSKTRWHFGIRSRSYPLDVMGEIYIALKNLGAEWAKPSEEDLWTIKLRWKYDIGNKTNTNEKIPDLMKMVIQLFQIETNNYLVDFKFDGWESSYGDDTTVSNISEDEMSTFSAYPFLHLTTKLIMELAVNS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein SIP2
Molecular weight formula_weight	28956.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SLMVPVEIRWQQGGSKVYVTGSFTKWRKMIGLIPDSDNNGSFHVKLRLLPGTHRFRFIVDNELRVSDFLPTATDQMGNFVNYIEVRQPEKNPTNEKIRSKEADSMRPPTSDRSSIALQIGKDPDDFGDGYTRFHEDLSPRPPLEYTTDIPAVFTDPSVMERYYYTLDRQQSNTDTSWLTPPQLPPQLENVILNKYYATQDQFNENNSGALPIPNHVVLNHLVTSSIKHNTLCVASIVRYKQKYVTQILYTPI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nuclear protein SNF4
Molecular weight formula_weight	35625.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SQEKVSIEQQLAVESIRKFLNSKTSYDVLPVSYRLIVLDTSLLVKKSLNVLLQNSIVSAPLWDSKTSRFAGLLTTTDFINVIQYYFSNPDKFELVDKLQLDGLKDIERALGVDQLDTASIHPSRPLFEACLKMLESRSGRIPLIDQDEETHREIVVSVLTQYRILKFVALNCRETHFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGIYNDLSLSVGEALMRRSDDFEGVYTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
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	111

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2qlva1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.6 — KA1-like
Family Family family	d.129.6.2 — Ssp2 C-terminal domain-like

Domain ID domain_id	d2qlvb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.21 — AMPK-beta glycogen binding domain-like

Domain ID domain_id	d2qlvb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.353 — AMPKBI-like
Superfamily Superfamily superfamily	d.353.1 — AMPKBI-like
Family Family family	d.353.1.1 — AMPKBI-like

Domain ID domain_id	d2qlvc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qlvc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qlvd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.6 — KA1-like
Family Family family	d.129.6.2 — Ssp2 C-terminal domain-like

Domain ID domain_id	d2qlve1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.21 — AMPK-beta glycogen binding domain-like

Domain ID domain_id	d2qlve2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.353 — AMPKBI-like
Superfamily Superfamily superfamily	d.353.1 — AMPKBI-like
Family Family family	d.353.1.1 — AMPKBI-like

Domain ID domain_id	d2qlvf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qlvf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

CATH v4.4 (10 domains)

Domain ID domain_id	2qlvA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	80 — Kinase associated domain 1, KA1

Domain ID domain_id	2qlvB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qlvB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	290 —

Domain ID domain_id	2qlvC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2qlvC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2qlvD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	80 — Kinase associated domain 1, KA1

Domain ID domain_id	2qlvE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2qlvE02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	290 —

Domain ID domain_id	2qlvF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2qlvF02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

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Unit-cell length a length_a	112.330 Å
Unit-cell length b length_b	81.840 Å
Unit-cell length c length_c	174.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.540 Å
R factor r_factor	—
R_work r_work	0.2390
R_free r_free	0.2990

Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1

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

Carbon catabolite derepressing protein kinase

State in the Current Structure

Other States of the Same Protein in the Database

Protein SIP2

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear protein SNF4

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

2qlv__assembly_2__model_1

2qlv__assembly_2__model_1 | I(q)

2qlv__assembly_2__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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1

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

Carbon catabolite derepressing protein kinase

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 SIP2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear protein SNF4

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

2qlv__assembly_2__model_1

2qlv__assembly_2__model_1 | I(q)

2qlv__assembly_2__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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)