8p4o

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx

Method: ELECTRON MICROSCOPY

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

Chaperonin GroEL

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Co-chaperonin GroES × 7 （P0A6F9） S-adenosylmethionine synthase × 1 （P0A817） ADENOSINE-5'-DIPHOSPHATE × 7 MAGNESIUM ION × 7 BERYLLIUM TRIFLUORIDE ION × 7 POTASSIUM ION × 7 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CH60_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–547； UniProt 2–548 Author chain B； PDBConstruct 1–547； UniProt 2–548 Author chain C； PDBConstruct 1–547； UniProt 2–548 Author chain D； PDBConstruct 1–547； UniProt 2–548 Author chain E； PDBConstruct 1–547； UniProt 2–548 Author chain F； PDBConstruct 1–547； UniProt 2–548 Author chain G； PDBConstruct 1–547； UniProt 2–548

Co-chaperonin GroES

Escherichia coli

UniProt P0A6F9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Chaperonin GroEL × 7 （P0A6F5） S-adenosylmethionine synthase × 1 （P0A817） ADENOSINE-5'-DIPHOSPHATE × 7 MAGNESIUM ION × 7 BERYLLIUM TRIFLUORIDE ION × 7 POTASSIUM ION × 7 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CH10_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain O； PDBConstruct 1–97； UniProt 1–97 Author chain P； PDBConstruct 1–97； UniProt 1–97 Author chain Q； PDBConstruct 1–97； UniProt 1–97 Author chain R； PDBConstruct 1–97； UniProt 1–97 Author chain S； PDBConstruct 1–97； UniProt 1–97 Author chain T； PDBConstruct 1–97； UniProt 1–97 Author chain U； PDBConstruct 1–97； UniProt 1–97

S-adenosylmethionine synthase

Escherichia coli

UniProt P0A817

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Chaperonin GroEL × 7 （P0A6F5） Co-chaperonin GroES × 7 （P0A6F9） ADENOSINE-5'-DIPHOSPHATE × 7 MAGNESIUM ION × 7 BERYLLIUM TRIFLUORIDE ION × 7 POTASSIUM ION × 7 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	METK_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 1； PDBConstruct 1–384； UniProt 1–384

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	8p4o
Deposition date deposition_date	2023-05-23
Structure title title	CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx
Keywords keywords	Chaperonin, Folding cage, proteostasis, heat shock, ATPase, CHAPERONE; CHAPERONE
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.

8p4o__assembly_1__model_1

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

Download this curve (.dat)

8p4o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8p4o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.28 Å
Rg (electron density)	55.52 Å
Total Rg	55.81 Å
Atom count	34584
Residues	4712
Excluded volume	618560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8p4o__assembly_1__model_1`	pentadecameric （15）	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 (8)

Entity 1 Entity 1 polymer

Description description	Chaperonin GroEL
Molecular weight formula_weight	57260.5 kDa
EC 编号 ec_number	5.6.1.7
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	34605

AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGGMGGMGGMM

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Co-chaperonin GroES
Molecular weight formula_weight	10400.9 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,S,T,U

MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	S-adenosylmethionine synthase
Molecular weight formula_weight	41998.5 kDa
EC 编号 ec_number	2.5.1.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

MAKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQGLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGHFGREHFPWEKTDKAQLLRDAAGLK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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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	triclinic

Resolution resolution	3.04 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	454545

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx

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

Chaperonin GroEL

State in the Current Structure

Other States of the Same Protein in the Database

Co-chaperonin GroES

State in the Current Structure

Other States of the Same Protein in the Database

S-adenosylmethionine synthase

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

8p4o__assembly_1__model_1

8p4o__assembly_1__model_1 | I(q)

8p4o__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx

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

Chaperonin GroEL

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Co-chaperonin GroES

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

S-adenosylmethionine synthase

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

8p4o__assembly_1__model_1

8p4o__assembly_1__model_1 | I(q)

8p4o__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)