7JHG

Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody

PDB DOI: https://doi.org/10.2210/pdb7JHG/pdb
EM Map EMD-22336: EMDB EMDataResource

Classification: TRANSFERASE/IMMUNE SYSTEM
Organism(s): Homo sapiens, Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2020-07-20 Released: 2021-07-21
Deposition Author(s): Yan, Y., Murkherjee, S., Zhou, X.E., Xu, T.H., Xu, H.E., Kossiakoff, A.A., Melcher, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.47 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 222.18 kDa
Atom Count: 13,457
Modelled Residue Count: 1,699
Deposited Residue Count: 1,972
Unique protein chains: 7

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-1	A	484	Homo sapiens	Mutation(s): 0 Gene Names: PRKAA1, AMPK1 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13131 (Homo sapiens) Explore Q13131 Go to UniProtKB: Q13131
PHAROS: Q13131 GTEx: ENSG00000132356
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13131
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-2	B	198	Homo sapiens	Mutation(s): 0 Gene Names: PRKAB2
UniProt & NIH Common Fund Data Resources
Find proteins for O43741 (Homo sapiens) Explore O43741 Go to UniProtKB: O43741
PHAROS: O43741 GTEx: ENSG00000131791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43741
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit gamma-1	C [auth G]	306	Homo sapiens	Mutation(s): 0 Gene Names: PRKAG1
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens) Explore P54619 Go to UniProtKB: P54619
PHAROS: P54619 GTEx: ENSG00000181929
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54619
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	D [auth M]	373	Escherichia coli K-12	Mutation(s): 0 Gene Names: malE
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEX9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	E [auth L]	215	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	F [auth H]	237	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	G [auth N]	159	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	H [auth D]	2		N/A	Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain J [auth G] MOL2 format, chain J [auth G]	J [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth G] Interactions & Density Focus chain J [auth G]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain K [auth G] MOL2 format, chain K [auth G]	K [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth G] Interactions & Density Focus chain K [auth G]
TAK (Subject of Investigation/LOI) Query on TAK Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine C₂₄ H₂₅ N₅ O XHBVYDAKJHETMP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain L [auth G] MOL2 format, chain L [auth G]	L [auth G]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain L [auth G] Interactions & Density Focus chain L [auth G]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	H [auth D]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.47 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM117372
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM129436

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2021-12-15
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

Prepare Data

Validate Data

Deposit Data

Help and Resources

7JHG

Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

Entity Groups

Sequence Annotations

Expand

Entity ID: 6

Entity Groups

Sequence Annotations

Expand

Entity ID: 7

Entity Groups

Sequence Annotations

Expand

Entity ID: 8

Glycosylation Resources

Entity ID: 8

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)