[English] 日本語
Yorodumi
- EMDB-22337: Cryo-EM structure of ATP-bound fully inactive AMPK in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22337
TitleCryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody
Map dataStructure of AMPK with Fab and nanobody
Sample
  • Complex: AMPK complex with Fab and nanobody
    • Complex: AMPK
      • Protein or peptide: 5'-AMP-activated protein kinase catalytic subunit alpha-1
      • Protein or peptide: 5'-AMP-activated protein kinase subunit beta-2
      • Protein or peptide: 5'-AMP-activated protein kinase subunit gamma-1
      • Protein or peptide: Maltodextrin-binding protein
    • Complex: Fab, nanobody
      • Protein or peptide: Fab light chain
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Nanobody
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsAMPK / ATP / fully inactive / KD-displaced / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy / CAMKK-AMPK signaling cascade / cAMP-dependent protein kinase regulator activity / negative regulation of hepatocyte apoptotic process / regulation of vesicle-mediated transport / Carnitine shuttle / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / nucleotide-activated protein kinase complex / protein kinase regulator activity / regulation of vascular permeability / motor behavior / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / protein localization to lipid droplet / protein localization to membrane / cholesterol biosynthetic process / regulation of glycolytic process / cAMP-dependent protein kinase activity / : / cellular response to stress / response to caffeine / tau-protein kinase activity / AMP binding / lipid biosynthetic process / Macroautophagy / negative regulation of ferroptosis / fatty acid homeostasis / cellular response to ethanol / carbohydrate transmembrane transporter activity / response to UV / maltose binding / negative regulation of lipid catabolic process / maltose transport / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / maltodextrin transmembrane transport / energy homeostasis / cellular response to glucose starvation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of protein localization / Activation of AMPK downstream of NMDARs / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / response to gamma radiation / cellular response to nutrient levels / positive regulation of autophagy / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / protein localization to plasma membrane / cellular response to starvation / regulation of microtubule cytoskeleton organization / neuron cellular homeostasis / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / cellular response to xenobiotic stimulus / ADP binding / positive regulation of cholesterol biosynthetic process / regulation of circadian rhythm / response to estrogen / Wnt signaling pathway / tau protein binding / cellular response to hydrogen peroxide / positive regulation of T cell activation / autophagy / fatty acid biosynthetic process / glucose homeostasis / rhythmic process / positive regulation of cold-induced thermogenesis / outer membrane-bounded periplasmic space / cellular response to oxidative stress / spermatogenesis / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / ciliary basal body / response to hypoxia / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / nuclear speck / apical plasma membrane / endoplasmic reticulum lumen / negative regulation of gene expression / protein serine kinase activity / axon
Similarity search - Function
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin E-set / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Maltodextrin-binding protein / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsYan Y / Murkherjee S / Zhou XE / Xu TH / Xu HE / Kossiakoff AA / Melcher K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM117372 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM129436 United States
CitationJournal: Science / Year: 2021
Title: Structure of an AMPK complex in an inactive, ATP-bound state.
Authors: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna ...Authors: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna Radziwon / Abigail Ellis / Scott J Novick / Irving E Vega / Russell G Jones / Laurence J Miller / H Eric Xu / Patrick R Griffin / Anthony A Kossiakoff / Karsten Melcher /
Abstract: Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in ...Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in which the kinase activation loop (AL) is protected from protein phosphatases, thus keeping the AL in its active, phosphorylated state. At low AMP:ATP (adenosine triphosphate) ratios, ATP inhibits AMPK by increasing AL dynamics and accessibility. We developed conformation-specific antibodies to trap ATP-bound AMPK in a fully inactive, dynamic state and determined its structure at 3.5-angstrom resolution using cryo-electron microscopy. A 180° rotation and 100-angstrom displacement of the kinase domain fully exposes the AL. On the basis of the structure and supporting biophysical data, we propose a multistep mechanism explaining how adenine nucleotides and pharmacological agonists modulate AMPK activity by altering AL phosphorylation and accessibility.
History
DepositionJul 20, 2020-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jhh
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22337.png

Downloads & links

-
Map

FileDownload / File: emd_22337.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of AMPK with Fab and nanobody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 240 pix.
= 246.96 Å		1.03 Å/pix.
x 240 pix.
= 246.96 Å		1.03 Å/pix.
x 240 pix.
= 246.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04410703 - 0.081703946
Average (Standard dev.)0.00027798326 (±0.0022904756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 246.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z246.960246.960246.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0440.0820.000

-
Supplemental data

-
Sample components

+
Entire : AMPK complex with Fab and nanobody

EntireName: AMPK complex with Fab and nanobody
Components
  • Complex: AMPK complex with Fab and nanobody
    • Complex: AMPK
      • Protein or peptide: 5'-AMP-activated protein kinase catalytic subunit alpha-1
      • Protein or peptide: 5'-AMP-activated protein kinase subunit beta-2
      • Protein or peptide: 5'-AMP-activated protein kinase subunit gamma-1
      • Protein or peptide: Maltodextrin-binding protein
    • Complex: Fab, nanobody
      • Protein or peptide: Fab light chain
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Nanobody
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE

+
Supramolecule #1: AMPK complex with Fab and nanobody

SupramoleculeName: AMPK complex with Fab and nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Molecular weightTheoretical: 220 KDa

+
Supramolecule #2: AMPK

SupramoleculeName: AMPK / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Fab, nanobody

SupramoleculeName: Fab, nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#7
Source (natural)Organism: synthetic construct (others)

+
Macromolecule #1: 5'-AMP-activated protein kinase catalytic subunit alpha-1

MacromoleculeName: 5'-AMP-activated protein kinase catalytic subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.004395 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: VKIGHYILGD TLGVGTFGKV KVGKHELTGH KVAVKILNRQ KIRSLDVVGK IRREIQNLKL FRHPHIIKLY QVISTPSDIF MVMEYVSGG ELFDYICKNG RLDEKESRRL FQQILSGVDY CHRHMVVHRD LKPENVLLDA HMNAKIADFG LSNMMSDGEF L RTSCGSPN ...String:
VKIGHYILGD TLGVGTFGKV KVGKHELTGH KVAVKILNRQ KIRSLDVVGK IRREIQNLKL FRHPHIIKLY QVISTPSDIF MVMEYVSGG ELFDYICKNG RLDEKESRRL FQQILSGVDY CHRHMVVHRD LKPENVLLDA HMNAKIADFG LSNMMSDGEF L RTSCGSPN YAAPEVISGR LYAGPEVDIW SSGVILYALL CGTLPFDDDH VPTLFKKICD GIFYTPQYLN PSVISLLKHM LQ VDPMKRA TIKDIREHEW FKQDLPKYLF PEDPSYSSTM IDDEALKEVC EKFECSEEEV LSCLYNRNHQ DPLAVAYHLI IDN RRIMNE AKDFYLATSP PDSFLDDHHL TRPHPERVPF LVAETPRARH TLDELNPQKS KHQGVRKAKW HLGIRSQSRP NDIM AEVCR AIKQLDYEWK VVNPYYLRVR RKNPVTSTYS KMSLQLYQVD SRTYLLDFRS IDDELTPRPG SHTIEFFEMC ANLIK ILAQ

UniProtKB: 5'-AMP-activated protein kinase catalytic subunit alpha-1, 5'-AMP-activated protein kinase catalytic subunit alpha-1

+
Macromolecule #2: 5'-AMP-activated protein kinase subunit beta-2

MacromoleculeName: 5'-AMP-activated protein kinase subunit beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.38465 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MARPTVIRWS EGGKEVFISG SFNNWSTKIP LIKSHNDFVA ILDLPEGEHQ YKFFVDGQWV HDPSEPVVTS QLGTINNLIH VKKSDFEVF DALKLDSMES SETSCRDLSS SPPGPYGQEM YAFRSAARFK SPPILPPHLL QVILNKDTNI SCDPALLPEP N HVMLNHLY ...String:
MARPTVIRWS EGGKEVFISG SFNNWSTKIP LIKSHNDFVA ILDLPEGEHQ YKFFVDGQWV HDPSEPVVTS QLGTINNLIH VKKSDFEVF DALKLDSMES SETSCRDLSS SPPGPYGQEM YAFRSAARFK SPPILPPHLL QVILNKDTNI SCDPALLPEP N HVMLNHLY ALSIKDSVMV LSATHRYKKK YVTTLLYKPI

UniProtKB: 5'-AMP-activated protein kinase subunit beta-2

+
Macromolecule #3: 5'-AMP-activated protein kinase subunit gamma-1

MacromoleculeName: 5'-AMP-activated protein kinase subunit gamma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.833359 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MGSNNSVYTS FMKSHRCYDL IPTSSKLVVF DTSLQVKKAF FALVTNGVRA APLWDSKKQS FVGMLTITDF INILHRYYKS ALVQIYELE EHKIETWREV YLQDSFKPLV CISPNASLFD AVSSLIRNKI HRLPVIDPES GNTLYILTHK RILKFLKLFI T EFPKPEFM ...String:
MGSNNSVYTS FMKSHRCYDL IPTSSKLVVF DTSLQVKKAF FALVTNGVRA APLWDSKKQS FVGMLTITDF INILHRYYKS ALVQIYELE EHKIETWREV YLQDSFKPLV CISPNASLFD AVSSLIRNKI HRLPVIDPES GNTLYILTHK RILKFLKLFI T EFPKPEFM SKSLEELQIG TYANIAMVRT TTPVYVALGI FVQHRVSALP VVDEKGRVVD IYSKFDVINL AAEKTYNNLD VS VTKALQH RSHYFEGVLK CYLHETLETI INRLVEAEVH RLVVVDENDV VKGIVSLSDI LQALVLTGG

UniProtKB: 5'-AMP-activated protein kinase subunit gamma-1

+
Macromolecule #4: Maltodextrin-binding protein

MacromoleculeName: Maltodextrin-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 40.827125 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPAAAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT W PLIAADGG ...String:
MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPAAAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT W PLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NGPWAWSNID TS AVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYEEELAKDP RIA ATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTNAAEF

UniProtKB: Maltodextrin-binding protein

+
Macromolecule #5: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.212715 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSGPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSGPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

+
Macromolecule #6: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.483488 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NIYYYSIHWV RQAPGKGLEW VASIYPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYYPYFISY YSKMEAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NIYYYSIHWV RQAPGKGLEW VASIYPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYYPYFISY YSKMEAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHT

+
Macromolecule #7: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.414383 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMHHHHHHG ENLYFQGSQV QLQESGGGLV QPGGSLRLSC AASGRTISRY AMSWFRQAPG KEREFVAVA RRSGDGAFYA DSVQGRFTVS RDDAKNTVYL QMNSLKPEDT AVYYCAIDSD TFYSGSYDYW GQGTQVTVSS

+
Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #11: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 7659 / Average exposure time: 0.2 sec. / Average electron dose: 88.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1501939
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 360824
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

4rer

source_name: PDB, initial_model_type: experimental model

6cmo

source_name: PDB, initial_model_type: experimental model

6h16

source_name: PDB, initial_model_type: experimental model
Output model

PDB-7jhh:
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more