[English] 日本語
Yorodumi
- PDB-7jij: ATP-bound AMP-activated protein kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jij
TitleATP-bound AMP-activated protein kinase
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
  • Maltose/maltodextrin ABC transporter substrate-binding protein MalE
KeywordsSIGNALING PROTEIN / AMPK / activation / ATP-binding
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 / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation ...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 / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / cellular response to organonitrogen compound / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / protein kinase regulator activity / cellular response to ethanol / protein localization to lipid droplet / negative regulation of TOR signaling / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / lipid biosynthetic process / negative regulation of tubulin deacetylation / AMP-activated protein kinase activity / Macroautophagy / positive regulation of protein localization / tau-protein kinase activity / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / cellular response to nutrient levels / carbohydrate transmembrane transporter activity / positive regulation of protein kinase activity / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to glucose starvation / positive regulation of autophagy / energy homeostasis / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / response to UV / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / negative regulation of insulin receptor signaling pathway / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / response to gamma radiation / cellular response to glucose stimulus / tau protein binding / regulation of circadian rhythm / ADP binding / fatty acid biosynthetic process / autophagy / Wnt signaling pathway / cellular response to hydrogen peroxide / neuron cellular homeostasis / response to estrogen / cellular response to prostaglandin E stimulus / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / periplasmic space / non-specific serine/threonine protein kinase / response to hypoxia / protein kinase activity / nuclear speck / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / 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
alpha-maltose / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 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 speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.5 Å
AuthorsYan, Y. / Zhou, X.E. / Powell, K. / Xu, T. / Brunzelle, J.S. / Xu, H.X. / Melcher, K.
Funding support United States, 1items
OrganizationGrant numberCountry
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 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: Maltose/maltodextrin ABC transporter substrate-binding protein MalE
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-2
G: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8148
Polymers154,1904
Non-polymers1,6244
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-68 kcal/mol
Surface area60990 Å2
Unit cell
Length a, b, c (Å)126.688, 126.688, 332.384
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 2 types, 2 molecules MA

#1: Protein Maltose/maltodextrin ABC transporter substrate-binding protein MalE


Mass: 40827.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, GRW33_05015 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6D0N546
#2: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-1 / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


Mass: 56084.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase

-
5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BG

#3: Protein 5'-AMP-activated protein kinase subunit beta-2 / AMPK subunit beta-2


Mass: 22384.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43741
#4: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 34893.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54619

-
Sugars , 1 types, 1 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 3 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M tri-lithium citrate,10% w/v PEG3350, pH7.5,0.01 M barium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07823 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07823 Å / Relative weight: 1
ReflectionResolution: 5.5→49 Å / Num. obs: 10563 / % possible obs: 99.5 % / Redundancy: 9.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.298 / Net I/σ(I): 4.7
Reflection shellResolution: 5.5→6.15 Å / Rmerge(I) obs: 3.1 / Num. unique obs: 2894 / CC1/2: 0.323

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RER

4rer


Resolution: 5.5→24.901 Å / SU ML: 1.02 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3227 537 5.18 %
Rwork0.2492 9824 -
obs0.2531 10361 99.04 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 971.36 Å2 / Biso mean: 429.4287 Å2 / Biso min: 166.08 Å2
Refinement stepCycle: final / Resolution: 5.5→24.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9268 0 104 0 9372
Biso mean--370.02 --
Num. residues----1161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.5002-6.04660.44691170.36122390250798
6.0466-6.90520.43541580.31862378253699
6.9052-8.6390.32891400.28924672607100
8.639-24.9010.27161220.20172589271199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0023-0.003-0.0078-0.00390.01020.0004-0.021-0.01070.1233-0.0772-0.1801-0.12590.0243-0.156203.49270.26440.4433.3572-0.06513.5578-18.8099-13.1693-47.1454
20.0076-0.005-0.0141-0.00920.00810.00470.090.04630.0750.02790.13250.06260.07320.0014-03.31280.12010.24463.3693-0.19623.4958-35.4282-12.3954-52.1218
30.00450.0081-0.03150.01830.00610.00980.1825-0.13560.02810.10830.13640.00750.0814-0.021501.7924-0.20440.00511.6326-0.21792.1308-30.416-25.2554-62.6097
40.0083-0.0090.0021-0.0282-0.0030.00130.0094-0.07270.23650.0751-0.06410.1080.01710.1349-03.3967-0.1904-0.22363.0784-0.08163.0607-34.8182-44.4993-39.6997
5-0.0274-0.0519-0.0377-0.01090.09390.02240.627-0.2767-0.46890.1776-0.0456-0.46350.12720.2956-01.9982-0.3773-0.27742.5004-0.48232.3839-36.9162-34.2637-45.3852
6-0.0062-0.05270.04550.0443-0.001-0.00550.26570.0949-0.3849-0.00240.11390.3682-0.02540.0818-01.7567-0.1740.1872.64110.13762.0251-23.4971-27.4078-60.0842
7-0.0114-0.0161-0.0053-0.0052-0.0001-0.0016-0.05760.0437-0.0496-0.01880.1105-0.1658-0.01460.0141-02.75950.2440.1262.3569-0.41152.5083-51.2186-27.7729-41.9547
80.0202-0.0115-0.00330.01580.03310.01860.01050.2347-0.0516-0.0997-0.00140.1203-0.01580.007903.6726-0.91380.03442.4231-0.89853.5191-59.2283-13.0951-40.6526
9-0.00840.0134-0.0148-0.0077-0.00210.00020.4038-0.0349-0.0829-0.05820.3835-0.2622-0.04480.052103.5591-0.73651.08693.2705-0.49242.3179-55.6334-6.7283-28.4458
100.05860.02350.04390.0150.047-0.02520.1192-0.1045-0.4174-0.17970.161-0.50540.0566-0.182302.3818-0.26920.27331.8984-0.28143.3339-70.42292.5578-32.5562
110.0135-0.0021-0.0062-0.0149-0.0033-0.003-0.1128-0.0304-0.0988-0.0856-0.0935-0.0160.10540.010902.639-0.45630.03072.06170.25032.5456-54.368711.8303-29.4119
120.0166-0.00320.0103-0.02560.01490.0068-0.00530.0256-0.4361-0.1409-0.0885-0.05390.0553-0.0116-03.1905-0.8453-0.54722.2730.26922.4296-68.19820.3995-36.423
130.00260.004-0.00030.001-0.00180.0101-0.01650.0717-0.04120.0665-0.0646-0.04650.0095-0.0498-02.8976-0.1776-0.08492.48130.42422.4383-69.084322.783-24.982
14-0.05430.1435-0.0322-0.03880.00810.0665-0.1289-0.1861-0.52330.3625-0.04680.5638-0.13530.068203.0007-0.53530.52592.753-0.25572.6839-73.355716.9081-5.1361
150.0372-0.0326-0.03690.03030.00490.04340.31030.1049-0.0187-0.23810.4598-0.192-0.3054-0.167903.396-1.09740.40783.2137-0.64243.4533-35.819218.3719-11.2068
160.0035-0.0056-0.00110.00710.0026-0.0009-0.01390.0235-0.11710.0455-0.08580.0933-0.0750.015305.3886-0.0233-0.04295.3695-0.0715.4188-23.783213.7733-26.1176
170.00110.0088-0.00080.0046-0.0018-0.0022-0.03410.0088-0.01480.0234-0.0624-0.11070.00890.0182-01.6415-0.1327-0.39531.81760.22862.0668-30.746123.4982-33.3104
18-0.02480.0526-0.0431-0.02540.0327-0.01620.0248-0.22210.01960.1840.11530.2188-0.0325-0.1878-03.2732-0.6396-0.0512.7199-0.68653.5702-56.6924.1433-10.2012
190.0159-0.0083-0.03750.01440.03210.0945-0.01070.00180.0126-0.00990.00720.0258-0.0016-0.0055-0.00013.98670.01830.14653.886-0.02494.0226-60.992719.29162.9439
200.0277-0.0119-0.0360.00610.0170.05250.0219-0.0134-0.00570.0540.00010.0203-0.01190.0055-0.00033.01-0.0502-0.10433.0690.01753.215-58.52714.723-10.686
210.00490.0082-0.0089-0.00120.0129-0.0039-0.0538-0.01570.2520.05260.064-0.1533-0.0517-0.020702.3625-0.06660.3832.7144-0.69032.6284-45.708723.7852-6.3373
220.0115-0.02850.00810.0120.0023-0.0083-0.2440.15360.04460.0448-0.2418-0.00520.0311-0.0247-02.5602-0.20720.41362.319-0.2463.0014-49.379713.5233-3.4428
230.0055-0.00280.00360.00920.00030.00480.08-0.0385-0.15530.00610.04910.2039-0.0568-0.0335-02.8431-0.1949-0.44092.64240.06383.2266-45.378819.62640.9941
24-0.0547-0.0985-0.04950.06490.0699-0.02830.14560.1714-0.71420.23180.26070.6646-0.18260.1433-02.76660.3546-0.0882.1792-0.582.6125-51.477112.876210.4305
25-0.00790.00870.00670.00290.0257-0.0103-0.1913-0.0659-0.15870.002-0.0723-0.29530.05380.0543-03.241-0.11610.12223.6156-0.53793.0392-43.807431.552324.0933
260.00420.0167-0.02130.0125-0.03830.0258-0.28860.0845-0.01330.0297-0.1441-0.10890.2068-0.051204.0229-0.8566-0.37074.12970.2843.6858-42.179512.355119.3739
270.0130.01430.0006-0.00570.00080.0285-0.0192-0.0709-0.14510.00520.0285-0.32790.0572-0.2557-03.8759-0.75260.14133.59350.21373.5864-57.226.21613.0322
28-0.18230.2491-0.0525-0.03570.08440.09620.4664-0.36260.5557-0.0291-0.05460.3138-0.1566-0.049303.7779-1.0540.17552.8028-0.30162.7052-68.133620.013425.9456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'M' and (resid 7 through 44 )M7 - 44
2X-RAY DIFFRACTION2chain 'M' and (resid 45 through 84 )M45 - 84
3X-RAY DIFFRACTION3chain 'M' and (resid 85 through 120 )M85 - 120
4X-RAY DIFFRACTION4chain 'M' and (resid 121 through 166 )M121 - 166
5X-RAY DIFFRACTION5chain 'M' and (resid 167 through 275 )M167 - 275
6X-RAY DIFFRACTION6chain 'M' and (resid 276 through 335 )M276 - 335
7X-RAY DIFFRACTION7chain 'M' and (resid 336 through 373 )M336 - 373
8X-RAY DIFFRACTION8chain 'A' and (resid 13 through 56 )A13 - 56
9X-RAY DIFFRACTION9chain 'A' and (resid 57 through 89 )A57 - 89
10X-RAY DIFFRACTION10chain 'A' and (resid 90 through 156 )A90 - 156
11X-RAY DIFFRACTION11chain 'A' and (resid 157 through 193 )A157 - 193
12X-RAY DIFFRACTION12chain 'A' and (resid 194 through 240 )A194 - 240
13X-RAY DIFFRACTION13chain 'A' and (resid 241 through 260 )A241 - 260
14X-RAY DIFFRACTION14chain 'A' and (resid 261 through 371 )A261 - 371
15X-RAY DIFFRACTION15chain 'A' and (resid 372 through 550 )A372 - 550
16X-RAY DIFFRACTION16chain 'B' and (resid 186 through 195 )B186 - 195
17X-RAY DIFFRACTION17chain 'B' and (resid 196 through 205 )B196 - 205
18X-RAY DIFFRACTION18chain 'B' and (resid 206 through 225 )B206 - 225
19X-RAY DIFFRACTION19chain 'B' and (resid 226 through 230 )B226 - 230
20X-RAY DIFFRACTION20chain 'B' and (resid 231 through 235 )B231 - 235
21X-RAY DIFFRACTION21chain 'B' and (resid 236 through 249 )B236 - 249
22X-RAY DIFFRACTION22chain 'B' and (resid 250 through 262 )B250 - 262
23X-RAY DIFFRACTION23chain 'B' and (resid 263 through 272 )B263 - 272
24X-RAY DIFFRACTION24chain 'G' and (resid 25 through 87 )G25 - 87
25X-RAY DIFFRACTION25chain 'G' and (resid 88 through 113 )G88 - 113
26X-RAY DIFFRACTION26chain 'G' and (resid 114 through 137 )G114 - 137
27X-RAY DIFFRACTION27chain 'G' and (resid 138 through 179 )G138 - 179
28X-RAY DIFFRACTION28chain 'G' and (resid 180 through 324 )G180 - 324

+
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