[English] 日本語
Yorodumi
- PDB-5iso: STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iso
TitleSTRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991)
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-2
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / ACTIVATOR / NON-PHOSPHORYLATION
Function / homology
Function and homology information


nail development / [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 / cAMP-dependent protein kinase regulator activity / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy ...nail development / [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 / cAMP-dependent protein kinase regulator activity / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy / regulation of carbon utilization / import into nucleus / nucleotide-activated protein kinase complex / negative regulation of hepatocyte apoptotic process / Carnitine shuttle / Energy dependent regulation of mTOR by LKB1-AMPK / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / cAMP-dependent protein kinase activity / regulation of glycolytic process / protein localization to lipid droplet / negative regulation of tubulin deacetylation / AMP binding / cholesterol biosynthetic process / Macroautophagy / lipid biosynthetic process / response to muscle activity / positive regulation of protein kinase activity / positive regulation of macroautophagy / regulation of macroautophagy / fatty acid homeostasis / cellular response to nutrient levels / cellular response to glucose starvation / energy homeostasis / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / negative regulation of TORC1 signaling / positive regulation of gluconeogenesis / positive regulation of autophagy / protein serine/threonine/tyrosine kinase activity / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / positive regulation of glycolytic process / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / regulation of circadian rhythm / ADP binding / autophagy / Wnt signaling pathway / cellular response to xenobiotic stimulus / cytoplasmic stress granule / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / regulation of cell cycle / nuclear speck / ciliary basal body / axon / negative regulation of gene expression / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / dendrite / chromatin binding / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, 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 ...PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, 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 / Ubiquitin-associated (UBA) domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Helicase, Ruva Protein; domain 3 / Immunoglobulin E-set / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-992 / ADENOSINE MONOPHOSPHATE / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-2 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsXiao, B. / Hubbard, J.A. / Gamblin, S.J.
CitationJournal: To Be Published
Title: STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991)
Authors: Xiao, B. / Hubbard, J.A. / Gamblin, S.J.
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2
B: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit gamma-1
C: 5'-AMP-activated protein kinase catalytic subunit alpha-2
D: 5'-AMP-activated protein kinase subunit beta-1
F: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,84716
Polymers264,9676
Non-polymers3,88010
Water1,44180
1
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2
B: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4238
Polymers132,4833
Non-polymers1,9405
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16640 Å2
ΔGint-100 kcal/mol
Surface area42190 Å2
MethodPISA
2
C: 5'-AMP-activated protein kinase catalytic subunit alpha-2
D: 5'-AMP-activated protein kinase subunit beta-1
F: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4238
Polymers132,4833
Non-polymers1,9405
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-97 kcal/mol
Surface area40810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.420, 129.390, 139.280
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AC

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-2 / AMPK subunit alpha-2 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-2 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase


Mass: 62408.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA2, AMPK, AMPK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P54646, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase

-
5'-AMP-activated protein kinase subunit ... , 2 types, 4 molecules BDEF

#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb


Mass: 32448.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: B 108 SER is phosphorylated, and renamed to SEP. THE 16 RESIDUES (MGLNDIFEAQKIEWHE) AT THE N-TERMINAL OF BETA-1 ARE EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 37626.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54619

-
Non-polymers , 4 types, 90 molecules

#4: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#5: Chemical ChemComp-992 / 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid


Mass: 431.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H18ClN3O3
#6: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.79 % / Description: rods like
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% PEG3350, 300 mM Guanidine in 100mM PIPES buffer at pH 7.2.
PH range: 7.0-7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.63→47.37 Å / Num. obs: 78641 / % possible obs: 99.9 % / Redundancy: 3.2 % / Net I/σ(I): 14.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
XSCALEdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CFE

4cfe


Resolution: 2.63→19.974 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2296 3884 4.95 %
Rwork0.1779 --
obs0.1804 78449 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.63→19.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14548 0 270 80 14898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615193
X-RAY DIFFRACTIONf_angle_d0.84720676
X-RAY DIFFRACTIONf_dihedral_angle_d15.4689003
X-RAY DIFFRACTIONf_chiral_restr0.0522346
X-RAY DIFFRACTIONf_plane_restr0.0062556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.6620.34811350.28292636X-RAY DIFFRACTION100
2.662-2.69560.36221590.26822709X-RAY DIFFRACTION100
2.6956-2.7310.34661310.26892654X-RAY DIFFRACTION100
2.731-2.76830.3121540.25882669X-RAY DIFFRACTION100
2.7683-2.80780.31951470.2582665X-RAY DIFFRACTION100
2.8078-2.84960.26681360.25242643X-RAY DIFFRACTION100
2.8496-2.8940.32371680.23152673X-RAY DIFFRACTION100
2.894-2.94130.28851400.22172650X-RAY DIFFRACTION100
2.9413-2.99180.24541450.21922689X-RAY DIFFRACTION100
2.9918-3.04610.34021370.22042675X-RAY DIFFRACTION100
3.0461-3.10440.26081330.22752682X-RAY DIFFRACTION100
3.1044-3.16760.25541130.2322715X-RAY DIFFRACTION100
3.1676-3.23620.28811220.21972684X-RAY DIFFRACTION100
3.2362-3.31110.29271300.21272691X-RAY DIFFRACTION100
3.3111-3.39350.2881360.21132681X-RAY DIFFRACTION100
3.3935-3.48480.21821330.20082670X-RAY DIFFRACTION100
3.4848-3.58680.27751380.19432698X-RAY DIFFRACTION100
3.5868-3.70180.23661540.18212608X-RAY DIFFRACTION99
3.7018-3.83330.23521440.17882665X-RAY DIFFRACTION99
3.8333-3.98560.22921610.16932646X-RAY DIFFRACTION99
3.9856-4.16540.22111420.15472647X-RAY DIFFRACTION99
4.1654-4.38280.23221370.15352655X-RAY DIFFRACTION99
4.3828-4.65420.18191390.14392650X-RAY DIFFRACTION98
4.6542-5.00830.17621120.13932688X-RAY DIFFRACTION98
5.0083-5.50270.20711340.15712621X-RAY DIFFRACTION98
5.5027-6.27720.23721400.17552657X-RAY DIFFRACTION97
6.2772-7.82870.22961000.16692634X-RAY DIFFRACTION96
7.8287-19.97420.15121640.13782610X-RAY DIFFRACTION95
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)
11.8567-0.45490.62548.2582-0.46151.5406-0.15630.0736-0.08520.13030.1799-0.3476-0.1925-0.1661-0.0340.46480.13550.04830.6466-0.01730.4159-44.1031-19.87084.4096
23.0018-0.00590.63433.576-0.77794.57440.0469-0.2986-0.62990.34980.29220.33180.0372-0.7625-0.30210.40140.1242-0.04350.6540.07810.6851-51.6259-39.222819.9759
35.14240.61310.75937.5026-1.39175.497-0.34270.67310.7918-1.6520.52750.10370.12660.2998-0.19870.8636-0.1549-0.09410.7614-0.01680.6152-24.6471-41.93497.9868
47.1986-1.0809-0.00152.2421-4.21029.98460.4022-1.087-0.14431.03180.05150.892-1.066-0.0346-0.51930.85240.0053-0.02860.7129-0.11690.6744-19.9192-58.254742.8087
55.39180.00050.52132.5867-0.1482.3877-0.2204-0.58950.78420.6470.0162-0.0293-0.7081-0.2710.19571.0430.2608-0.25290.6643-0.14030.622-27.6564-24.337645.0893
60.841-0.66452.37083.0912-1.62476.252-0.5314-0.30230.21980.55160.1984-0.407-0.7391-0.01230.29470.62310.1445-0.04660.612-0.01590.539-43.7456-0.09166.9132
75.1749-1.5192-0.98963.63660.60320.8869-0.1816-0.24180.02740.31760.1150.1887-0.3627-0.36750.05630.62060.1-0.13320.560.04060.4619-27.5724-38.973538.7046
85.7282-3.1767-5.32476.98483.26644.92770.1150.5771-0.1528-0.7322-0.41090.1761-0.7586-0.08240.16430.5609-0.0427-0.07910.5550.02950.4748-12.4719-46.136418.919
93.3133-3.00492.62097.7769-4.55726.0755-0.5716-0.43150.54250.8953-0.0053-0.8589-0.82270.3420.53070.67630.0558-0.22390.5608-0.01490.563-5.1984-44.623548.5082
103.9684-1.9135-1.85998.91043.78356.9255-0.17040.26720.3335-0.1383-0.0061-0.2059-0.20690.05950.20750.3795-0.0312-0.08830.41970.05860.4381-8.6746-45.843824.7624
114.0884-4.0976.10687.8367-5.62799.28490.69371.2488-1.0253-0.8847-0.1163-0.46911.82441.8795-0.39860.73760.24280.03271.1091-0.16760.74530.5284-65.272217.295
127.4636-0.5373-1.39483.73741.11676.3566-0.0282-0.0044-0.67390.29270.033-0.00760.8093-0.02590.02950.67810.0771-0.1210.41480.0640.4493-5.3121-65.688545.0444
133.0443-2.49250.34344.52080.59826.1941-0.01370.4163-0.84750.02080.1155-0.2641.21240.3326-0.15210.76080.1309-0.01280.5511-0.09280.6875-4.9698-66.850225.1996
142.97921.8274-0.19355.1584-2.61574.8702-0.28650.2799-0.10340.0677-0.0003-0.4780.5512-0.0360.29560.4985-0.1215-0.02450.5546-0.0710.515-9.0828-1.288963.7487
153.0033-0.3614-0.55672.9524-0.29943.4885-0.06660.46920.1778-0.12910.03460.2607-0.0278-0.52060.05550.3539-0.1009-0.03060.72010.04790.652-14.277916.016245.2813
161.7341.38930.92382.53460.43934.49380.681-0.1870.42571.470.0360.5712-0.2718-0.3875-0.79551.10430.20420.30720.87570.16220.975310.85923.488557.2276
179.8713-1.4062-1.57874.72484.70214.692-0.53710.7190.3544-0.80540.37951.054-1.8281-0.91890.0750.91230.17590.06470.95320.20670.844117.553937.415329.0299
186.60312.4161-0.4483.69320.31882.3597-0.29591.1559-1.17-0.48680.1672-0.19650.3904-0.37820.08140.6777-0.09440.14710.8881-0.2470.749114.15532.201124.906
191.7206-0.0401-2.28751.589-0.69462.6988-1.39770.2281-1.1379-0.42190.2905-0.51711.7428-0.44970.98021.4924-0.24780.38420.6925-0.08161.0832-8.9808-20.995364.1908
205.55161.9860.45624.2821.1583.4589-0.04370.70620.0345-0.35110.050.33120.0699-0.6882-0.00450.35540.03960.0770.73740.07410.492112.12816.955930.7531
217.29634.11794.4285.89072.93475.47310.2363-0.94370.13761.1452-0.3690.64120.7320.19520.20080.67290.13540.19430.80740.06320.449424.231726.224351.34
222.3283.7315-2.4587.9456-3.6035.3008-0.15350.4814-0.3757-0.37220.0732-0.73120.05910.44240.05740.38170.050.07620.7770.02540.49834.67624.308322.7471
233.32170.92290.29436.92511.26933.8210.0119-0.4613-0.17920.89220.0612-0.13570.00340.3254-0.04670.5040.14040.05290.66910.10080.39828.686226.122545.9983
244.14850.0743-3.60484.8859-0.03183.33781.4888-1.31131.32341.1888-0.04850.2332-1.95641.3382-1.50191.1775-0.26530.22021.3201-0.33470.865935.149346.937153.7052
255.52422.15482.33186.21852.82557.98190.03690.06690.8561-0.33730.06070.5018-1.2359-0.1105-0.05050.7490.09770.19320.61510.1760.574432.084945.249425.0313
268.72540.66942.54098.59543.01126.66570.5146-0.62721.4126-0.0789-0.1093-0.1087-0.99830.0855-0.42780.86960.02640.30750.5801-0.07990.606530.239646.590645.3644
276.95191.9947-3.5244.5431-3.68263.59411.00130.54591.3211.4949-0.5154-0.0896-1.52050.0115-0.64170.90850.10690.05620.75880.02850.7702-3.5259-56.725235.0894
289.98680.04366.39829.1273-4.47587.71531.0049-0.2175-0.5511-1.3704-0.0672-0.89191.38321.0576-0.88090.85210.01390.07490.7456-0.12240.623933.723337.176435.7347
297.85220.68883.80783.7437-1.45843.15360.60382.06950.67640.27730.1425-0.1981-0.4907-0.5703-0.33350.4620.16080.07770.76590.04210.5377-52.3559-25.9326.5292
304.7158-2.7096-1.62035.2945-0.22241.15890.6071-0.4331-0.3678-0.3430.0826-0.10840.8126-1.3481-0.50.3758-0.1863-0.04420.5915-0.01160.4962-16.51394.034659.7093
311.86353.1950.29385.55680.78271.1901-0.2211-1.41051.13220.85690.35610.5675-0.6685-0.5204-0.28450.69610.29280.26740.8532-0.19480.812-51.2102-10.97815.0351
327.0876-0.3936-3.85917.7511-4.10884.5115-0.26210.7604-1.5504-0.0699-0.3156-0.39093.755-3.03070.94460.9203-0.4894-0.04670.9108-0.02240.9313-15.9442-10.627663.0688
33-0.14160.0528-0.08490.2041-0.02760.0184-0.00270.0857-0.0808-0.02570.0028-0.07470.04440.06760.00920.30320.0248-0.11290.47230.04570.309-13.6473-10.20841.3848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 9:100)
2X-RAY DIFFRACTION2(chain A and resid 101:276)
3X-RAY DIFFRACTION3(chain A and resid 277:346)
4X-RAY DIFFRACTION4(chain A and resid 363:377)
5X-RAY DIFFRACTION5(chain A and resid 397:551)
6X-RAY DIFFRACTION6(chain B and resid 77:193)
7X-RAY DIFFRACTION7(chain B and resid 201:270)
8X-RAY DIFFRACTION8(chain E and resid 27:47)
9X-RAY DIFFRACTION9(chain E and resid 48:128)
10X-RAY DIFFRACTION10(chain E and resid 129:183)
11X-RAY DIFFRACTION11(chain E and resid 184:203)
12X-RAY DIFFRACTION12(chain E and resid 204:274)
13X-RAY DIFFRACTION13(chain E and resid 275:324)
14X-RAY DIFFRACTION14(chain C and resid 9:100)
15X-RAY DIFFRACTION15(chain C and resid 101:276)
16X-RAY DIFFRACTION16(chain C and resid 277:345)
17X-RAY DIFFRACTION17(chain C and resid 363:374)
18X-RAY DIFFRACTION18(chain C and resid 396:550)
19X-RAY DIFFRACTION19(chain D and resid 78:193)
20X-RAY DIFFRACTION20(chain D and resid 202:270)
21X-RAY DIFFRACTION21(chain F and resid 27:47)
22X-RAY DIFFRACTION22(chain F and resid 48:128)
23X-RAY DIFFRACTION23(chain F and resid 129:183)
24X-RAY DIFFRACTION24(chain F and resid 184:203)
25X-RAY DIFFRACTION25(chain F and resid 204:274)
26X-RAY DIFFRACTION26(chain F and resid 275:325)
27X-RAY DIFFRACTION27(chain G and resid 1:4)
28X-RAY DIFFRACTION28(chain H and resid 1:4)
29X-RAY DIFFRACTION29(chain I and resid 1:1)
30X-RAY DIFFRACTION30(chain J and resid 1:1)
31X-RAY DIFFRACTION31(chain K and resid 1:1)
32X-RAY DIFFRACTION32(chain L and resid 1:1)
33X-RAY DIFFRACTION33(chain W and resid 1:80)

+
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