[English] 日本語
Yorodumi
- PDB-8dgp: 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dgp
Title14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide
Components
  • 14-3-3 protein epsilon
  • Phosphorylated PEAK3 (pS69) peptide
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of heart rate by hormone / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / protein localization to endoplasmic reticulum / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / intracellular potassium ion homeostasis / Signaling by Hippo ...regulation of heart rate by hormone / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / protein localization to endoplasmic reticulum / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / intracellular potassium ion homeostasis / Signaling by Hippo / regulation of potassium ion transmembrane transport / negative regulation of calcium ion export across plasma membrane / protein phosphatase inhibitor activity / cytoplasmic pattern recognition receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of heart rate by cardiac conduction / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / regulation of cytosolic calcium ion concentration / HSF1 activation / potassium channel regulator activity / calcium channel inhibitor activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / signaling adaptor activity / calcium channel regulator activity / substantia nigra development / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / regulation of mitotic cell cycle / AURKA Activation by TPX2 / hippocampus development / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / mitochondrial membrane / cerebral cortex development / histone deacetylase binding / MHC class II protein complex binding / MAPK cascade / Regulation of PLK1 Activity at G2/M Transition / protein localization / melanosome / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / protein domain specific binding / protein heterodimerization activity / focal adhesion / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsRoy, M.J. / Hardy, J.M. / Lucet, I.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1144149 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling.
Authors: Roy, M.J. / Surudoi, M.G. / Kropp, A. / Hou, J. / Dai, W. / Hardy, J.M. / Liang, L.Y. / Cotton, T.R. / Lechtenberg, B.C. / Dite, T.A. / Ma, X. / Daly, R.J. / Patel, O. / Lucet, I.S.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein epsilon
B: 14-3-3 protein epsilon
C: 14-3-3 protein epsilon
D: 14-3-3 protein epsilon
E: Phosphorylated PEAK3 (pS69) peptide
F: Phosphorylated PEAK3 (pS69) peptide
G: Phosphorylated PEAK3 (pS69) peptide
H: Phosphorylated PEAK3 (pS69) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,20913
Polymers127,7968
Non-polymers4125
Water2,306128
1
A: 14-3-3 protein epsilon
B: 14-3-3 protein epsilon
E: Phosphorylated PEAK3 (pS69) peptide
F: Phosphorylated PEAK3 (pS69) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3109
Polymers63,8984
Non-polymers4125
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-59 kcal/mol
Surface area23500 Å2
MethodPISA
2
C: 14-3-3 protein epsilon
D: 14-3-3 protein epsilon
G: Phosphorylated PEAK3 (pS69) peptide
H: Phosphorylated PEAK3 (pS69) peptide


Theoretical massNumber of molelcules
Total (without water)63,8984
Polymers63,8984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-32 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.532, 155.532, 58.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w

-
Components

#1: Protein
14-3-3 protein epsilon / 14-3-3E


Mass: 29454.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62258
#2: Protein/peptide
Phosphorylated PEAK3 (pS69) peptide


Mass: 2494.931 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.35
Details: 2M ammonium sulfate, 0.1 M sodium bicine pH 9.35, 5% (v/v) 2-methyl-2,4,-pentandiol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.69→49.18 Å / Num. obs: 38786 / % possible obs: 99.6 % / Redundancy: 13.9 % / Biso Wilson estimate: 48.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.256 / Rrim(I) all: 0.266 / Net I/σ(I): 9.71
Reflection shellResolution: 2.69→2.86 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.786 / Num. unique obs: 82902 / CC1/2: 0.546 / Rrim(I) all: 1.854 / % possible all: 97.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.7 Å49.18 Å
Translation3.7 Å49.18 Å

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20161205data reduction
Aimless0.5.21data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BR9

2br9


Resolution: 2.7→49.18 Å / SU ML: 0.3637 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.6838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1985 5.15 %
Rwork0.1874 36526 -
obs0.1898 38511 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.89 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7505 0 23 128 7656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617642
X-RAY DIFFRACTIONf_angle_d0.770910362
X-RAY DIFFRACTIONf_chiral_restr0.04371199
X-RAY DIFFRACTIONf_plane_restr0.00691330
X-RAY DIFFRACTIONf_dihedral_angle_d3.71791080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.41031330.30242379X-RAY DIFFRACTION90.39
2.76-2.840.30291510.25192550X-RAY DIFFRACTION100
2.84-2.920.27131410.21982632X-RAY DIFFRACTION100
2.92-3.020.24521300.21622612X-RAY DIFFRACTION100
3.02-3.130.2531480.21122580X-RAY DIFFRACTION100
3.13-3.250.26991870.20612574X-RAY DIFFRACTION100
3.25-3.40.2861200.23612657X-RAY DIFFRACTION100
3.4-3.580.24831170.18032587X-RAY DIFFRACTION100
3.58-3.80.21121570.16572624X-RAY DIFFRACTION100
3.8-4.090.19341270.15472648X-RAY DIFFRACTION100
4.09-4.510.18311370.15632650X-RAY DIFFRACTION100
4.51-5.160.20851550.16822621X-RAY DIFFRACTION100
5.16-6.50.2821370.21192680X-RAY DIFFRACTION100
6.5-49.180.19771450.16432732X-RAY DIFFRACTION99.55
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)
13.3055577018-1.269209561611.745684603977.775069381390.4651286891551.595313100470.168731906479-0.372467129115-0.09638272401650.229465819593-0.1187522621160.311859967943-0.0498007271502-0.392710059856-0.1036065386780.381145977085-0.05571493609050.01043999701060.4214988804930.03504615956130.197158602907-83.979960383448.38012914212.36112511721
21.402104447830.363264344895-1.750471219030.5008450599810.9744600505936.616333483060.04119867398810.093600389463-0.0231866224494-0.274773890729-0.06724077463750.0450283692393-0.407138405350.278811780108-0.03983261254080.3910944251910.00999342033644-0.06221397679690.3946563319170.04205118042710.209085455764-70.834746008556.1068853731-16.1229713004
33.57511816507-0.6813724807371.316752404822.50050717725-0.0460471703572.19583859831-0.0933699413028-0.02697286820410.136121583132-0.1146819141150.01712990177-0.259367675451-0.1472908042780.2531596242580.07763062893370.343693812392-0.0540196425785-0.003957516255030.31973040278-0.03808092955420.196634042871-62.316278797962.28167917930.913322483379
46.609016266192.138947574971.927485304955.304175086351.706545622323.37476666511-0.588755862325-0.975493113936-0.9461390640230.390199293366-0.148986111644-0.1926582924231.013286130050.4389158710210.0887388829830.4551573778160.1495296072590.01968299021520.3311159939230.07279035911030.354831280595-53.516124145949.02824301755.58945123838
57.856808899911.933093135920.7368230966715.88547002934-0.2476832157783.1566409441-0.1803974718950.25792161736-0.0754764287268-0.2028672573880.1466666563570.342363839208-0.218492336056-0.1933362514150.006467249066640.419867155822-0.0308651908029-0.02101227830630.391725433241-0.01347720236950.208426514544-76.196871154244.340677605-32.8199204179
62.838104481150.305966161519-2.372590688152.28270006182-0.05167049423218.0800042598-0.317335353232-0.160819746511-0.6160346772930.19584443994-0.1941404588-0.2290337532940.517191206181-0.02941915859410.0669601033010.443489084706-0.00896135885991-0.08256409992520.3930766630740.0113948674560.299497091493-80.163095518433.085995738-14.8796378186
72.57427368252-0.0133650845007-1.274908464562.274645035751.071257677237.41939991325-0.178706942797-0.120433937261-0.1089463202320.200469638864-0.3095506332060.3367531677480.141652427254-0.5833683621310.09614252097410.365483240047-0.08122643855-0.003175649527960.2925647091490.03249999938840.366648105523-89.694032449835.3791657627-13.522140591
83.986901765911.494260580671.013166337344.31005265148-1.259894022231.4946290646-0.1511750977550.287785147958-0.578751093560.013302402969-0.150928478799-0.0612998616267-0.358943970324-0.085913631471-0.002961146437230.418049924408-0.0132521395382-0.07151131481460.301400539078-0.08334395300070.327751444424-83.157302412627.7500200258-30.4604733778
94.178537440791.47343054166-3.401321365173.35971011898-0.6349680950614.166439435460.1621395438980.36084685318-0.518477544474-0.3142489234320.02159831562210.3204586977630.238770687958-0.3811642401540.2056071714370.5283335702120.0474500104547-0.147739110620.372038829438-0.0996552192780.591462680019-86.849728097219.431608437-28.8743630428
105.84572447163-1.22307680365-0.6685522967163.351583932860.2145769223941.86704203481-0.0479541524482-0.465896034594-1.541180933670.4547246276310.149413031662-0.4527191540810.7849218928540.5725894173480.1854337855650.6024067987940.149840363447-0.1359274994380.419950291557-0.08609868229650.740234766491-74.927189659914.8576649458-26.1636501678
112.235141533491.57847329219-2.608449711346.529450567-1.650049887465.14797629471-0.21196331709-0.708346939406-0.500680248417-0.584237816325-0.278392828183-0.2751571248950.2697155008411.540822519490.3637314903310.5160964865320.137027927781-0.09526630050450.8050026050480.04084370788060.897787440543-64.876595915917.5186784535-25.4939413912
121.099269536981.994903383440.9591112237835.9739608268-1.849645674676.61816175601-0.0882707737911-0.259909189399-0.1535457395341.5490988069-0.2352012833521.575166146570.285939677658-0.0819585803010.4950592647730.67308474671-0.02315784368590.2092106934250.3079725483940.003139486683310.8508831838-56.706456860426.4574292145-1.73172742893
132.42829244422-0.860331742223-0.6464030836296.753946896693.205355322074.3946794068-0.0453511343215-0.127808151918-0.0135485367498-0.07563621158530.02526780493240.381573840715-0.3509549489520.166370322150.1083008052610.406971648839-0.008639198811180.05172168490840.3174185143240.0775953488320.593317963182-47.468790215721.6732346823-16.9644142836
142.3944622035-0.614075745013-0.1807204571777.348694707433.14505170285.20957784538-0.1825820377660.4668859659860.222642148307-0.7052688512170.01001283216280.396768267363-0.2387696249810.0539327761652-0.01805380081130.516191483708-0.06769443666010.1016758546440.3874315817320.09649650810120.575371089072-46.137787147626.4917473793-23.8611124766
152.6924875487-0.26090588217-0.8368663828831.2864152218-0.9267272421546.7271469260.1828269793630.134503092192-0.118207451931-0.153523734802-0.0872216881099-0.446676191015-0.0371338399662-0.246351771997-0.2274998090380.544869404735-0.03576763505940.06071969924710.3462514616910.06198240667010.792623908709-33.310859679533.7733076981-19.9850912338
162.58543089158-0.393462843217-1.46465773493.889036117921.164977621788.100995012040.0100832500384-0.758547064005-0.2833447955670.5176831296290.0160683270273-0.39621066980.1342866003290.845102284733-0.2154902418520.521594030963-0.069116390878-0.0906463747370.5474580053940.1475805328821.01895553787-24.22758921728.0655071875-11.0109657149
176.372907220710.879772556218-0.5143540161885.074049864440.955935514474.80277597904-0.4759189108130.358267543491-0.382651769197-1.363596804460.7379571846650.147437790858-0.1345213495880.261981943754-0.3538489089670.765270978693-0.0912618908659-0.09094107918110.384096969310.05131155848860.864300478944-53.91316966310.573100930748-27.7716388894
185.51963274883-0.853356290159-1.174530614640.170032656850.2896727346830.554159070253-0.1959245730440.449419333118-1.00720854013-0.7061358390530.41694378740.3597834060590.754762034899-0.5738637714650.006346075826790.756732105666-0.351276552771-0.1587793895280.605959268804-0.161571911911.46952108051-59.0694229867-12.4343608485-27.3473935884
191.820587965460.3181696830.1192988112085.36894678892.094917896213.95480491284-0.02911968082-0.281067816843-0.4227158410970.339487061925-0.1775064050141.06635947468-0.196609408232-0.0660329259211-0.2419882433010.6002458042660.005533298024110.1479347477940.3956254753480.2375954508981.07216448653-54.39509359543.91280857258-8.03584631759
201.830615470280.8911441926540.4488414013917.226549950782.876425914923.777878148570.0277191241055-0.1038401831190.2740307833550.4164066126870.03629880210231.45689081149-0.440542336582-0.282613411977-0.1788135200390.6635429338520.07275553710730.3000880462670.3900453070640.3410257631641.31709724211-63.41009875739.47458340618-5.00449419556
212.389216919770.07246020653640.2324140563342.05901826523-1.887934989151.765735492960.3016337402130.153718265461-0.505224570133-0.2088116449550.3604401496440.9857037461460.282886106927-0.349024970491-0.04427485641490.441181657453-0.04340737542730.0411730966830.4426607901180.3063371079431.534836217-60.5887198271-9.60450216697-12.8404040989
221.037569107620.678115785677-0.2001713982631.98218304771-0.3681221716491.533071029730.174548726526-0.00577242227891-0.1710854648910.1173828250980.3787866011150.8345645015860.0798382522119-0.4121345129690.823087125760.579150851816-0.05329195464070.159610813910.3353924181090.2845692008581.56479083451-62.6139128397-13.8010794464-4.45164299466
232.297814890510.177556286739-0.9209536703792.51919691097-1.900318158475.917343020910.175029331284-0.2273792936680.03495986978070.2625193620760.09786728545030.2758567257360.1293397178350.540258325378-0.2523976732430.5045400853930.02793839410210.05667106467010.4320515036320.2177451958861.13803635636-48.1847953354-17.2395657686-3.85593809241
241.82623833729-2.01988097884-2.22756426513.464025585962.483877802357.155621664050.0230405363038-0.05570714190790.167799310408-0.0926728140215-0.0243304933406-0.0265869790579-0.3439319450820.4403460291460.1247086245470.4403611616280.02269145363820.08931536349040.4093611351830.2025701784731.04150647874-40.9347590032-12.0023120163-2.28963767806
258.277416683685.10293879702-4.225983092274.85906714003-1.70067759515.3835097145-0.460827860174-0.901284107276-0.2893909402771.25731254559-0.977499569537-1.78789705399-0.955384895870.9428287329971.078499692960.6013950944870.0471260719046-0.130550762820.5534795618580.04587192526970.727080569111-72.432917657824.9937899869-19.2697437941
269.84772446722-3.43282875305-4.310402244944.26516223975-1.7206698055.27704816276-0.4951023184670.581303242817-1.34409314436-0.8478072825020.188653368137-0.0177719845840.523631683917-0.4733966872270.4920615055790.493447277548-0.03624823662340.01544786560350.405125509244-0.16532663920.315965444595-60.369710998150.0860470597-5.47445288478
275.57117834616-4.33664697929-3.960830813214.173738795745.387991713759.47006896302-0.3281378196790.277158079249-0.09016286216980.3143301585430.983166061382-1.023222210381.1641553558-0.283088774297-0.7520766474190.608437666797-0.0321107151560.1669643373360.4842267902240.07732239272271.24776640148-33.2767625620.5500692272-15.2280642227
280.5446141993291.33151885186-0.8580384977477.244513350731.590683043627.718265142180.867221940909-0.03291644252680.1283512485680.977282061170.424855615686-0.688928991621-0.76379441546-0.13662166833-0.4037517621960.584183956316-0.0841597179476-0.08393434606640.3566159304030.2446822638291.34226374829-46.500227775-4.26080096736-4.70028722634
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 38 )AA-2 - 381 - 41
22chain 'A' and (resid 39 through 106 )AA39 - 10642 - 109
33chain 'A' and (resid 107 through 204 )AA107 - 204110 - 207
44chain 'A' and (resid 205 through 233 )AA205 - 233208 - 236
55chain 'B' and (resid 2 through 38 )BD2 - 381 - 37
66chain 'B' and (resid 39 through 73 )BD39 - 7338 - 72
77chain 'B' and (resid 74 through 106 )BD74 - 10673 - 105
88chain 'B' and (resid 107 through 137 )BD107 - 137106 - 136
99chain 'B' and (resid 138 through 162 )BD138 - 162137 - 161
1010chain 'B' and (resid 163 through 204 )BD163 - 204162 - 203
1111chain 'B' and (resid 205 through 234 )BD205 - 234204 - 233
1212chain 'C' and (resid -1 through 17 )CE-1 - 171 - 19
1313chain 'C' and (resid 18 through 73 )CE18 - 7320 - 75
1414chain 'C' and (resid 74 through 138 )CE74 - 13876 - 140
1515chain 'C' and (resid 139 through 187 )CE139 - 187141 - 189
1616chain 'C' and (resid 188 through 234 )CE188 - 234190 - 236
1717chain 'D' and (resid 0 through 33 )DF0 - 331 - 34
1818chain 'D' and (resid 34 through 38 )DF34 - 3835 - 39
1919chain 'D' and (resid 39 through 73 )DF39 - 7340 - 74
2020chain 'D' and (resid 74 through 104 )DF74 - 10475 - 105
2121chain 'D' and (resid 105 through 137 )DF105 - 137106 - 138
2222chain 'D' and (resid 138 through 162 )DF138 - 162139 - 163
2323chain 'D' and (resid 163 through 213 )DF163 - 213164 - 214
2424chain 'D' and (resid 214 through 234 )DF214 - 234215 - 235
2525chain 'E' and (resid 66 through 72 )EG66 - 721 - 7
2626chain 'F' and (resid 65 through 73 )FH65 - 731 - 9
2727chain 'G' and (resid 65 through 72 )GI65 - 721 - 8
2828chain 'H' and (resid 65 through 72 )HJ65 - 721 - 8

+
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