[English] 日本語
Yorodumi
- PDB-6twz: 14-3-3 sigma complexed with a phosphorylated 16E6 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6twz
Title14-3-3 sigma complexed with a phosphorylated 16E6 peptide
Components
  • 14-3-3 protein sigma
  • phosphorylated 16E6 peptide
KeywordsPEPTIDE BINDING PROTEIN / phosphorylation / motif / 14-3-3 protein
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
Similarity search - Domain/homology
D(-)-TARTARIC ACID / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGogl, G. / Cousido-Siah, A. / Sluchanko, N.N. / Trave, G.
CitationJournal: Structure / Year: 2020
Title: Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study.
Authors: Gogl, G. / Jane, P. / Caillet-Saguy, C. / Kostmann, C. / Bich, G. / Cousido-Siah, A. / Nyitray, L. / Vincentelli, R. / Wolff, N. / Nomine, Y. / Sluchanko, N.N. / Trave, G.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: phosphorylated 16E6 peptide
F: phosphorylated 16E6 peptide
G: phosphorylated 16E6 peptide
D000: phosphorylated 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,17813
Polymers110,2968
Non-polymers8835
Water0
1
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
E: phosphorylated 16E6 peptide
D000: phosphorylated 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4486
Polymers55,1484
Non-polymers3002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-13 kcal/mol
Surface area22890 Å2
MethodPISA
2
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
F: phosphorylated 16E6 peptide
G: phosphorylated 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7307
Polymers55,1484
Non-polymers5833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-13 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.580, 107.420, 79.600
Angle α, β, γ (deg.)90.000, 109.289, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-302-

B3P

-
Components

#1: Protein
14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin / CLU1


Mass: 26257.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide
phosphorylated 16E6 peptide


Mass: 1316.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.1M Bis-Tris-Propane (pH 6.5), 0.2M K/Na-tartarate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49 Å / Num. obs: 34835 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 70.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.23
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2543 / CC1/2: 0.458

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LU2

5lu2


Resolution: 2.8→48.56 Å / SU ML: 0.4231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4234
RfactorNum. reflection% reflection
Rfree0.2356 1761 5.06 %
Rwork0.2027 --
obs0.2043 34827 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7527 0 59 0 7586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367684
X-RAY DIFFRACTIONf_angle_d0.554710358
X-RAY DIFFRACTIONf_chiral_restr0.03311153
X-RAY DIFFRACTIONf_plane_restr0.00231349
X-RAY DIFFRACTIONf_dihedral_angle_d19.16632903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.37111450.33672504X-RAY DIFFRACTION99.07
2.88-2.960.3621200.30452540X-RAY DIFFRACTION99.14
2.96-3.060.37031290.29232525X-RAY DIFFRACTION99.03
3.06-3.170.33061220.2872537X-RAY DIFFRACTION99.22
3.17-3.290.31291350.28022544X-RAY DIFFRACTION99.33
3.29-3.440.28421390.24622518X-RAY DIFFRACTION99.4
3.44-3.620.26861310.22172557X-RAY DIFFRACTION99.48
3.62-3.850.2531370.20552548X-RAY DIFFRACTION99.44
3.85-4.150.21641390.18122518X-RAY DIFFRACTION99.48
4.15-4.560.1761390.15832543X-RAY DIFFRACTION99.59
4.56-5.220.19721360.16392554X-RAY DIFFRACTION99.67
5.22-6.580.23181390.20532584X-RAY DIFFRACTION99.67
6.58-48.560.18791500.16352594X-RAY DIFFRACTION99.42
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)
16.72871327341.01049794874-2.016872119865.75852280204-0.648251614755.2970033410.7966430629981.004612205670.0622020136764-2.52489878911-0.4057041328130.735252835685-0.3839140043640.288417392746-0.3656471481472.056433820020.314464871115-0.1701623642020.637772122952-0.1019512149010.756963508726-79.82464562637.7827859999510.9190632239
23.64997600332-0.570190597281-1.189312166868.365591063521.468477327613.724314031720.1038642659840.0422318143405-0.265660259826-0.690086762819-0.2206039096921.285984832310.0875166900488-0.3880188395150.1104746801560.632157740374-0.0576982888902-0.1551044807910.451204117822-0.06284943134370.922421528937-86.17748540585.0478845971230.5490601613
35.98995114379-1.5102941003-0.9753145359226.751375732280.948747244895.87274657311-0.441967855957-0.1738637029880.1511807735641.258787210030.393915663144-0.1303651597930.8994069198220.3126209961660.03939065905120.9134895349120.0493233482667-0.1721840311910.353266541433-0.0304244058810.76847673216-74.6208998795-9.6670313692437.5912238692
41.60059896961-2.29146630746-3.33809866063.114082368424.573066199916.82239833143-0.33132745858-1.474008439241.428439874431.132933653080.3148982906140.5404768797310.330217742359-0.06925206379290.05440591849120.903223783807-0.05333556705220.1300068795840.51658968802-0.1793366861081.17159647295-91.135855058128.586948138142.1024314309
57.24960967028-0.463102311923-3.430353824215.542584554131.598535848829.07336335403-0.1782310423380.0642813571336-0.0282463051654-0.940874804294-0.05573059359980.6484317521440.13960535084-0.1831556245510.2576605499840.708653389661-0.0335772960995-0.1363112329930.336001652103-0.05225623161480.806634540065-81.9784377828.839000745228.3788103163
62.85400350121-1.36064558192-4.216275263517.541142106331.488864521176.31068875489-1.235529656970.487087284226-0.382126727021-0.616035134111-0.319226168997-1.312153563791.40382997541.225865475321.572860894231.283410709960.1572259983350.1169738984431.297969053730.06464564599850.964898024877-71.942675325415.78877215360.858076835017
74.608168043970.157714355851-1.659255739486.0312367924.877877304385.29621742668-0.08430500027630.5241470771740.565972305131-2.877928708430.07244778255430.957378391103-0.174721793945-0.410423498070.2273707113381.666996511050.00170153206809-0.489674956380.540761280370.001537320345060.857973413381-84.230665481927.724029168316.4545313144
86.487652952117.803996264873.144498300499.529867911163.80162900371.587911304350.300691897154-1.43492992421-0.106948712147-0.371143859999-0.4415727760171.15399584891-0.380836257286-1.177927831620.2262055966710.5959587631850.255793397481-0.02931355715320.8525956289390.008111400123391.46684969989-89.212826266846.349370784732.4531206337
93.848265620152.3462252591-1.182162090156.779478908823.087826534433.65807746826-0.3222928751670.2547726746920.299889976535-1.718797302110.3091597418760.655869380017-0.0665465221384-0.1370185399740.0127753744571.097749800820.00936834259473-0.1953525225360.3951493497710.03220355110770.804406490351-77.646257016443.990671380923.1844839507
109.09433440815-1.06923330847-1.099307549928.54320342428-1.157980673938.162949322010.306603031430.92100909690.220217738292-1.368242171370.137022336944-0.3589951638250.8393134139180.129081529639-0.4574727581450.5849459145840.01921537022640.03379705111420.371192785484-0.0172999011470.505113703465-68.792318856542.657978764922.8303419082
116.111231689191.802885541043.573638325314.989684229175.390198345787.388324335620.2352154150650.1827195813821.52656895005-1.740858214690.108398901567-0.798391737231-1.898073290791.42347501725-0.1312012919110.745878214038-0.08063146890550.2489074814330.56013520407-0.001668457968010.992404718234-60.67933953548.1314994926.1376069771
125.04208944417-0.05703140226711.558901161199.201428628295.569242225874.03831869025-0.155416100894-0.66355611683-0.161453955927-0.1091098776310.252684653152-0.09967777102260.0584597557571.400478889430.02251647878610.635467372897-0.05258897113480.06947132610750.6669050958930.01541301486290.872942428289-61.216817876241.714305326135.6477704931
135.97715992231-1.87763757537-3.182449916297.30766793205-2.799820984953.899118286680.1291430546780.204244388791-0.547274596948-0.154082105147-0.4445328934430.845921330490.954687996075-0.5306428087810.1798487226520.713499777053-0.1842498524410.05365156916550.480769367508-0.08501215502330.615210263515-34.59647286330.8227480057747.58565634366
143.35989565315-3.34131136728-0.1840721250984.610018204342.173382139053.024217866990.000928851859420.248808881528-0.4860534093390.0181939938992-0.2315107071810.9274142796120.410701877491-0.7374223737750.06988654390110.5916224978-0.09450034436630.04631455640760.509065696333-0.0672358634740.574854186351-39.15066954283.927514441213.524948568
153.071240405111.15670527393-0.9909754760432.4264251543-3.359487467564.916586141950.005327988075990.2117947889480.3747847916432.085908312580.134604656102-0.201015895522-1.02385859953-0.064182608602-0.09452652038920.5664816984210.08517051604580.0213728671250.4419971406020.004247263185950.569382964823-31.981106149719.950457755916.4651570941
167.42729501136-3.02106218583-2.378580664133.50310325575-0.6165500262732.296608066660.177135765184-0.4109189460951.04468576396-0.3817857545581.20718675138-1.7316115681-0.632250278388-0.324578866812-1.159046226891.58443842999-0.01872952723790.4629351189950.5124541076760.2271884030541.56587207731-33.031678829146.185134408412.3095395772
172.503767614-1.30328279393-2.521931780437.99666267943-0.9083156671033.69870543147-0.004881206355361.09120856080.6672122541730.1773021994641.009958574790.535391310525-0.790721775851-1.39559662721-1.037316434990.4992475134120.1592946921520.05387974191890.6266549836440.1316356685360.601237110804-41.126348188323.714771841214.0303602675
186.869036544751.103767499610.004105192095566.17590529188-1.877187196377.644725063740.0434121866192-0.3429736638020.037765365670.9874116183280.09756341331990.50420422804-0.636533619705-0.836305213845-0.1124624291320.579485640380.06087861320670.1332592260560.512650854659-0.0627367142780.412660848456-40.271679401214.500500660329.4407121445
197.148191250671.113913104232.382737936244.08601612581-1.460798027096.351123661860.045217564457-0.5948660171920.2388896015540.693144812646-0.186561604641-0.20571715356-0.923816946256-0.190839896170.1460857639540.724290653758-0.0884450275450.05579392999710.464684900268-0.07515758762060.506617537597-27.663371498416.657160802936.8446320294
204.584620439-4.244498433931.739047186324.20410530669-2.133306830445.421575739460.2500440633880.0213241892507-0.3149399868851.18756336142-0.409379828093-0.678250732467-0.3834270037690.4898301943280.172952280880.573763795521-0.179015712903-0.02471606548680.5871875405040.08837822536790.713918865979-18.22622929111.208419045833.3431646656
215.60287552994-1.41859072251-1.653206546428.89961726293-2.213671945456.604861557-0.3145834320680.9618666789591.001047725460.382269506415-0.0113458099996-0.732098760945-1.4635545618-0.6742601093150.2822210901620.9335184252710.2144413253150.08644581439580.6489929073250.2815366709780.84234268667-33.074319076336.8974193569-1.67254551688
224.084036187861.82249523801-2.405791805234.477202010173.524085806229.48416195561-0.1464089424660.6574016022461.202682041210.378417997842-0.08688552167180.258663808499-0.563516192867-0.2911025483390.4576568980580.4772788355580.1520442543780.04060768750020.5259526380190.25788920270.88762483247-31.368284095329.7366474127-4.78262842967
233.5757211149-0.124747962095-0.7544966713127.91700680085-2.170121139846.15308274174-0.02547225205160.393984979421-0.2251845423150.108106089544-0.0880503506544-0.1954627655260.727343331479-0.3606613720920.05398863393980.359908567045-0.03538060471580.06431475236630.487431400385-0.03973933140490.386074681777-27.06911905610.5980756398-4.98641561743
248.43843881689-0.1008350928291.118192073545.21725373105-1.896412876682.56506707927-0.2303731333631.190903759120.627744401159-0.6682798999810.2575161816780.0280625622693-0.0924730404891-0.319046057697-0.03629761881220.601850642826-0.002968035245980.09121380252750.8203516107850.1260715353830.411453645786-20.649429887820.2441057179-18.6251075054
257.811101015050.7549645951183.164751893858.476233180382.030871539656.35802178562-0.3504719987540.7516815804740.937959340417-0.04074226583530.15649970445-0.758014985166-0.341823557510.316440674660.1443594746480.365829572637-0.007065613023580.1024335607260.56316153870.1848810556120.708664457485-4.6785821602921.58020345-11.2624660331
263.564178255660.691701512531-2.851337452543.12691697428-2.962453675774.45714677621.01529222342-2.50657098465-2.01571116532-0.5984942045350.354282463025-0.2660742044841.244828702420.0804448471197-1.126700669280.655488700994-0.0135038363833-0.09905542615490.766747158270.01693979143680.879085853687-67.298603128832.822468766926.1589488187
274.92454897286-5.45862211169-2.982322593926.206134151613.650757681692.64354968390.2475212655562.00516329674-0.820875753817-0.1059306324680.10987128403-2.532383469070.4871598500061.34360265448-0.1649529656850.814132352679-0.0348184830504-0.2709044890190.824906832282-0.09001370565640.947273722294-24.658938598520.220980297724.8230056551
283.47206851874-3.71874915322-0.608698616044.249569735471.544972542172.59658672114-1.19479285484-2.132241109180.2825006673411.637050632110.7860416014140.1743195057570.349077242374-1.836782684330.4881155337810.5511782743210.0516343157839-0.003684902392990.703248987885-0.1603924168330.909895998547-12.409419432915.6281359096-3.75385496721
295.3726275638-5.22247291141-4.451982580745.094199951794.338697192753.686044359780.3431171326770.4109892467312.35674392194-0.3112389470851.18239993608-2.86029964384-1.914699658561.83579379077-1.573415549240.795518680122-0.0349057000814-0.1228801830970.923313689788-0.0922034091631.23894907752-74.45560154272.1656251470238.8901021653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 231 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 15 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 79 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 105 )
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 166 )
10X-RAY DIFFRACTION10chain 'B' and (resid 167 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 187 through 203 )
12X-RAY DIFFRACTION12chain 'B' and (resid 204 through 231 )
13X-RAY DIFFRACTION13chain 'C' and (resid -1 through 18 )
14X-RAY DIFFRACTION14chain 'C' and (resid 19 through 37 )
15X-RAY DIFFRACTION15chain 'C' and (resid 38 through 69 )
16X-RAY DIFFRACTION16chain 'C' and (resid 70 through 79 )
17X-RAY DIFFRACTION17chain 'C' and (resid 80 through 105 )
18X-RAY DIFFRACTION18chain 'C' and (resid 106 through 161 )
19X-RAY DIFFRACTION19chain 'C' and (resid 162 through 203 )
20X-RAY DIFFRACTION20chain 'C' and (resid 204 through 231 )
21X-RAY DIFFRACTION21chain 'D' and (resid -2 through 15 )
22X-RAY DIFFRACTION22chain 'D' and (resid 16 through 37 )
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 105 )
24X-RAY DIFFRACTION24chain 'D' and (resid 106 through 161 )
25X-RAY DIFFRACTION25chain 'D' and (resid 162 through 231 )
26X-RAY DIFFRACTION26chain 'E' and (resid 151 through 158 )
27X-RAY DIFFRACTION27chain 'F' and (resid 151 through 158 )
28X-RAY DIFFRACTION28chain 'G' and (resid 151 through 158 )
29X-RAY DIFFRACTION29chain 'I' and (resid 151 through 158 )

+
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