[English] 日本語
Yorodumi
- PDB-6z3u: Structure of the CAK complex form Chaetomium thermophilum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z3u
TitleStructure of the CAK complex form Chaetomium thermophilum
Components
  • CYCLIN domain-containing protein
  • Protein kinase domain-containing protein
  • RING-type domain-containing protein
KeywordsTRANSCRIPTION / CAK complex / Kinase / TFIIK / cell cycle / trnascription / DNA repair
Function / homology
Function and homology information


transcription factor TFIIK complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RNA polymerase II CTD heptapeptide repeat kinase activity / nucleotide-excision repair / protein phosphorylation / regulation of transcription by RNA polymerase II / ATP binding ...transcription factor TFIIK complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RNA polymerase II CTD heptapeptide repeat kinase activity / nucleotide-excision repair / protein phosphorylation / regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus
Similarity search - Function
Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, N-terminal / Cyclin, N-terminal domain ...Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
RNA polymerase II transcription factor B subunit 3 / [RNA-polymerase]-subunit kinase / CYCLIN domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPeissert, S. / Kuper, J. / Kisker, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for CDK7 activation by MAT1 and Cyclin H.
Authors: Peissert, S. / Schlosser, A. / Kendel, R. / Kuper, J. / Kisker, C.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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: CYCLIN domain-containing protein
B: Protein kinase domain-containing protein
C: RING-type domain-containing protein
D: CYCLIN domain-containing protein
E: Protein kinase domain-containing protein
F: RING-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,0547
Polymers208,0186
Non-polymers351
Water37821
1
A: CYCLIN domain-containing protein
B: Protein kinase domain-containing protein
C: RING-type domain-containing protein


Theoretical massNumber of molelcules
Total (without water)104,0093
Polymers104,0093
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-36 kcal/mol
Surface area30240 Å2
MethodPISA
2
D: CYCLIN domain-containing protein
E: Protein kinase domain-containing protein
F: RING-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0444
Polymers104,0093
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-35 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.436, 85.240, 160.401
Angle α, β, γ (deg.)90.000, 96.931, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "D" and (resid 5 through 262 or resid 312 through 390))
d_1ens_2chain "B"
d_2ens_2(chain "E" and resid 78 through 399)
d_1ens_3chain "C"
d_2ens_3(chain "F" and resid 273 through 338)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEGLYA1 - 312
d_21ens_1ILETYRD2 - 234
d_22ens_1SERGLYD236 - 314
d_11ens_2PROSERB1 - 322
d_21ens_2PROSERE2 - 323
d_11ens_3ASPGLYC1 - 66
d_21ens_3ASPGLYF2 - 67

NCS ensembles :
ID
ens_1
ens_2
ens_3

-
Components

#1: Protein CYCLIN domain-containing protein


Mass: 46931.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0069020 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SH78
#2: Protein Protein kinase domain-containing protein


Mass: 49133.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0061570 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SFC6
#3: Protein RING-type domain-containing protein


Mass: 7944.815 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0060790 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SF48
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.0-8.0, 0.2 M sodium formate, 15-22% PEG 3350.
PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.6→75.9 Å / Num. obs: 33808 / % possible obs: 83.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.25 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.198 / Net I/σ(I): 6.6
Reflection shellResolution: 2.604→2.816 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.776 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1690 / CC1/2: 0.249 / Rpim(I) all: 1.164 / % possible all: 64.4

-
Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.18rc4_3812refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ua2
Resolution: 2.6→75.87 Å / SU ML: 0.2901 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1653 4.89 %
Rwork0.2027 32121 -
obs0.205 33774 50.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.61 Å2
Refinement stepCycle: LAST / Resolution: 2.6→75.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 1 21 11398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002511651
X-RAY DIFFRACTIONf_angle_d0.507415740
X-RAY DIFFRACTIONf_chiral_restr0.03781667
X-RAY DIFFRACTIONf_plane_restr0.00342042
X-RAY DIFFRACTIONf_dihedral_angle_d29.15224421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.572901775633
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.751849955081
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.495517563851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.4346210.3104526X-RAY DIFFRACTION9.86
2.68-2.770.3344350.3444651X-RAY DIFFRACTION12.44
2.77-2.870.3744470.3108957X-RAY DIFFRACTION18.04
2.87-2.980.3546780.28811292X-RAY DIFFRACTION24.79
2.98-3.120.3681710.28671686X-RAY DIFFRACTION31.45
3.12-3.280.26661080.27662042X-RAY DIFFRACTION38.6
3.28-3.490.31581240.24792515X-RAY DIFFRACTION47.68
3.49-3.760.28531830.21993215X-RAY DIFFRACTION61.12
3.76-4.130.23091990.18654110X-RAY DIFFRACTION76.97
4.13-4.730.21352440.16644602X-RAY DIFFRACTION86.14
4.73-5.960.2312680.19595081X-RAY DIFFRACTION95.36
5.96-75.870.22542750.17975444X-RAY DIFFRACTION99.5
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.601178103820.4107484496250.6943312697684.221492255950.9206380435721.95313221098-0.0885921668432-1.10657651498-0.2560397557170.295178752601-0.0856562274664-0.0773283676074-0.2707206564960.3314762549920.1623209245850.7003231272430.09514172948340.2007812705280.716154538775-0.05774636207530.35731402069765.620890202819.362417113722.4327424277
28.294202679936.620932770686.776807310625.285981707565.412164774675.544265772480.599941586810.027096568004-1.31890682154-0.07635766305660.433720471302-1.473911482070.4320250754580.915740825613-0.855024456160.5253803377120.08342859088320.03669072775550.786167733798-0.07619257718830.61549158177967.94123779610.4098332891493.83763461711
32.54191457533-0.246162870718-0.3557236015261.745803866110.3125953107971.158627281130.03903213813050.10327875101-0.133217424035-0.5329415066120.238948215794-0.3784922111920.1581468708970.773498214888-0.1343039340870.57337712897-0.003622158062690.2370202468220.549959487255-0.1106399466790.27525021328460.121925110714.2674327898-0.6654673269
42.93327059592-0.624014292792-0.5677767818223.36206667528-0.3816840766640.2544096362360.19091317140.610121102443-0.102982210148-0.43864812389-0.251994471340.2862017071060.1844773042850.353934691042-0.1455010243070.590504854254-0.03517931962090.2519975305420.414386592368-0.1636935047960.24103221386849.235227918916.83767216712.88932199743
54.33065664771-1.289051074830.6185085350290.449943119679-0.04100279065610.3996367401610.153362771686-0.3659805878690.940253333689-0.594028916835-0.0321320411279-0.46120139189-0.7708238321610.471834248482-0.4718988152720.972492975064-0.4215146192990.3765090041210.778739717635-0.2012889299970.57557933817968.815551298241.844589424611.7538473438
62.139693855950.4513968020080.6363062196962.898841966311.976863433982.428192712170.1707513054630.513307115784-0.211410945873-0.3267724043120.0272837232075-0.795858613853-0.6049216757470.726877956184-0.1696386972030.365429410999-0.2200735370150.04184642736170.818907438629-0.07810255664340.41869059272270.762651087327.17038651299.54623108128
71.00690337558-0.926160370791-0.7275463800651.25759329596-0.2173610786142.51034949324-0.12135109382-0.2311621103210.297824899603-0.1480770280360.180495125574-0.746787953221-0.337510661371.07433611721-0.297620309010.495725172667-0.2793694403030.2279361217621.03662783094-0.2691005618430.73896388302676.07547981328.69776111427.36050432832
81.105045844810.2295310775331.755029284694.972014303771.283061145092.957941737-0.2111820586880.326670874887-0.425818259477-0.2096548932550.0174975863534-0.2291044414380.9792613620750.5303223797730.03347964771150.846449653884-0.01227306122720.2887113394550.593701834219-0.2346311193810.51416771352861.19283167533.335411432-9.44308189387
94.433131503414.482324560943.921970155185.022849072374.065330776653.491221463960.928389019599-0.7557744254450.04184053406731.37870427604-0.6238306160240.595351124580.286653466045-0.466231879296-0.05273144990850.8360334560730.02875604773130.08286400900580.747417035316-0.1447606884180.40264943124441.0624341209-4.8391794123-0.401107779614
107.17536651517-0.440679715029-3.144049655632.327859341810.241772250776.56817939057-0.5766288646630.383690464213-1.25493408536-0.1574780365240.135606956378-0.05150987454181.766294671120.09070679372190.3579196995340.9899569433330.01807161072770.05877885750450.336690036396-0.07026033999810.50851734338546.65618518051.0266934336722.6870639061
111.14049404052-0.443058565839-0.9766712924730.9121799295770.3603186020281.13968049961-0.01875481060530.153045201822-0.337948234551-0.0649610007182-0.0106304098877-0.009229510820730.236961835036-0.04943340405640.05491325378860.442863448588-0.1493792600290.04975417444520.33085613368-0.1013256061310.10823028892641.876117558617.930386030127.7992149341
121.37258411143-0.0849874112677-0.6730242161480.924732200523-0.03810023820072.036914740530.3150698300890.07555166119980.253963808113-0.08276524437890.033697116703-0.0336712215727-0.493629970736-0.0195710073137-0.00274685396510.546134080147-0.1746050565820.2567870649510.247175367821-0.0488643417340.016080373570235.354595073436.335073435230.000086227
137.797122556432.731806143953.209045167743.01152836502-0.5283162127892.650324524910.382088148915-0.40000897025-0.0373725896183-0.1208072518550.4183253184-0.535145526309-0.7007616733041.06902611584-0.6445658314950.725298549523-0.157251213766-0.01558478573960.858685441132-0.3003329794250.48542620483557.769008674229.509065735337.0504723363
142.8501060578-1.577939575291.088632285341.96765777716-0.3469092961292.214497388660.258571128799-0.04326279010270.4938934644960.131018947081-0.0164503481608-0.458241606343-0.54839210290.7276170233560.08284506709330.747704943924-0.3258404729650.2592421008640.495874916965-0.1392200996990.4210530429660.676889401336.823865602820.2780403207
153.8062962503-3.71633953259-1.115652295467.228581196591.200286522751.34919920503-0.0446803373253-0.3013037525540.7679271378990.2661878604080.0130581427355-0.578024295131-0.3896026112810.0946476874281-0.0707771250830.415322962885-0.00774462374858-0.01630523643810.260765220765-0.1170761025640.33354762686212.979659843438.118783047597.5956235799
161.78619869036-0.931229949967-0.8180487411163.910450253520.9541100849342.5471924078-0.190262996442-0.342536049230.1140081481260.1155190550110.05463012779310.2305003766380.0311605939408-0.2027474629560.1156623729150.243133409130.0887236447473-0.002298065727320.2117475308830.001719467439060.129242438186-2.5628716284132.03801588793.2799415558
170.860995654313-0.65796335241-0.2565531847763.8131958-0.7303118945250.925089821729-0.278203482683-0.474620101337-0.06582111154070.6095819709920.288683699161-0.2005692287950.3438164095390.2417092066930.009058468884160.5306201024250.1642597663530.07409596396510.3989551938840.09897817720560.12990401704216.298862989713.692022505103.322456452
180.381060519532-0.8029805760040.5412555155751.85354222027-0.9649282347540.918538948455-0.131876305147-0.3640052989820.03805806772590.4418975297690.2462726386420.407260587297-0.446349099471-0.421224224922-0.06535951618830.5322708924070.1565254158670.1772605561680.48844247876-0.01236653885190.204330767639-8.0839327752334.0336079072106.584709827
198.92483080999-7.430334949970.1664188839538.672141349411.000595429560.5248262647790.3732655257961.305160550831.06442275203-1.51628658504-0.459295529357-1.21342625438-0.30291143706-0.04310505023430.1634973476180.6380792832030.1695104832270.1612233162760.7561789979710.07237221070070.563538389974-9.935846866652.242484282679.9244669515
203.1147652565-0.2151651845-1.322224141962.91139726131-0.2456851608172.409995658030.1417510581610.1502112048250.711484314019-0.3256912668030.1694988084680.230151360588-0.809628365801-0.248062967455-0.1886781099380.4259038911430.06277515539840.03813644370380.1889158350290.01989838697630.34705065776810.563554235240.40693586975.818081159
211.991315080120.52466783742-0.5487990023051.956792966070.03252233429832.51044389438-0.2277170695130.217778355947-0.0695064660455-0.1394734474640.1266022091680.005722775650580.180941353480.03800972914360.05202730196340.09453964311590.01830959239740.02828524927960.05294978913140.03643415270740.06961833490316.946678418515.057766087162.1178980271
228.576687659273.79385788446-1.14893495412.18463950604-1.609268386543.91945926425-0.9058653940490.906275266369-1.18144924609-1.033259370990.341244974518-0.689047202450.2994745695550.9373727168970.5643678776490.5850323437530.08020269872880.08696741625030.719173458607-0.1396147651970.50459664518332.234744913518.371206763477.0568021359
233.488901901575.209332849643.182221622859.316189328034.307243643683.067550784720.404835366294-0.388540241002-0.697831151781-0.800224010210.0925159808567-1.875343459860.9297380037331.03939855951-0.3924315849560.5336244006540.1572596806490.1559818974010.4430879371520.09054761118470.52802421473828.133738720212.096176071191.8686277944
240.9073103120740.5996042481360.9967890666734.77424981338-0.6269899417761.868506361270.272925177749-0.0725480669639-0.580989236041-0.09211003731390.0491939098827-0.03584632511690.4071583496230.1098053501120.3633277931260.6402493208510.3192217988910.1392852193860.5103494833540.2222273943710.4640671220820.2777184491.5169653266289.3269463693
251.167941039560.4488045490670.5766812981693.18365092035-0.2806591184370.937645655397-0.00996018237828-0.0711182380139-0.09417747179840.379194153307-0.0641737199594-0.07485832346330.200212821519-0.005582272152790.1127516246430.449613802185-0.02888241557440.1515504538340.1081251238230.06126923541420.3286659452537.670051654961.0490716413480.7081461753
260.834414399778-0.122357083834-0.2823584222020.2134692524540.4953902398811.141311452630.152619036160.02014920633940.208102316610.04507482174810.195916139853-0.196081047923-0.1016011839680.1981328429840.2243348923010.3073207489320.1743269961450.1578845913960.2044192552910.008543257250190.17785322611517.627323805111.178237229887.5017133828
272.574836210530.3980582680260.6572788012291.29475060229-0.01224906420561.03961241618-0.0628800421549-0.4811250160170.4250010089590.07815175248180.07908495346960.0167384825443-0.119819960539-0.1970316080840.2580921682450.23053123420.115220650903-0.1512153648320.627304269568-0.03593262120630.58909843533824.115561065429.4811313368100.652401124
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 24 )AA5 - 241 - 20
22chain 'A' and (resid 25 through 47 )AA25 - 4721 - 43
33chain 'A' and (resid 48 through 147 )AA48 - 14744 - 118
44chain 'A' and (resid 148 through 188 )AA148 - 188119 - 159
55chain 'A' and (resid 189 through 221 )AA189 - 221160 - 192
66chain 'A' and (resid 222 through 248 )AA222 - 248193 - 219
77chain 'A' and (resid 249 through 350 )AA249 - 350220 - 272
88chain 'A' and (resid 351 through 367 )AA351 - 367273 - 289
99chain 'A' and (resid 368 through 390 )AA368 - 390290 - 312
1010chain 'B' and (resid 78 through 124 )BB78 - 1241 - 47
1111chain 'B' and (resid 125 through 233 )BB125 - 23348 - 156
1212chain 'B' and (resid 234 through 399 )BB234 - 399157 - 322
1313chain 'C' and (resid 273 through 282 )CC273 - 2821 - 10
1414chain 'C' and (resid 283 through 338 )CC283 - 33811 - 66
1515chain 'D' and (resid 4 through 48 )DD4 - 481 - 45
1616chain 'D' and (resid 49 through 188 )DD49 - 18846 - 160
1717chain 'D' and (resid 189 through 332 )DD189 - 332161 - 256
1818chain 'D' and (resid 333 through 367 )DD333 - 367257 - 291
1919chain 'D' and (resid 368 through 390 )DD368 - 390292 - 314
2020chain 'E' and (resid 77 through 172 )EE77 - 1721 - 96
2121chain 'E' and (resid 173 through 399 )EE173 - 39997 - 323
2222chain 'F' and (resid 272 through 281 )FF272 - 2811 - 10
2323chain 'F' and (resid 282 through 286 )FF282 - 28611 - 15
2424chain 'F' and (resid 287 through 293 )FF287 - 29316 - 22
2525chain 'F' and (resid 294 through 311 )FF294 - 31123 - 40
2626chain 'F' and (resid 312 through 324 )FF312 - 32441 - 53
2727chain 'F' and (resid 325 through 338 )FF325 - 33854 - 67

+
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