[English] 日本語
Yorodumi
- PDB-8fy2: E3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fy2
TitleE3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2)
Components
  • Apoptosis regulator Bcl-2
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsTRANSCRIPTION / ternary complex / degrader
Function / homology
Function and homology information


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / negative regulation of calcium ion transport into cytosol / lymphoid progenitor cell differentiation / regulation of cellular response to hypoxia / melanocyte differentiation / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / regulation of nitrogen utilization / negative regulation of dendritic cell apoptotic process / glomerulus development / focal adhesion assembly / regulation of transmembrane transporter activity / negative regulation of T cell apoptotic process / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / regulation of viral genome replication / transcription elongation factor activity / target-directed miRNA degradation / endoplasmic reticulum calcium ion homeostasis / elongin complex / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / negative regulation of ossification / response to UV-B / Replication of the SARS-CoV-1 genome / response to iron ion / VCB complex / negative regulation of mitochondrial depolarization / epithelial cell apoptotic process / axon regeneration / motor neuron apoptotic process / Cul5-RING ubiquitin ligase complex / positive regulation of smooth muscle cell migration / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / organ growth / hair follicle morphogenesis / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / negative regulation of G1/S transition of mitotic cell cycle / digestive tract morphogenesis / SUMOylation of ubiquitinylation proteins / pore complex / negative regulation of intrinsic apoptotic signaling pathway / BH3 domain binding / T cell homeostasis / regulation of calcium ion transport / B cell homeostasis / humoral immune response / B cell proliferation / negative regulation of anoikis / negative regulation of apoptotic signaling pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
Similarity search - Function
Apoptosis regulator, Bcl-2 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Apoptosis regulator, Bcl-2/ BclX ...Apoptosis regulator, Bcl-2 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Elongin-C / Elongin B / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Apoptosis regulator Bcl-2 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsNayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Ruben, E. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. ...Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Ruben, E. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. / Zhou, D. / Olsen, S.K.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115568 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM128731 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR200030 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA242003 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA241191 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG063801 United States
CitationJournal: Nat Commun / Year: 2024
Title: Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL.
Authors: Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Nayak, A. / Ruben, E.A. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. / Zhou, D. / Olsen, S.K.
History
DepositionJan 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: von Hippel-Lindau disease tumor suppressor
B: Elongin-B
C: Elongin-C
D: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4205
Polymers67,7394
Non-polymers1,6821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.278, 102.604, 167.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 20729.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#4: Protein Apoptosis regulator Bcl-2


Mass: 23017.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10415
#5: Chemical ChemComp-YFH / N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide


Mass: 1681.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C83H105ClF3N13O11S4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.98→167.5 Å / Num. obs: 17444 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 92.16 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.199 / Net I/σ(I): 11.5
Reflection shellResolution: 2.98→3.14 Å / Rmerge(I) obs: 2.21 / Num. unique obs: 2476

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→83.68 Å / SU ML: 0.5468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2786 1728 9.99 %
Rwork0.2294 15577 -
obs0.2344 17305 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.21 Å2
Refinement stepCycle: LAST / Resolution: 2.98→83.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 115 0 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224131
X-RAY DIFFRACTIONf_angle_d0.52055620
X-RAY DIFFRACTIONf_chiral_restr0.0387601
X-RAY DIFFRACTIONf_plane_restr0.0036718
X-RAY DIFFRACTIONf_dihedral_angle_d15.19391543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.060.53691350.54361218X-RAY DIFFRACTION96.16
3.06-3.160.4181430.42621289X-RAY DIFFRACTION99.17
3.16-3.280.40021380.33871243X-RAY DIFFRACTION99.71
3.28-3.410.32131450.29921305X-RAY DIFFRACTION99.66
3.41-3.560.34911410.28891271X-RAY DIFFRACTION99.86
3.56-3.750.33021420.28511276X-RAY DIFFRACTION100
3.75-3.990.35711440.27351303X-RAY DIFFRACTION99.79
3.99-4.290.29241460.19641306X-RAY DIFFRACTION99.52
4.29-4.720.25431430.17181301X-RAY DIFFRACTION99.86
4.73-5.410.19361460.18621309X-RAY DIFFRACTION99.93
5.41-6.810.26141480.22431342X-RAY DIFFRACTION100
6.81-83.680.2191570.17741414X-RAY DIFFRACTION99.56
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)
10.3111677321430.4446492964380.3741768277320.4977394589730.4931896006060.3614049262080.387970509658-0.1621319724840.06355723745510.15107937160.06448249860420.657714750918-0.1781077190250.383664428365-6.3860878426E-60.619417012696-0.02242902074870.009310090031680.5575043568070.1171374237430.6408553499467.06492379068-13.8032513637-17.6042195869
21.033619703390.979135634917-0.4688587607060.543186251318-0.4861636269080.0686404517902-0.2330593876840.222802989443-0.256892080570.09967211848290.02381123895780.103040923720.1821914237940.149765281854-7.2410868579E-60.6373440857440.02868959228050.01493097423680.8578006660920.06673621099960.532353106599.75741111442-16.4084739754-25.3240920548
30.2016870373750.322020859883-0.2595103414940.464230461757-0.4854743005470.366354970570.142509736592-0.179219364561-0.0995444985898-0.071804614248-0.323959807165-0.450830672892-0.8611192270030.83665434344-6.62304775021E-50.746999304238-0.0912893165164-0.02057453280380.977418795752-0.01711046789750.9067183456314.611916-10.0508289536-24.0429175291
40.205076942956-0.3488954062370.465006241743-0.173940722764-0.3939631516410.9488474126540.356313687097-0.385633876607-0.25621369832-0.373519092858-0.1932229510480.549488122034-0.5837585988430.817995501450.002866291541220.684881050855-0.06538649470650.0143105073720.6315556625030.1512837128990.97567871057820.2444700959-9.37513832973-31.59131682
50.1133202155370.01987418553930.06748770310440.403846629789-0.1958861162430.173233120629-0.01162081200850.238081132169-0.248901120558-0.4163826876760.275162480839-0.475328858032-0.07646978885750.06872239159115.05109717884E-50.7809177646090.0937464413343-0.07859453399780.825783542890.07102659029221.0163039251936.3730478789-24.3497864233-35.168195678
60.14886398298-0.2379791125620.004292910870080.8508819528780.6663889520750.694662815181-0.131542105093-0.812046633097-0.306694300373-0.339345923574-0.2065612911540.228619782386-0.9347158296690.964999198221-0.0166498270520.412765484629-0.0898946376603-0.1263513417751.074842014950.1160397026660.6114779921524.3580740207-15.3030110538-14.7872442732
70.4662316872220.1453998541360.02010460835430.406215886866-0.3984871930830.443025018585-0.199169840497-0.1265563031420.695950705649-0.5632427469620.340452721925-0.187592127821-0.164460750841-0.2173737369690.002239663312130.680255354121-0.08107774461730.06506042001150.4658357213970.001025603321440.64800062929832.669651468610.5294711936-46.7989174603
80.5991165563360.4513254321090.1613902299220.3896405788480.1674273212170.06910611092080.1949479306240.7043912855130.3483424507870.02011962187160.203561645212-0.07144043380640.1731734897840.04802324871590.0001014420849040.6617265351810.094383093941-0.06589606180990.5763160741710.01138886495930.74751828587638.268571584620.2351948437-49.9924527974
90.6080992207060.2618670608370.456836474850.89918657496-0.297944908441.614597345580.2262045162640.6902600191870.228843013326-0.2585822985031.235410662370.529769922693-0.38867702295-1.148845144240.6015347393890.747089486861-0.212503730748-0.02119159417440.7445411306060.216270689890.87245010493727.493460067316.0973001654-56.8268613551
100.08552786159050.09729136704870.01411382197350.104619248358-0.03852795027130.0289101362670.09455198800840.107082774270.648429185805-0.536975482868-0.246493522966-0.296787385817-0.717280495083-0.4980373538441.7858331898E-50.51530373901-0.068914000667-0.02877008093850.919739550983-0.01461379950290.61340960579824.22729822764.79165783281-47.0291144018
110.09897489049990.1184402276070.11000304130.0401765382808-0.05275316208850.115021357197-0.07614287374670.723035891651-0.513990991404-0.44008051139-0.220521304305-0.6861095792150.9109497398970.8139141100020.0001088616627660.647710822008-0.00916011329853-0.1196022460331.044542956330.009459196026180.55920291563837.365854759411.9132384535-53.7513424156
120.02575231937580.0325853477112-0.02096354386860.0250390190553-0.03145658572440.06680992571820.00725784195632-0.1692393853030.708729331489-0.3679864952060.0365743616821-0.3673607792190.3563365261520.6656985396270.001082375229471.006776215390.0132847790883-0.01378043646260.970549647671-0.08533069699480.93814806438947.804677903222.1677396768-61.5986207623
13-0.00888643186759-0.006788665711420.01227500958690.0288501039697-0.08378879021160.1108228739730.2683788410460.5377344795940.2913185096260.166427603226-0.332252494167-1.98760033427-0.8612937796370.0920357737529-7.14130100535E-50.9436456620140.1769030968430.2236548740520.7493155098970.1031504204760.71899965088942.361644038913.6775691793-60.9943814517
140.08804385545040.193380513443-0.01470091462510.138079423126-0.1773173316520.1718446356610.107207765703-0.436254391886-0.921644418835-0.778535985456-0.7791338765270.1059903799910.2577213709741.12202768082-0.005719273741110.9136063433140.1447092221010.2301721398330.7076312329580.04787355013690.75968992696241.0482035733-7.37650121856-53.3627403489
150.42063195572-0.168894560236-0.5868102895740.3963821891550.6432346879371.308939266970.763242760792-0.4024552057140.0471582288989-0.3260274289680.985780895394-0.264555130986-0.2792127810740.2871431761740.03905384616821.10363568508-0.0445955496147-0.1350427336690.5327130337770.05410837568810.95357497627633.8380532903-24.2911950485-49.0449740495
160.5724277073190.05562665898920.2491701497490.4761144196290.0439559834920.0266113027491-0.157202223160.38240739052-0.387669425294-0.419553568449-0.07055279988190.0474098975349-0.05578529240510.101173770973-7.0707970296E-60.590573792699-0.003206869372210.002175678791950.7328981116420.1515091140230.53732358865543.22953712014.40968200458-37.2449597881
170.3188565321480.4341891537980.10060060490.5741672442170.1660688556070.0313978463404-0.3416630653140.384692883498-0.314989329658-0.4546873230360.273977825905-0.2689976854490.135087381740.694397548790.01173635001290.559734061530.08713906391980.01098908389131.041026484120.3272611455570.74832052286949.3679484091-0.372190996152-39.0219874698
180.3344482897950.3837139710210.4915633512580.571522655990.2077014554270.6736134150270.667803812522-0.02905370321750.282912719675-0.388814654946-0.4727079909450.183224588337-0.770319219139-0.2316947077820.0001126503217220.7243439751860.1215989447890.1476559257160.8766026571490.08554580163260.64308311007629.561066792-1.56314385492-38.0789834009
191.287108776350.125671937981-1.110993426290.0603335110146-0.1399148491920.942094966452-0.704109106303-1.424788193210.483368741036-0.466812218345-0.2860907695410.172399233284-0.9463194315660.970094872309-0.02808030297010.5526419242450.06438040145030.042162938270.4881392232950.1898618823130.63455355989339.3641523538-10.931882459-38.6860078193
200.54752756259-0.08794300475610.08941376557260.0204957357817-0.0203680810588-0.05756341411270.4393771912560.0825946973198-0.4122241648310.753449244751.00391346931-0.550019891670.142066091769-0.4271993724940.8743518442491.2631577433-0.06790498700550.240009031240.9537837963530.2008768452990.93671834816-13.1145577192-48.0003087176-7.78766726127
210.342332511241-0.147393270824-0.4300315086270.1914427499360.1786011593170.213257714574-0.115591740658-1.1122541303-0.08303479495170.114070656320.5176395663040.329024354059-0.281141095406-0.1392608180720.00274229832271.15427201863-0.1239515567760.1138761840220.8941003005470.2160689815321.0486125679-14.0370844783-46.7326603657-2.21161213742
221.028613248160.07466719626850.419873795061-0.0117246021549-0.009598339324590.0514023469072-0.946983807198-1.200770847210.60755178324-0.1036228965170.60367717029-0.2029583106010.3948624595350.00732867056408-0.02322487079031.179361852490.1922516427360.04298201075711.036819541540.0701268143040.614295005841-2.14538974337-46.053373691-10.1724770144
230.288049559085-0.1565959728860.1528135103250.0626626195955-0.1336580359520.06314774485680.07095146653331.50136807103-0.519979443353-0.08134879859830.1675532037520.525982974261-0.2584219245490.2325533929010.003465655980840.8352103318420.05905257148970.08311984958730.509860447559-0.003804576859480.681165860684-6.66488015315-28.0196048262-9.01644966736
240.544197655373-0.1096649303-0.212880585003-0.004907591878310.0352678353205-0.0886986674489-0.4611533842041.38928472446-0.677151679463-0.5720568570110.2336390650161.128998732060.237118430483-0.1353578557480.003973313423630.8764385464520.034710696218-0.07370212394280.7241084835870.01818416920350.7629365232-15.7600681574-32.1193415303-18.6189978031
250.0747830764325-0.1419750219870.05972148119311.44521280246-0.3623524585790.07331440634760.1296195041970.0564115767907-0.203138065795-0.0893731053715-0.2116979838140.4907058689640.075043622207-1.201609296291.07602464195E-50.883164346527-0.2591971403490.1008350094231.043186092770.0297656654560.755670460717-15.9210151116-38.0977198512-10.6434192269
260.7184187899230.5288945414391.031098009220.4787758852330.7939332809591.535056275060.2759446841080.706890807436-1.08763903908-0.2889655007940.725234085196-1.373035388280.7303129471010.5640679441120.3747290951160.998900593407-0.5815260160150.3109696724191.42918470635-0.3793570002241.22789834264-12.6668853621-49.1820154206-25.9763672876
270.1055278589890.02188340920710.01301084222320.3240567698880.2543567704490.226129232003-0.0176499911719-0.194287527697-0.6461506858460.240522559681-0.123247451023-0.03478408812231.023408245930.07996131054080.02597192398061.671182569880.232980408450.2186076071050.5577695187220.1740826648711.02023926858-2.81932810143-52.2422840556-18.5413525345
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 60 through 79 )AA60 - 791 - 20
22chain 'A' and (resid 80 through 121 )AA80 - 12121 - 62
33chain 'A' and (resid 122 through 141 )AA122 - 14163 - 82
44chain 'A' and (resid 142 through 169 )AA142 - 16983 - 110
55chain 'A' and (resid 170 through 193 )AA170 - 193111 - 134
66chain 'A' and (resid 194 through 208 )AA194 - 208135 - 149
77chain 'B' and (resid 1 through 23 )BB1 - 231 - 23
88chain 'B' and (resid 24 through 45 )BB24 - 4524 - 45
99chain 'B' and (resid 46 through 60 )BB46 - 6046 - 60
1010chain 'B' and (resid 61 through 72 )BB61 - 7261 - 72
1111chain 'B' and (resid 73 through 79 )BB73 - 7973 - 79
1212chain 'B' and (resid 80 through 84 )BB80 - 8480 - 84
1313chain 'B' and (resid 85 through 89 )BB85 - 8985 - 89
1414chain 'B' and (resid 90 through 99 )BB90 - 9990 - 99
1515chain 'B' and (resid 100 through 105 )BB100 - 105100 - 105
1616chain 'C' and (resid 17 through 45 )CC17 - 451 - 29
1717chain 'C' and (resid 46 through 66 )CC46 - 6630 - 39
1818chain 'C' and (resid 67 through 96 )CC67 - 9640 - 69
1919chain 'C' and (resid 97 through 112 )CC97 - 11270 - 85
2020chain 'D' and (resid 8 through 25 )DD8 - 251 - 18
2121chain 'D' and (resid 26 through 90 )DD26 - 9019 - 28
2222chain 'D' and (resid 91 through 107 )DD91 - 10729 - 45
2323chain 'D' and (resid 108 through 122 )DD108 - 12246 - 60
2424chain 'D' and (resid 123 through 143 )DD123 - 14361 - 81
2525chain 'D' and (resid 144 through 184 )DD144 - 18482 - 122
2626chain 'D' and (resid 185 through 193 )DD185 - 193123 - 131
2727chain 'D' and (resid 194 through 203 )DD194 - 203132 - 141

+
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