[English] 日本語
Yorodumi
- PDB-8buj: Structure of DDB1 bound to DS06-engaged CDK12-cyclin K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8buj
TitleStructure of DDB1 bound to DS06-engaged CDK12-cyclin K
Components
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
KeywordsLIGASE / kinase / cyclin / ubiquitin / degrader
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / viral release from host cell / regulation of signal transduction / ectopic germ cell programmed cell death / proteasomal protein catabolic process / cyclin-dependent kinase / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of gluconeogenesis / RNA Polymerase II Pre-transcription Events / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA processing / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein autophosphorylation / chromosome, telomeric region / damaged DNA binding / protein kinase activity / protein ubiquitination / nuclear speck / cell cycle / cell division / DNA repair / protein serine kinase activity / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Cyclin, N-terminal ...Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / 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
Chem-RUW / Cyclin-K / DNA damage-binding protein 1 / Cyclin-dependent kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsKozicka, Z. / Kempf, G. / Petzold, G. / Thoma, N.H.
Funding supportEuropean Union, Switzerland, 7items
OrganizationGrant numberCountry
European Research Council (ERC)666068European Union
Swiss National Science Foundation31003A_179541 Switzerland
Swiss National Science Foundation310030_301206 Switzerland
Swiss Cancer League4980-02-2020 Switzerland
Swiss National Science FoundationCRSII5_186230 Switzerland
Marie Sklodowska-Curie Actions, FragNET ITN765445European Union
Other private Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Design principles for cyclin K molecular glue degraders.
Authors: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / ...Authors: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / Haussinger, D. / Winter, G.E. / Fischer, E.S. / Slabicki, M. / Gillingham, D. / Ebert, B.L. / Thoma, N.H.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,03226
Polymers496,5589
Non-polymers2,47417
Water00
1
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,3769
Polymers165,5193
Non-polymers8576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,2808
Polymers165,5193
Non-polymers7615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,3769
Polymers165,5193
Non-polymers8576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.353, 249.353, 218.417
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 393 or resid 709 through 1140))
d_2ens_1(chain "D" and (resid 1 through 393 or resid 709 through 1140))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1140))
d_1ens_2chain "B"
d_2ens_2(chain "E" and (resid 715 through 1041 or resid 1101))
d_3ens_2(chain "H" and (resid 715 through 1041 or resid 1101))
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLYGLYAA1 - 3935 - 397
d_12ens_1LYSLYSHISHISAA709 - 1140409 - 840
d_21ens_1METMETGLYGLYDD1 - 3935 - 397
d_22ens_1LYSLYSHISHISDD709 - 1140409 - 840
d_31ens_1METMETGLYGLYGG1 - 3935 - 397
d_32ens_1LYSLYSHISHISGG709 - 1140409 - 840
d_11ens_2THRTHRASPASPBB715 - 10327 - 324
d_12ens_2RUWRUWRUWRUWBM1101
d_21ens_2THRTHRASPASPEE715 - 10327 - 324
d_22ens_2RUWRUWRUWRUWES1101
d_31ens_2THRTHRASPASPHH715 - 10327 - 324
d_32ens_2RUWRUWRUWRUWHW1101
d_11ens_3THRTHRHISHISCC20 - 26724 - 271
d_21ens_3THRTHRHISHISFF20 - 26724 - 271
d_31ens_3THRTHRHISHISII20 - 26724 - 271

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.475509504409, -0.511067619121, 0.716031144506), (0.506307831203, 0.506627720123, 0.697840048483), (-0.719404678383, 0.694361751459, 0.0178512417196)-127.3751185, 79.7985126517, -108.159966986
2given(-0.508659446524, 0.502535122402, -0.699087990324), (-0.554746806985, 0.429659817149, 0.712494506412), (0.658423532084, 0.750233891716, 0.0602292297655)-178.726096771, -28.9330307557, 33.8669459493
3given(-0.510838806481, -0.519933627185, 0.684625983377), (0.494427990501, 0.473793031721, 0.728739408363), (-0.703267144122, 0.71076661881, 0.0150378716398)-129.320432221, 79.3433048373, -107.289621609
4given(-0.513036266849, 0.506141058663, -0.693264031688), (-0.536276125052, 0.441628087341, 0.719286139287), (0.670225116357, 0.740800824248, 0.0448601404041)-179.307116849, -28.0780595029, 34.3295147446
5given(-0.546994078541, -0.512028720522, 0.66228699776), (0.483529647192, 0.452573914798, 0.749250246534), (-0.683371464379, 0.730070846566, 2.58150893107E-5)-131.927604295, 79.6972443074, -107.072110459
6given(-0.494346936173, 0.518028364232, -0.698045643598), (-0.520868883058, 0.466375121651, 0.714975420952), (0.695928669734, 0.717036163492, 0.0392737429745)-179.045097273, -28.2761610422, 36.3683335513

-
Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 93675.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#2: Protein Cyclin-dependent kinase 12 / Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 ...Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 / CDC2-related protein kinase 7 / Cell division protein kinase 12 / hCDK12


Mass: 40143.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK12, CRK7, CRKRS, KIAA0904 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#3: Protein Cyclin-K


Mass: 31700.471 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75909
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-RUW / (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol


Mass: 376.539 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H36N6O / 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: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99995 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 3.618→215.946 Å / Num. obs: 81004 / % possible obs: 95.8 % / Redundancy: 21.1 % / CC1/2: 0.99 / Net I/σ(I): 11.6
Reflection shellResolution: 3.618→3.784 Å / Num. unique obs: 4053 / CC1/2: 0.41

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Cootmodel building
STARANISOdata scaling
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.62→76.78 Å / SU ML: 0.4013 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 4039 4.99 %
Rwork0.164 76916 -
obs-80955 90.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 158.71 Å2
Refinement stepCycle: LAST / Resolution: 3.62→76.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33696 0 151 0 33847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534542
X-RAY DIFFRACTIONf_angle_d0.850246704
X-RAY DIFFRACTIONf_chiral_restr0.05085169
X-RAY DIFFRACTIONf_plane_restr0.00565976
X-RAY DIFFRACTIONf_dihedral_angle_d11.739312899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.02482687802
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.08580747802
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.958772135804
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.897705491673
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.703613257438
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.571117681238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.62-3.660.3891120.3258215X-RAY DIFFRACTION7.4
3.66-3.710.3322480.3081812X-RAY DIFFRACTION28.45
3.71-3.750.3579860.30081527X-RAY DIFFRACTION52.47
3.75-3.80.32521030.2912049X-RAY DIFFRACTION71.14
3.8-3.850.35091420.27932387X-RAY DIFFRACTION81.92
3.85-3.910.33381360.26542581X-RAY DIFFRACTION89.4
3.91-3.970.31561540.252762X-RAY DIFFRACTION94.52
3.97-4.030.26681490.23142834X-RAY DIFFRACTION97.9
4.03-4.10.2471430.22792914X-RAY DIFFRACTION99.45
4.1-4.170.24991580.20392889X-RAY DIFFRACTION99.93
4.17-4.240.23511350.20352915X-RAY DIFFRACTION100
4.24-4.320.21911340.17712960X-RAY DIFFRACTION100
4.32-4.410.2171570.17442880X-RAY DIFFRACTION100
4.41-4.510.20651730.16572880X-RAY DIFFRACTION100
4.51-4.610.20151400.15792967X-RAY DIFFRACTION100
4.61-4.730.20741730.15372885X-RAY DIFFRACTION100
4.73-4.860.19921490.14862928X-RAY DIFFRACTION100
4.86-50.20441550.14242931X-RAY DIFFRACTION100
5-5.160.19831770.14022896X-RAY DIFFRACTION100
5.16-5.340.18631070.15422990X-RAY DIFFRACTION100
5.34-5.560.21861340.16152930X-RAY DIFFRACTION100
5.56-5.810.20171520.16192931X-RAY DIFFRACTION100
5.81-6.120.20411530.17282955X-RAY DIFFRACTION100
6.12-6.50.26851680.16482920X-RAY DIFFRACTION100
6.5-70.20571550.16192958X-RAY DIFFRACTION100
7-7.70.20451760.16532954X-RAY DIFFRACTION100
7.71-8.820.17691670.13372964X-RAY DIFFRACTION100
8.82-11.10.13841660.10672986X-RAY DIFFRACTION99.84
11.11-76.780.17861370.14893116X-RAY DIFFRACTION99
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)
12.411084420941.655624998290.002808615939331.52996588827-0.1393303384161.55732930618-0.10521394314-0.383419793137-0.3010831219240.2579527462950.00241861648465-0.2541060506110.2336840444310.2792369990490.008299522717711.553653527720.221265282645-0.2723888922521.3574190230.02130232957411.56595738199-57.3730690186-7.8104008884427.953982616
20.926958201069-0.384139983141-0.6399118244162.31571476055-0.2218503919370.859031059754-0.0201667569112-0.4045640273810.04930591043850.2861013974930.131336397745-0.0619791348324-0.09025547119410.0121104327346-0.006143802839241.536119856320.00796522128117-0.03999595587071.32584327254-0.1319786698021.19919173812-81.23667984813.02169737231.8615312648
31.96379066678-0.298464810071-0.1019556567750.143608623564-0.2191643346021.635445722640.0927338623443-0.04905697050730.4578271119490.2150220181440.0287237592211-0.398471352182-0.3065798973450.368083793840.06875177029951.65266918286-0.078095837844-0.1185719601121.27300255035-0.2406293479661.58170971326-63.311138302429.204046064521.2802578663
41.88905054246-0.147568583204-1.234507048510.914865727282-0.2769532861191.606721160280.418252676996-0.201366981302-0.0643355314596-0.107296341230.0132606818831-0.106364713641-0.648674622084-0.003702474448070.005142289689921.50315075235-0.056902808091-0.06014744165851.34660024551-0.06916109247551.54558071542-61.851343797231.3975492015-14.7936295646
52.452547978740.6222494001890.8933485685412.62539919991-1.456628266620.14748257336-0.1210954176360.269476174835-0.210792652954-0.02788040314290.3924348141710.315584001809-0.2495119746790.0378706166172-0.0109469599421.58732629785-0.004934309538890.04827776586711.36344694704-0.274194422981.40677926236-59.043909177120.1583646743-10.5967514523
60.6868541334150.06861468690090.2154599770661.20501335828-0.4696896554640.2002561452940.732515085078-0.2241173730420.4168108008030.184642524593-0.162912146137-1.140460393341.369193537562.11211759572-0.04456024195421.75072527859-0.08011934226060.1004479819991.98141970915-0.07469964349192.103322096-40.953708897218.3146346347-15.8435730756
72.04924851547-1.24649460178-0.7900049242112.75329182490.5686746159572.90770325763-0.0148161960859-0.05908520771740.06760027056010.125900034428-0.0669516976797-0.2226533774480.2628499996970.375972646432-0.01213896988231.37672167295-0.0181456906898-0.09941607311631.32934301938-0.2492978649471.79850370225-45.26993771315.58272420867-4.74284407503
81.84374101925-0.7648996458320.3960740526261.15939771721-0.4617950203542.0508539294-0.163654919580.5759364668490.198819733387-0.6476327265880.0910214570475-0.7578367038310.06156618765830.349108990360.03704059836431.53690944764-0.1312476867040.1556192992541.26191623558-0.2130105844361.4417495328-51.010296200539.9403444872-39.3388334218
91.297369141130.530892147895-0.6132166716581.67648852851-0.775935393141.76670225140.0570888490913-0.3235520686480.4830428029980.9253368867180.217697813433-0.325329085448-0.8374625514690.4925202047690.03408301331791.58200060944-0.184650509797-0.1020656578811.2637471724-0.1804612224871.63806835798-45.443116087345.590369744-28.1291586673
100.705126852472-1.09109976482-0.590073494512.276358803041.349582283051.86138699554-0.2671725478490.301319465167-0.405089931785-0.01845963231420.0498444061284-0.6893102231990.1712361743690.1866970696650.03656910835481.5144295307-0.0443757651380.2435005788351.42917691276-0.1137864349981.7848493494-43.487722473722.2618043937-42.5921459862
111.48274800858-0.7697643016520.3796319004924.271665829170.3723246509181.58424155521-0.0200748123520.313229426166-0.41725640253-0.2180801138710.10664709133-0.202977167735-0.2604395455050.1239824420180.04053806330451.56977888333-0.008905321212920.156638798281.22704994206-0.2150964276161.73902595119-48.238304037420.6585019909-52.0501501199
121.6641373358-1.349368876712.285324809912.93746542859-2.108679354623.14563926041-0.8340603690350.288243777293-2.10065266198-0.2757303222650.1823908704890.2331714818860.897961691723-0.193943451778-0.01077805957981.45173971125-0.000677078833042-0.2226988698711.64926195573-0.1240880370271.69340848123-54.683664763116.0510093795-50.3700620748
131.523507659020.776648065578-0.7577509838683.12412770083-0.7131987781831.28868333942-0.3653115637351.096367308991.91637018937-0.648114994360.0253963207661-1.61630323556-0.7685349138430.2038848221460.00752334644751.96116314178-0.0913250094157-0.09769632277561.50578719097-0.04484743300352.19780306224-45.162157343432.9868877721-55.1764144047
142.26005860168-1.02601043268-0.005551478732951.390413902970.1268518068581.39545447034-0.1444685164660.4331064651410.0503776528604-0.4194017898940.100505645229-0.253509919362-0.2582341803010.350555882351-0.01341524065391.67544006375-0.269635227020.1261596607251.38252104251-0.003416990577991.28127925435-74.450638578567.1680960179-69.1246604523
152.66650685103-1.06852907884-0.07872403607552.2841244355-0.1484125304562.47489478263-0.0607115700281-0.3670818468740.0830524330432-0.3528467892030.0659082037549-0.135083802483-0.09874159195690.1357095282210.001026808813861.30035481885-0.152205891034-0.02088233511851.27804860956-0.1642631954311.25265017659-75.507137016165.8429261159-34.5148703189
161.37335348930.1545952213860.1161277927860.998649424956-1.001377487112.34049981967-0.0530045042504-0.05713940784220.419008244663-0.0367667721113-0.0712670022140.0926118919071-0.557327831289-0.458408252495-0.06429885168331.58412297236-0.0209399845214-0.1337060058091.27779105756-0.177624538331.42131048291-96.946930587977.4126235799-41.9284102228
174.377895734330.8421890059811.590487657010.3846553421280.2815074146482.46535581928-0.273346669108-0.179319320016-0.1151213262060.1450489651930.02994369137480.386823234997-0.01002985066970.22850458582-0.02181998094811.38731654193-0.0322751599074-0.07664680816121.313902265410.008626556806851.42487155031-123.52634909655.2971190697-38.2346614554
182.466706763290.336474395002-0.2630361926281.242225428210.3342242842141.51496040427-0.104506747596-0.545274379108-0.0369073910838-0.05951521375890.130678609087-0.1214186624040.03671449136570.20757601877-0.08018583174181.4117861708-0.0819624542695-0.1399470368111.35058741141-0.03140485968351.29033678697-121.70991849253.2514817713-45.0108741413
192.841081039710.433551572867-0.672625061712.232413736130.2284003852891.88035469766-0.6138415044010.363915338147-0.3629057435590.2282503069440.3938288235820.2428647353270.1082317645510.384331913909-0.04488751472951.466675405960.0973368142149-0.2740786686211.21673028505-0.1057171889731.40161811908-115.03091474148.2657249258-58.6437062542
200.481768122272-0.293525222921-0.1677422182620.525007404492-0.2561467199510.28391764668-0.3379707694050.2849638569750.320845889232-0.1146973040020.6562195376270.4676361515660.107922534823-1.40110987830.0232200895212.018660684830.10639990862-0.2230400979361.968325566070.1724437819822.21590411716-129.1635856456.344471497-65.7951326766
211.661357382270.01258089460350.1132542595112.05331561325-0.505524963821.975663792730.3844484299380.8455242642840.391363898113-1.081143556810.187983483072-0.0748777262384-0.832519610768-0.239677543843-0.01372047264762.183723037620.133046670364-0.2765804363581.486125218260.1116093222771.34720678579-117.69035292861.7724471821-74.8501900924
223.319611838150.428764348975-0.01279178573472.605774336331.11048739651.603042273520.2636500793170.258729626801-0.279988453112-1.302712321380.1135465034870.2489269051490.2687458790660.33131022602-0.02676961017191.66018077419-0.0707196081971-0.1852697446281.22319332372-0.1259511980721.22919197504-109.23544616547.5970051139-73.4158317258
232.023725199190.00174537112883-0.4932179868780.275870927278-0.9107972558972.78297202602-0.2218212551120.2533186844660.9591038043910.7955016034550.2138557149380.36951100299-0.6215169504110.776471932346-0.04002692780491.916154645790.146931841111-0.04350500679862.33499475258-0.05746127825252.42867672211-92.42766670453.9588250598-49.4162326112
242.90355237397-0.422643270434-2.07706978222.804892178480.8314804945974.07245844811-0.163287540363-0.507931515692-0.9065104897740.5421392354280.341034437634-0.1805540345750.251419151852-0.03874417240850.02573897873431.2915719857-0.09534633433730.09490159807051.36955384270.04297583045551.45770924265-147.48641893636.7884599336-35.807941954
250.862061174810.978998625614-1.242640902162.93073630291-2.870071037663.7327077029-0.4561937532150.555036645869-0.213664050415-0.9383373773710.2724671326730.1958866618210.554646122737-1.37524496205-0.1659266056121.370766995960.2131932613630.01435030886391.35959161449-0.05885578533071.70076757048-157.30826604647.6027529411-45.4545703431
262.570325787910.2912539403390.05140403863572.573687769860.1776750592472.33866920495-0.05208075097890.2428893409810.13526774826-0.1686218506960.03741102207460.0289530732429-0.545873113996-0.327849483689-0.06997532088961.199233100490.0875200445557-0.1466376695061.192192927060.07950329996581.34270525099-148.21282125252.8264096682-46.407896914
272.40839117955-0.534414330221-0.2691371488711.926828877460.5602368227390.827928903401-0.204500954567-0.2479561682951.068744467420.327912998683-0.1161831284620.188385303378-1.08491138966-0.785185035146-0.04807118970071.542361851250.207182773343-0.07106721622681.47405248227-0.1413312024461.37970432015-149.46036734259.3492785664-39.1693181861
281.325887018111.211749983780.4305911609082.091435726692.594766955154.122752769040.2569696394180.6008443862070.351252969505-0.876574516776-0.147331084314-0.700221950198-0.665387654016-0.326704613692-0.2591731012771.080882399340.0590456331308-0.1325039652731.354138846590.06278845936361.42737931115-142.20044806937.5166880269-58.7121034997
291.756299200370.220223934701-0.3930250026052.107560870020.8728836595463.31199188813-0.1069156742880.4044601184690.09153138185380.04574486797140.2807928249290.06937916764620.116174566822-0.23774357559-0.05457718264791.34115931212-0.0796399253499-0.0338021288951.27252830380.0121179011091.35625853925-152.70069254533.5797974443-57.9915034978
300.554069637561-0.99209360013-0.4511003899231.881976215180.8368064464392.49809809453-0.0480636141095-0.0560482009487-1.06531425224-0.2386127360990.49217201444-0.06356405071610.35174492954-0.0255463697529-0.1637712539791.481503425450.0923210936916-0.01506387610031.39115596569-0.01889872360521.50629730924-147.68678759721.0967393769-63.5360866979
312.636042340730.246566580242-1.484503583751.533782491461.740719291753.518049616390.77919356005-0.2709906361550.5405807867950.887884939336-0.7934760708531.85017848634-1.32356611129-1.68577437808-0.123931930961.60613221427-0.00328242844055-0.03905014105061.76520812088-0.170090894341.67134293034-160.58589857331.5822886014-51.9815130775
320.640571833351-0.19487044430.2415171638091.23037634570.02837750094124.13511858391-0.0472291483229-0.111582315112-0.057862858272-0.03871044973560.1340503288130.6827476756050.0885767024285-0.606285973779-0.0696219650411.382352580240.05936118512440.05407897905061.385596444770.1628173898741.6928850485-173.00829561518.9511438698-7.24208217556
330.81511116960.196781461572-0.380691738570.899423081344-0.06876336840090.917125611753-0.1471663031480.1604418011520.6630306184010.2345894503670.1151312186290.55098048347-0.635924317499-0.2008841186210.03295363387661.764920147090.2137014450650.01639286149651.149072684280.09849061206611.53865467764-161.4781773543.1943607156-6.8326729359
341.588684833111.664220155571.186189348831.507191915780.7552379100452.884786968040.1144211457180.5084362919270.1881059765870.0176261625367-0.261517760842-0.372345010666-0.169316901911-0.184767570653-0.08885741344181.465913384750.0158228063998-0.02621922059181.148075955880.1402524354761.39091818868-140.9580434842.0905625956-17.6149575786
351.78272307514-0.1102013540140.2111176737152.06742764365-0.8407627684261.9598984539-0.0392146737837-0.03095662667410.27190634190.223947642364-0.117661924261-0.533921425736-0.3680599987190.15036082037-0.007578541997231.61723077983-0.0467502603861-0.1916502061370.996730479048-0.0393165689421.41424661449-132.68855611839.98387071662.81441981453
361.672392343211.21795362855-0.2090818073650.3619216185390.1331959704682.141311639830.128456790292-0.674622795850.1113416197540.7518736552870.0205373084460.119347820284-0.478452357587-0.204748751117-0.0907788289252.09843411840.2575332981340.2244509242881.494769843250.0326495650261.41605664982-157.32378740430.947494040322.6890861474
371.71425534286-0.4072724831331.238995809153.18235219135-1.872745568311.529276762170.1966576751620.2983056784980.1715657069260.2344191577110.368039981583-0.010925449328-0.1590580074920.334582977633-0.04971664953351.577040274120.01962960383250.006078517860121.249268043770.04054949078661.55027295587-120.53563654112.119856597616.8342123275
383.862553260410.5232366653671.5278632632.873972730850.6217841257372.66207250391-0.124843353938-0.1153806060110.05204066438360.131727342810.0698982930021-0.289475228641-0.06451523603520.211734503706-0.01766111677261.36519296986-0.009686432871050.09700090548981.077191446040.01381812116321.2104188349-130.9997504661.6342615432111.6556645086
392.191518162520.568763889453-0.1042797793533.30889436148-0.4614324185262.45400613001-0.061889834967-0.159457785183-0.158072648618-0.0271934002771-0.01788157076160.6759247058570.100079958494-0.216789690743-0.08639814584191.25125755118-0.0334367985380.06678307669971.019724154220.05666178687241.25227995241-149.993506129-4.079453107337.66705079368
404.623418892990.7787842118960.7533521116651.701369295090.06615916975741.90546757829-0.167906071397-0.520564878205-0.137989978540.3911546561780.0133537505053-0.204847115030.1991815060120.0060699069565-0.03152531616691.540092465310.0452043645992-0.04291155368611.19371755926-0.02773106803681.10250655316-109.529507922-7.3640178525832.1346359657
411.625069794860.7640263150870.2195521354432.572348619830.7948588636911.04069963158-0.252961749117-0.113715458477-0.109418733782-0.1696673889150.08565425228730.6072273683050.290294519177-0.266434815179-0.03438694818571.55045820226-0.04950521319270.06597496118491.106848877340.023804768641.38031068315-112.723192075-25.31409138120.1821170916
423.492082464310.8330196999760.4649525337471.543316332361.917967010732.67187274485-0.2234638827360.0687752096078-0.25519116709-0.1033422824490.5588345632220.4541742801230.7441961392760.08318608076810.002721028155811.60964107635-0.01004041911090.1472308909151.48141794677-0.09471133508931.25042695504-109.830576602-34.89955127118.90987210887
433.093418260920.5534158322841.699181109673.701996723450.2040256379073.502018158620.0724727843581-1.07731124799-0.3961607627881.39811012821-0.883242868132-2.119960951910.4584492885311.143315309610.08573241288651.831500299510.0927365238996-0.03108475102871.396037215180.1057346095821.59930597211-100.966992359-28.754350655426.445147717
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 307 )AA1 - 3071 - 307
22chain 'A' and (resid 308 through 819 )AA308 - 819308 - 505
33chain 'A' and (resid 820 through 1140 )AA820 - 1140506 - 826
44chain 'B' and (resid 715 through 794 )BB715 - 7941 - 80
55chain 'B' and (resid 795 through 880 )BB795 - 88081 - 166
66chain 'B' and (resid 881 through 901 )BB881 - 901167 - 187
77chain 'B' and (resid 902 through 1041 )BB902 - 1041188 - 327
88chain 'C' and (resid 20 through 83 )CD20 - 831 - 64
99chain 'C' and (resid 84 through 150 )CD84 - 15065 - 131
1010chain 'C' and (resid 151 through 192 )CD151 - 192132 - 173
1111chain 'C' and (resid 193 through 233 )CD193 - 233174 - 214
1212chain 'C' and (resid 234 through 243 )CD234 - 243215 - 224
1313chain 'C' and (resid 244 through 267 )CD244 - 267225 - 248
1414chain 'D' and (resid 1 through 365 )DE1 - 3651 - 365
1515chain 'D' and (resid 366 through 819 )DE366 - 819366 - 506
1616chain 'D' and (resid 820 through 1140 )DE820 - 1140507 - 827
1717chain 'E' and (resid 715 through 768 )EF715 - 7681 - 54
1818chain 'E' and (resid 769 through 832 )EF769 - 83255 - 118
1919chain 'E' and (resid 833 through 880 )EF833 - 880119 - 166
2020chain 'E' and (resid 881 through 901 )EF881 - 901167 - 187
2121chain 'E' and (resid 902 through 980 )EF902 - 980188 - 266
2222chain 'E' and (resid 981 through 1026 )EF981 - 1026267 - 312
2323chain 'E' and (resid 1027 through 1043 )EF1027 - 1043313 - 329
2424chain 'F' and (resid 20 through 42 )FH20 - 421 - 23
2525chain 'F' and (resid 43 through 63 )FH43 - 6324 - 44
2626chain 'F' and (resid 64 through 123 )FH64 - 12345 - 104
2727chain 'F' and (resid 124 through 150 )FH124 - 150105 - 131
2828chain 'F' and (resid 151 through 174 )FH151 - 174132 - 155
2929chain 'F' and (resid 175 through 217 )FH175 - 217156 - 198
3030chain 'F' and (resid 218 through 243 )FH218 - 243199 - 224
3131chain 'F' and (resid 244 through 267 )FH244 - 267225 - 248
3232chain 'G' and (resid 1 through 294 )GI1 - 2941 - 294
3333chain 'G' and (resid 295 through 743 )GI295 - 743295 - 429
3434chain 'G' and (resid 744 through 795 )GI744 - 795430 - 481
3535chain 'G' and (resid 796 through 947 )GI796 - 947482 - 633
3636chain 'G' and (resid 948 through 1140 )GI948 - 1140634 - 826
3737chain 'H' and (resid 715 through 768 )HJ715 - 7681 - 54
3838chain 'H' and (resid 769 through 901 )HJ769 - 90155 - 187
3939chain 'H' and (resid 902 through 1043 )HJ902 - 1043188 - 329
4040chain 'I' and (resid 20 through 150 )IL20 - 1501 - 131
4141chain 'I' and (resid 151 through 218 )IL151 - 218132 - 199
4242chain 'I' and (resid 219 through 243 )IL219 - 243200 - 224
4343chain 'I' and (resid 244 through 267 )IL244 - 267225 - 248

+
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://pdbjlvh1.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