[English] 日本語
Yorodumi
- PDB-7b48: Structural basis of reactivation of oncogenic p53 mutants by a sm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b48
TitleStructural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (II)
ComponentsCellular tumor antigen p53P53
KeywordsTRANSCRIPTION / P53 / TUMOR SUPPRESSOR / DNA BINDING PROTEIN / PROTEIN DNA COMPLEX / MICHAEL ACCEPTOR / MICHAEL REACTION / PROTEIN-DRUG COMPLEX / PROTEIN-DNA-DRUG COMPLEX / LOOP-SHEET-HELIX MOTIF / DNA TARGET / ACTIVATOR / HOOGSTEEN BASE-PAIRING
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDegtjarik, O. / Rozenberg, H. / Shakked, Z.
Funding support1items
OrganizationGrant numberCountry
Aprea Therapeutics AB
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ).
Authors: Degtjarik, O. / Golovenko, D. / Diskin-Posner, Y. / Abrahmsen, L. / Rozenberg, H. / Shakked, Z.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,29521
Polymers89,9464
Non-polymers1,34917
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint16 kcal/mol
Surface area36370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.249, 72.003, 85.233
Angle α, β, γ (deg.)90.000, 90.066, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22486.535 Da / Num. of mol.: 4 / Fragment: p53 human DNA binding domain / Mutation: R273H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: pET-27-b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637

-
Non-polymers , 6 types, 486 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QNN / (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one


Mass: 139.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Nonpolymer detailsTwo enantiomers, QNN and QN8 are produced by addition reaction of the michael acceptor compound "2- ...Two enantiomers, QNN and QN8 are produced by addition reaction of the michael acceptor compound "2-methylenequinuclidin-3-one" with cysteine or lysine. As such, QNN and QN8 bind covalently to the thiol group of cysteine or amino group of lysine. The chiral definitions of QNN and QN8 bound to cysteines are reversed to that of the pseudo free ligands.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.01 % / Mosaicity: 0.64 °
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.1
Details: 0.2M Li Acetate, 2.0% w/v Agarose, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.756
11-h,-k,l20.244
ReflectionResolution: 2.05→39 Å / Num. obs: 49698 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.073 / Rrim(I) all: 0.136 / Χ2: 1.094 / Net I/σ(I): 10.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.0930.25421270.910.1620.3030.68381.1
2.09-2.123.10.25922110.9260.1610.3070.68884.5
2.12-2.1630.2523420.9210.1570.2970.73988.7
2.16-2.2130.27623630.9150.1750.3280.78392.4
2.21-2.263.10.22225340.9250.1410.2640.77695.1
2.26-2.313.20.23825460.9340.1510.2830.83296.3
2.31-2.373.20.22525070.9370.1420.2670.82596.8
2.37-2.433.10.18825740.9550.120.2250.93496.6
2.43-2.52.90.17425020.9510.1160.2110.99696
2.5-2.582.90.16125190.9510.1070.1951.08295.9
2.58-2.683.20.15725420.9620.0980.1861.07296.3
2.68-2.783.10.1425340.9610.090.1671.14196.2
2.78-2.9130.12724910.9620.0820.1521.28195.3
2.91-3.063.30.12325720.9720.0770.1461.34497.6
3.06-3.253.30.11425570.9750.0710.1351.48397.2
3.25-3.53.20.10625480.9790.0670.1261.4696.6
3.5-3.863.20.09825730.9780.0630.1171.44296
3.86-4.4130.08825230.9810.0580.1061.40895.6
4.41-5.562.90.08425300.9820.0560.1021.36694.7
5.56-393.10.08326030.9880.0540.11.30595.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IBS

4ibs


Resolution: 2.05→36.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1744 / FOM work R set: 0.8089 / SU B: 7.979 / SU ML: 0.127 / SU R Cruickshank DPI: 0.0447 / SU Rfree: 0.0383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2400 4.8 %RANDOM
Rwork0.1762 ---
obs0.1787 47284 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 31.036 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1--7.59 Å2-0 Å2-4.02 Å2
2--11 Å20 Å2
3----3.41 Å2
Refinement stepCycle: final / Resolution: 2.05→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 77 477 6509
Biso mean--36.83 33.37 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136283
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175694
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.6658535
X-RAY DIFFRACTIONr_angle_other_deg1.441.57813145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0195790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80520.583343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.253151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7041562
X-RAY DIFFRACTIONr_chiral_restr0.0970.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021466
LS refinement shellResolution: 2.05→2.101 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 91 -
Rwork0.174 2947 -
all-3038 -
obs--78.04 %
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)
121.8898-1.1436-2.38831.55890.55730.4548-0.13180.3771-0.478-0.28690.1284-0.26060.07910.05350.00330.40820.00440.11460.26830.02870.09056.483-22.807-23.724
27.6101-0.11910.98485.65263.328512.3446-0.0739-0.3679-0.0626-0.0527-0.08950.03560.0112-0.12770.16340.0717-0.00190.06880.2131-0.01520.0691.208-11.235-16.551
31.7475-0.35810.63130.3934-0.15031.98650.00040.05930.084-0.0363-0.02220.0388-0.0484-0.0160.02190.0623-0.00250.05680.2997-0.00640.0847-0.102-8.967-32.109
40.7672-2.03820.75865.7373-0.94724.45610.0880.0113-0.0691-0.1423-0.01890.14050.54880.0453-0.0690.1640.04910.07870.2855-0.04330.1529.97-26.568-36.425
58.0619-8.1845-4.075827.27518.56553.09590.71790.022-0.1967-0.2017-0.5726-0.8638-0.2372-0.107-0.14530.315-0.11740.12290.7969-0.05920.186316.398-16.599-48.784
60.2934-0.19860.10720.1397-0.07240.04030.14880.0932-0.0669-0.1355-0.09770.01090.05640.0423-0.05110.5034-0.19360.17670.7698-0.02380.466218.261-5.789-44.167
71.82170.68880.93991.77021.82182.6076-0.05430.08250.1601-0.25440.1096-0.0725-0.23440.2705-0.05530.0847-0.01450.06760.36250.00740.085116.073-8.328-34.647
81.9316-0.2289-0.1261.08980.92171.95830.04420.0730.1936-0.0638-0.0253-0.1008-0.0970.139-0.01890.05910.0040.06210.28050.00580.09258.756-8.11-30.774
91.375-1.63291.03943.93092.23187.78070.25820.1168-0.1681-0.2495-0.0072-0.03380.31670.3328-0.2510.14310.01640.03520.2821-0.07420.18516.537-22.538-40.903
106.12760.17311.42740.014-0.03353.45870.0427-0.204-0.2239-0.00310.0318-0.00280.33940.3599-0.07460.12260.04120.05930.35290.01040.073810.821-11.763-18.69
114.3232-0.87991.03581.6349-1.89913.02380.10180.2623-0.2645-0.2058-0.0920.10020.2318-0.0636-0.00970.1013-0.01250.04490.2677-0.05860.0764-3.651-15.248-40.934
1214.19816.7974-2.32878.98456.380710.4528-0.22340.4132-1.3353-0.025-0.3002-0.34940.27-0.56370.52360.122-0.0525-0.02710.3673-0.07490.5389-12.375-21.163-41.927
133.055-3.6881-4.42678.04616.869314.1079-0.0425-0.269-0.44410.230.111-0.21220.3206-0.3351-0.06840.1121-0.03810.0710.21580.13280.37890.493-20.07520.326
1410.6287-4.36723.45311.947-0.97322.4354-0.1639-0.3988-0.54630.05020.20940.2712-0.1207-0.0469-0.04560.08070.00660.03680.25230.01660.1722-9.188-8.30112.521
157.2992-1.1237-2.1393.2133-1.22452.4528-0.11840.477-0.22050.03020.1228-0.1135-0.0277-0.0647-0.00450.07740.00540.06250.4184-0.09160.0811-10.06-9.6783.036
163.72870.5545-1.28540.7373-0.05081.4758-0.0109-0.0711-0.18330.08350.02960.1045-0.07-0.0793-0.01870.08310.02450.0820.2420.00140.10591.386-9.96813.049
176.33531.47365.111610.2122-1.78945.02940.47150.3724-0.7238-0.31420.1575-0.11510.51630.2799-0.6290.2403-0.02620.10660.2201-0.1470.3336.175-26.8360.385
183.08060.5903-1.60720.1713-0.34210.87840.13450.1194-0.16410.079-0.1837-0.0735-0.16670.04580.04920.2189-0.09090.02380.73180.03830.141214.2-7.682-3.479
193.6088-0.0276-0.51233.33111.04762.6423-0.09410.0427-0.14080.04390.0194-0.0739-0.01790.13730.07470.0517-0.0080.0420.2779-0.00070.080713.448-10.5939.293
2017.2541-2.65931.83741.3155-0.87954.45670.1584-0.63591.98770.0801-0.3412-0.2448-0.55790.2550.18280.40570.09730.1020.5855-0.03760.2621-0.385-0.25823.621
212.2437-0.7701-1.71.0141.89326.0967-0.11670.2433-0.01750.09440.00220.06250.1747-0.28710.11440.084900.04110.2687-0.00130.07882.487-8.7163.721
221.20960.871-0.95451.63581.430912.569-0.11520.2008-0.3949-0.04270.0688-0.00520.602-0.31040.04640.0932-0.01210.03330.2225-0.07570.32512.266-18.1434.421
234.64-0.55140.51330.2724-0.05591.4495-0.08870.223-0.56930.01310.02640.06040.0391-0.07490.06220.0712-0.01010.07450.2131-0.04890.1336-1.568-13.798.579
248.131110.5423-4.135222.80320.90226.4107-0.07460.7502-0.06970.20170.0803-0.12570.2989-0.9635-0.00570.2670.0566-0.00840.4948-0.11780.1605-16.859-17.569-2.434
255.3027-0.7331-1.16071.0005-1.32732.7159-0.19770.67480.04020.21540.33450.0766-0.2626-0.8524-0.13680.11760.1160.00450.7746-0.09820.0507-32.139-2.665-46.704
263.38590.6858-0.21610.1398-0.04080.3794-0.02620.0149-0.25790.0015-0.0056-0.0437-0.03190.08920.03180.071-0.01940.07260.4037-0.04530.1165-38.166-7.663-29.326
273.26553.0473.864815.28647.280411.37770.11540.0961-0.2349-0.0862-0.48231.1667-0.2204-0.12320.36690.0926-0.0126-0.04660.4052-0.130.2525-35.682-13.373-49.084
282.2674-0.47-1.06086.08263.43422.48280.0970.20880.0526-0.3805-0.16320.2458-0.2822-0.06620.06620.05790.02820.03070.38380.02530.073-25.415-1.112-39.115
293.28870.2426-0.10832.7168-0.60612.27240.1389-0.17380.04760.0376-0.1636-0.37460.19570.1420.02460.062-0.040.01250.3734-0.02750.0676-19.4190.53-25.114
307.8411-4.2502-0.51169.3178-4.43895.5692-0.2611-0.30020.3580.38370.0287-0.2927-0.09980.31470.23240.0943-0.04320.01950.2693-0.01730.0529-17.081-4.436-27.349
313.43660.3624-0.87352.52971.39251.4336-0.00490.43-0.16420.0226-0.1125-0.06440.069-0.2550.11740.0386-0.0020.04460.412800.0896-19.585-8.343-36.838
323.21780.21980.26822.72753.20186.201-0.10980.2343-0.60120.211-0.13090.18590.0749-0.2350.24070.0541-0.03560.07180.3763-0.06560.1924-30.606-12.684-33.259
333.7319-2.67950.80444.048-5.381711.14770.297-0.24640.5590.18840.0731-0.1776-0.66070.1487-0.37010.402-0.08360.0970.3393-0.09580.1322-27.5786.169-22.471
343.0908-0.4394-4.59221.55121.84847.78350.02620.15590.0881-0.10740.02190.0879-0.1209-0.1987-0.04810.06430.0561-0.00580.4277-0.0080.0229-24.889-4.216-45.815
354.64331.0769-2.37120.9172-2.54327.4305-0.01030.11410.09470.0074-0.1267-0.01050.04280.1190.13690.0652-0.03520.06530.3524-0.05020.0728-35.514-1.96-27.613
364.4126-1.3061.208211.0484-0.83673.253-0.0109-0.38620.5560.2999-0.0042-0.0114-0.4265-0.24060.01510.0899-0.03180.05430.3019-0.05070.1487-45.80.946-23.591
372.34662.59212.42593.81021.66628.10090.02610.38910.17030.11650.27540.0578-0.2534-0.085-0.30160.05820.0466-0.03560.37530.1890.2199-33.5374.964-0.724
384.5091.22290.45830.4560.37912.0568-0.035-0.15590.0737-0.0684-0.0330.0548-0.01880.03510.0680.07350.01790.02890.28950.00080.0885-44.187-6.91512.026
393.02340.1517-0.57890.9363-0.37192.2111-0.09910.36130.1073-0.05010.0146-0.05820.1741-0.12070.08440.0396-0.00720.03320.36260.02320.0455-33.563-7.6944.02
405.3731-2.2039-2.815315.92440.13611.54580.1620.37330.64720.46210.21510.1365-0.1322-0.2278-0.37710.18980.04390.01250.2005-0.0460.4519-31.0949.66917.506
411.48010.5419-1.04593.1975-2.53743.82250.0981-0.39860.49790.1256-0.2216-0.1954-0.07250.84610.12360.0849-0.01360.02710.4556-0.02810.2468-23.065-0.62621.511
420.12440.2294-0.35490.9416-3.535418.36880.05460.0163-0.22860.07820.0627-0.3359-0.27280.353-0.11730.11930.0402-0.0040.4611-0.06430.5305-18.489-12.07919.336
433.6490.3594-0.23061.73161.10842.5177-0.04770.18380.0943-0.0239-0.0303-0.05250.06650.06080.0780.0381-0.00330.03940.30650.02150.0676-21.291-5.6269.136
443.46740.89740.87670.2761-0.21665.0179-0.07140.2648-0.1944-0.0340.085-0.04150.2680.0636-0.01360.1060.02580.04860.2972-0.00880.0897-33.375-10.5537.553
453.036-0.27590.80032.88434.777716.9499-0.0904-0.16310.58240.13450.06270.18430.1473-0.11290.02770.0396-0.01040.0250.1902-0.01050.1951-31.6471.91415.175
4615.16258.7767-4.09785.0812-2.3781.17120.2910.13240.79150.17390.09320.4775-0.1606-0.0767-0.38430.1912-0.00820.17390.53830.2310.5486-25.1880.424-5.532
474.29680.782-1.09781.28610.04470.55170.0183-0.32410.37620.17080.00030.0513-0.054-0.1214-0.01860.0920.0487-0.03730.3421-0.05290.1157-40.87-3.80617.255
4813.8063-11.47932.239617.46582.44022.73230.0163-0.48860.3478-0.2921-0.11250.0187-0.1763-0.32510.09620.44870.17820.06550.5146-0.06970.4974-51.1831.18921.331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 102
2X-RAY DIFFRACTION2A103 - 110
3X-RAY DIFFRACTION3A111 - 162
4X-RAY DIFFRACTION4A163 - 175
5X-RAY DIFFRACTION5A176 - 181
6X-RAY DIFFRACTION6A182 - 188
7X-RAY DIFFRACTION7A189 - 208
8X-RAY DIFFRACTION8A209 - 241
9X-RAY DIFFRACTION9A242 - 254
10X-RAY DIFFRACTION10A255 - 267
11X-RAY DIFFRACTION11A268 - 283
12X-RAY DIFFRACTION12A284 - 288
13X-RAY DIFFRACTION13B97 - 109
14X-RAY DIFFRACTION14B110 - 117
15X-RAY DIFFRACTION15B118 - 133
16X-RAY DIFFRACTION16B134 - 164
17X-RAY DIFFRACTION17B165 - 172
18X-RAY DIFFRACTION18B173 - 188
19X-RAY DIFFRACTION19B189 - 219
20X-RAY DIFFRACTION20B220 - 227
21X-RAY DIFFRACTION21B228 - 246
22X-RAY DIFFRACTION22B247 - 257
23X-RAY DIFFRACTION23B258 - 284
24X-RAY DIFFRACTION24B285 - 289
25X-RAY DIFFRACTION25D97 - 111
26X-RAY DIFFRACTION26D112 - 145
27X-RAY DIFFRACTION27D146 - 150
28X-RAY DIFFRACTION28D151 - 167
29X-RAY DIFFRACTION29D168 - 188
30X-RAY DIFFRACTION30D189 - 194
31X-RAY DIFFRACTION31D195 - 223
32X-RAY DIFFRACTION32D224 - 239
33X-RAY DIFFRACTION33D240 - 251
34X-RAY DIFFRACTION34D252 - 267
35X-RAY DIFFRACTION35D268 - 279
36X-RAY DIFFRACTION36D280 - 288
37X-RAY DIFFRACTION37C96 - 109
38X-RAY DIFFRACTION38C110 - 133
39X-RAY DIFFRACTION39C134 - 161
40X-RAY DIFFRACTION40C162 - 169
41X-RAY DIFFRACTION41C170 - 179
42X-RAY DIFFRACTION42C180 - 188
43X-RAY DIFFRACTION43C189 - 219
44X-RAY DIFFRACTION44C220 - 244
45X-RAY DIFFRACTION45C245 - 257
46X-RAY DIFFRACTION46C258 - 266
47X-RAY DIFFRACTION47C267 - 283
48X-RAY DIFFRACTION48C284 - 289

+
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