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- PDB-5lpk: Crystal structure of the bromodomain of human EP300 bound to the ... -

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Basic information

Entry
Database: PDB / ID: 5lpk
TitleCrystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1
ComponentsHistone acetyltransferase p300
KeywordsTRANSCRIPTION / bromodomain / protein-inhibitor complex / epigenetics
Function / homology
Function and homology information


behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation ...behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation / histone H2B acetyltransferase activity / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / thigmotaxis / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / positive regulation of TORC2 signaling / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / cellular response to L-leucine / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / TGFBR3 expression / positive regulation by host of viral transcription / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / face morphogenesis / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / megakaryocyte development / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase activity / acetyltransferase activity / PI5P Regulates TP53 Acetylation / FOXO-mediated transcription of cell death genes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / fat cell differentiation / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / histone acetyltransferase complex / canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / NF-kappaB binding / negative regulation of gluconeogenesis / cellular response to nutrient levels / somitogenesis / negative regulation of protein-containing complex assembly / pre-mRNA intronic binding / Attenuation phase / positive regulation of T-helper 17 cell lineage commitment / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / skeletal muscle tissue development / regulation of cellular response to heat
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-XDM / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHuegle, M. / Wohlwend, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWO2012/1-1 Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles.
Authors: Hugle, M. / Lucas, X. / Ostrovskyi, D. / Regenass, P. / Gerhardt, S. / Einsle, O. / Hau, M. / Jung, M. / Breit, B. / Gunther, S. / Wohlwend, D.
History
DepositionAug 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase p300
B: Histone acetyltransferase p300
C: Histone acetyltransferase p300
D: Histone acetyltransferase p300
E: Histone acetyltransferase p300
F: Histone acetyltransferase p300
G: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,14139
Polymers101,0567
Non-polymers4,08532
Water8,701483
1
A: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2589
Polymers14,4371
Non-polymers8218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3229
Polymers14,4371
Non-polymers8858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9134
Polymers14,4371
Non-polymers4773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9425
Polymers14,4371
Non-polymers5054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2325
Polymers14,4371
Non-polymers7964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9765
Polymers14,4371
Non-polymers5394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4992
Polymers14,4371
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.600, 61.040, 135.680
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300


Mass: 14436.515 Da / Num. of mol.: 7 / Fragment: bromodomain, UNP residues 1040-1161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09472, histone acetyltransferase

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Non-polymers , 5 types, 515 molecules

#2: Chemical
ChemComp-XDM / ~{N}-[(3-chlorophenyl)methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide / XDM1


Mass: 318.798 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C17H19ClN2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 % / Mosaicity: 0.71 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5 / Details: PEG 3350, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→41.52 Å / Num. obs: 104124 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.813.92.9861961650940.1681.6823.4470.499.8
9.74-41.524.90.03633236820.9990.0170.0428.998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å41.52 Å
Translation2.1 Å41.52 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.5phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-p300 (pdb 3I3J)
Resolution: 2.1→41.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.891 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 3107 4.9 %RANDOM
Rwork0.1764 ---
obs0.1778 60323 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.75 Å2 / Biso mean: 41.958 Å2 / Biso min: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å20.96 Å2
2--1.08 Å20 Å2
3----2.02 Å2
Refinement stepCycle: final / Resolution: 2.1→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 268 483 7473
Biso mean--41.57 41.99 -
Num. residues----799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027206
X-RAY DIFFRACTIONr_bond_other_d0.0010.026802
X-RAY DIFFRACTIONr_angle_refined_deg1.3012.0099744
X-RAY DIFFRACTIONr_angle_other_deg0.783315709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42324.504353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.577151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8771545
X-RAY DIFFRACTIONr_chiral_restr0.070.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021621
X-RAY DIFFRACTIONr_mcbond_it0.8892.1193209
X-RAY DIFFRACTIONr_mcbond_other0.8892.1193208
X-RAY DIFFRACTIONr_mcangle_it1.4023.1674006
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 223 -
Rwork0.243 4418 -
all-4641 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.69410.0123-0.04093.6928-1.10183.93840.1799-0.0974-0.12250.1461-0.12470.13090.14360.122-0.05530.056-0.03630.00860.1362-0.04430.0258144.2521-72.8537154.3665
22.07371.0094-0.50981.7517-0.62333.24750.0367-0.02990.11790.02420.01680.0802-0.0240.069-0.05350.0157-0.02620.01540.0479-0.02420.0187141.7192-69.5084147.335
36.48812.8142-1.21287.1162-1.77464.1745-0.029-0.0814-0.50910.0455-0.1086-0.28280.37510.1010.13760.14080.0373-0.02610.1623-0.01310.1402147.8796-82.5927147.5919
48.10631.01934.10676.5574-1.56668.3493-0.019-0.37820.23230.7316-0.2106-0.3925-0.19990.71980.22960.28940.0877-0.01090.39860.0350.2986178.0128-64.0933149.5109
52.159-0.79140.9372.0001-1.36383.94320.0557-0.05320.09640.013-0.1369-0.2807-0.06160.30950.08130.0088-0.01410.00620.08930.01690.0527164.5022-52.6028138.1121
61.92460.4078-1.05856.049-4.76827.27150.0001-0.0784-0.44890.2485-0.2612-0.17530.6240.16950.2610.34450.0482-0.05130.21980.01460.2941166.6103-69.0767141.1139
72.4558-1.7809-0.88096.88652.71353.56260.11520.13720.18570.0703-0.21580.7365-0.6006-0.6460.10060.23390.05090.02350.28830.04120.2467146.0026-48.3644166.5107
81.0386-0.3122-0.51763.02572.01123.15430.0777-0.2141-0.02230.1903-0.12110.20210.1566-0.08940.04330.0347-0.0693-0.00150.18120.03540.0606151.8056-59.4586171.7077
96.1435-2.0108-2.9176.17463.42235.28350.0498-0.04940.1252-0.10260.1033-0.2301-0.20760.4111-0.15310.026-0.064-0.00590.1620.02360.0208162.0238-56.1054161.6696
1010.8398-3.3436-0.138311.71610.82836.80980.1213-0.58170.68220.3406-0.02820.042-0.30160.0212-0.09310.3484-0.02410.03510.2499-0.0420.3719153.0564-39.4137170.4557
113.49580.336-1.17771.88981.0013.78070.1793-0.24730.08340.084-0.0946-0.06190.13230.028-0.08470.1189-0.12260.02440.23080.0110.0266136.0392-69.5888180.2478
124.7458-1.5464-4.542310.23671.39244.3497-0.1530.0012-0.15730.4189-0.00550.12440.12850.00990.15850.2732-0.0092-0.0230.2370.00470.2686136.1959-83.021185.8637
1312.0769-10.2249-8.781214.08233.57659.840.1347-0.7283-0.3232-0.27910.150.25540.41720.7638-0.28470.5279-0.0313-0.08450.4020.09440.5643144.5556-85.824182.8462
149.0718-3.18225.63845.38130.05444.5011-0.5366-0.04590.9973-0.4101-0.0005-0.8983-0.7267-0.10540.53720.7519-0.0062-0.13020.4655-0.14440.7055181.4457-25.2668197.5804
1510.46483.61274.98734.73613.587610.646-0.4166-0.10040.47160.05020.00670.3236-0.3908-0.15960.40980.21580.00190.04610.18990.00630.1511169.149-33.2077191.3254
163.07111.13440.90382.01310.58414.14530.09680.0221-0.34290.02540.11350.07070.2363-0.1539-0.21020.0791-0.07190.02890.2316-0.01680.1056171.0239-49.7537187.2306
172.97151.8313.41833.70213.32476.3907-0.1370.18380.0337-0.16180.27550.1227-0.42280.0971-0.13850.107-0.11060.05980.2824-0.01780.0563173.7165-43.2829180.311
188.80116.25381.84359.8673.93672.7303-0.06070.13980.6333-0.3084-0.0137-0.1869-0.58920.27510.07450.4031-0.0440.01540.34940.04570.3755172.8144-29.2997181.6678
1910.086-0.38021.61120.76752.864511.7494-0.06410.10750.402-0.02940.04390.022-0.0750.30970.02020.3730.0174-0.02540.2473-0.01420.4179128.9474-47.0598143.9606
201.6055-1.76920.85353.4622-0.4743.84950.1313-0.1660.44740.024-0.2251-0.3869-0.45-0.19690.09380.1351-0.04890.10120.2368-0.01930.2269125.8712-60.1064163.7257
213.68851.8012-0.76655.0607-1.44992.0060.11970.25650.1709-0.30920.03420.0774-0.0522-0.3784-0.15390.1092-0.01520.06630.2205-0.0120.0757123.3887-64.6335156.0199
221.60442.5828-0.46627.6123-3.43894.53570.1097-0.07010.49050.1540.13720.6504-0.5218-0.6943-0.24690.15280.04010.11520.3287-0.01820.2314113.9292-60.7661165.2086
230.8341-2.15012.08165.6519-5.39655.20450.1035-0.012-0.1302-0.47210.23950.41870.2966-0.1037-0.3430.8299-0.13270.01980.60080.13090.6322116.7466-46.6182150.3549
242.36890.21830.13724.8571-0.86844.0846-0.0777-0.2336-0.49730.43220.13-0.47450.4718-0.1878-0.05240.16160.01050.00240.32890.02810.2781160.2565-58.9567200.5083
252.3847-1.58281.83976.0664-2.57164.507-0.1152-0.3032-0.14730.53810.2518-0.0086-0.066-0.527-0.13660.13740.05150.06650.34030.04560.12154.8759-51.8976204.0877
261.2755-0.50780.71287.8643-3.56916.1720.0694-0.1571-0.53820.35880.17710.37010.5121-0.4748-0.24650.1417-0.06680.02650.37390.05350.3187149.71-59.7121195.2813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1046 - 1088
2X-RAY DIFFRACTION2A1089 - 1143
3X-RAY DIFFRACTION3A1144 - 1161
4X-RAY DIFFRACTION4B1049 - 1059
5X-RAY DIFFRACTION5B1060 - 1146
6X-RAY DIFFRACTION6B1147 - 1160
7X-RAY DIFFRACTION7C1048 - 1077
8X-RAY DIFFRACTION8C1078 - 1132
9X-RAY DIFFRACTION9C1133 - 1149
10X-RAY DIFFRACTION10C1150 - 1161
11X-RAY DIFFRACTION11D1047 - 1149
12X-RAY DIFFRACTION12D1150 - 1155
13X-RAY DIFFRACTION13D1156 - 1161
14X-RAY DIFFRACTION14E1047 - 1052
15X-RAY DIFFRACTION15E1053 - 1068
16X-RAY DIFFRACTION16E1069 - 1109
17X-RAY DIFFRACTION17E1110 - 1146
18X-RAY DIFFRACTION18E1147 - 1159
19X-RAY DIFFRACTION19F1047 - 1051
20X-RAY DIFFRACTION20F1052 - 1087
21X-RAY DIFFRACTION21F1088 - 1133
22X-RAY DIFFRACTION22F1134 - 1155
23X-RAY DIFFRACTION23F1156 - 1161
24X-RAY DIFFRACTION24G1047 - 1085
25X-RAY DIFFRACTION25G1086 - 1133
26X-RAY DIFFRACTION26G1134 - 1160

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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