[English] 日本語
Yorodumi
- PDB-5ktw: CREBBP bromodomain in complex with Cpd 44 (3-((5-acetyl-1-(cyclop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ktw
TitleCREBBP bromodomain in complex with Cpd 44 (3-((5-acetyl-1-(cyclopropylmethyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl)amino)-N-isopropylbenzamide)
ComponentsCREB-binding protein
KeywordsTRANSFERASE / CREBBP bromodomain
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...peptide lactyltransferase (CoA-dependent) activity / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / protein acetylation / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / histone acetyltransferase activity / FOXO-mediated transcription of cell death genes / positive regulation of transforming growth factor beta receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / homeostatic process / histone acetyltransferase complex / Attenuation phase / cAMP/PKA signal transduction / protein-lysine-acetyltransferase activity / histone acetyltransferase / regulation of cellular response to heat / positive regulation of double-strand break repair via homologous recombination / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / canonical NF-kappaB signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / cellular response to nutrient levels / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Formation of the beta-catenin:TCF transactivating complex / Transcriptional regulation of white adipocyte differentiation / chromatin DNA binding / positive regulation of protein localization to nucleus / NOTCH1 Intracellular Domain Regulates Transcription / Evasion by RSV of host interferon responses / protein destabilization / Pre-NOTCH Transcription and Translation / tau protein binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription coactivator binding / p53 binding / cellular response to UV / transcription corepressor activity / rhythmic process / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / TRAF3-dependent IRF activation pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to hypoxia / transcription coactivator activity / nuclear body / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II
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 finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6XG / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.087 Å
AuthorsMurray, J.M. / Boenig, G.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Discovery of a Potent and Selective in Vivo Probe (GNE-272) for the Bromodomains of CBP/EP300.
Authors: Crawford, T.D. / Romero, F.A. / Lai, K.W. / Tsui, V. / Taylor, A.M. / de Leon Boenig, G. / Noland, C.L. / Murray, J. / Ly, J. / Choo, E.F. / Hunsaker, T.L. / Chan, E.W. / Merchant, M. / ...Authors: Crawford, T.D. / Romero, F.A. / Lai, K.W. / Tsui, V. / Taylor, A.M. / de Leon Boenig, G. / Noland, C.L. / Murray, J. / Ly, J. / Choo, E.F. / Hunsaker, T.L. / Chan, E.W. / Merchant, M. / Kharbanda, S. / Gascoigne, K.E. / Kaufman, S. / Beresini, M.H. / Liao, J. / Liu, W. / Chen, K.X. / Chen, Z. / Conery, A.R. / Cote, A. / Jayaram, H. / Jiang, Y. / Kiefer, J.R. / Kleinheinz, T. / Li, Y. / Maher, J. / Pardo, E. / Poy, F. / Spillane, K.L. / Wang, F. / Wang, J. / Wei, X. / Xu, Z. / Xu, Z. / Yen, I. / Zawadzke, L. / Zhu, X. / Bellon, S. / Cummings, R. / Cochran, A.G. / Albrecht, B.K. / Magnuson, S.
History
DepositionJul 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CREB-binding protein
B: CREB-binding protein
C: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,31914
Polymers40,6363
Non-polymers1,68311
Water10,683593
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1275
Polymers13,5451
Non-polymers5824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1275
Polymers13,5451
Non-polymers5824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0654
Polymers13,5451
Non-polymers5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.614, 44.395, 66.811
Angle α, β, γ (deg.)90.000, 106.500, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CREB-binding protein


Mass: 13545.468 Da / Num. of mol.: 3 / Fragment: bromodomain (UNP residues 1085-1196)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-6XG / 3-[[1-(cyclopropylmethyl)-5-ethanoyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]amino]-~{N}-propan-2-yl-benzamide


Mass: 395.498 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H29N5O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris pH 5.5, 5% v/v ethylene glycol, 23% PEG 3350

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.087→44.395 Å / Num. obs: 137643 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 13.2 / Num. measured all: 486509
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.087-1.0913.40.53195.2
5.045-44.3953.30.037192.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1492refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.087→36.489 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 16.27
RfactorNum. reflection% reflection
Rfree0.1758 6903 5.02 %
Rwork0.1625 --
obs0.1632 137612 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.23 Å2 / Biso mean: 15.0416 Å2 / Biso min: 3.97 Å2
Refinement stepCycle: final / Resolution: 1.087→36.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 119 594 3575
Biso mean--11.21 25.71 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123046
X-RAY DIFFRACTIONf_angle_d1.5634151
X-RAY DIFFRACTIONf_chiral_restr0.072424
X-RAY DIFFRACTIONf_plane_restr0.011536
X-RAY DIFFRACTIONf_dihedral_angle_d13.7621151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0874-1.09980.2272090.22734256446596
1.0998-1.11270.24512180.20994264448296
1.1127-1.12630.20942120.20834267447996
1.1263-1.14050.20392310.19414258448996
1.1405-1.15550.20342390.1934255449497
1.1555-1.17140.18482390.18844293453297
1.1714-1.18810.18842220.17854280450297
1.1881-1.20580.18992170.17594281449897
1.2058-1.22470.1982370.17534333457097
1.2247-1.24480.18212310.16944307453897
1.2448-1.26620.18822440.16994354459898
1.2662-1.28920.18392200.16364313453398
1.2892-1.3140.16182220.16074376459898
1.314-1.34090.17072300.16084340457098
1.3409-1.370.19472330.15684373460698
1.37-1.40190.17222550.15584339459498
1.4019-1.4370.17942250.16044389461499
1.437-1.47580.16952260.14814405463199
1.4758-1.51920.15772050.1444442464799
1.5192-1.56830.16412340.13924387462199
1.5683-1.62430.14352180.13554422464099
1.6243-1.68940.1652530.14684408466199
1.6894-1.76620.1642500.15164412466299
1.7662-1.85940.17382550.15264429468499
1.8594-1.97580.1672410.15494386462799
1.9758-2.12840.16582300.14954460469099
2.1284-2.34250.16922180.14964422464099
2.3425-2.68140.16782460.16424441468799
2.6814-3.37790.16562300.16184483471399
3.3779-36.50940.19162130.17644334454794
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)
12.39840.44570.03441.0633-0.09680.7604-0.07130.28420.0294-0.10890.0504-0.1392-0.10340.20420.01710.0874-0.0280.01090.15140.00650.0562-19.851810.88-15.0547
23.28211.01120.60852.3040.22082.7434-0.0771-0.06960.11190.09120.03030.2207-0.0829-0.22760.05580.06090.0206-0.00410.05550.01590.0688-39.251611.7112-7.514
31.83660.92190.01630.9242-0.93221.9926-0.23940.38790.3733-0.2080.19730.0513-0.29330.15540.09490.1181-0.0384-0.01030.14440.05240.115-21.34419.543-14.757
43.51871.6808-0.74811.72-0.49541.26640.03130.01630.09810.00310.00120.0017-0.06620.0971-0.03170.0542-0.0032-0.00010.04750.00050.0414-24.555512.3085-4.13
54.0242-0.6848-1.08546.233-1.12455.08130.0092-0.1402-0.04920.30590.0420.27260.0584-0.1049-0.01280.069-0.0066-0.00450.04910.00190.053-35.2849-1.3572-0.959
66.2453.08830.13932.08110.11460.82990.00420.1227-0.12090.00780.0437-0.1281-0.01540.198-0.03210.04940.0024-0.00370.073-0.00810.0519-18.4034.7588-6.208
71.55410.8294-0.05661.1596-0.05980.9764-0.0870.1229-0.0308-0.0650.0707-0.1412-0.10950.15720.00730.0683-0.0277-0.00070.0865-0.00130.051-8.035610.85995.8307
82.76310.5407-0.05982.07730.06643.0603-0.0228-0.08250.10280.06270.01430.2334-0.0239-0.31380.03730.04930.01330.00180.06470.00610.0706-26.548511.624514.395
92.57811.3297-0.08312.9365-0.05822.1522-0.03960.13640.1372-0.08060.0783-0.0553-0.30870.1302-0.00520.0863-0.0210.00560.06820.00560.0515-9.619719.37466.2787
102.22751.5044-0.7061.835-0.5631.36580.0738-0.0850.02970.072-0.0472-0.0105-0.13890.1144-0.03640.0627-0.0102-0.00430.0557-0.00580.0432-11.824812.465317.0984
111.96220.28910.22382.8386-0.84882.6055-0.0438-0.158-0.01340.1880.11220.0575-0.0016-0.1519-0.09060.0722-0.0021-0.00590.06210.01090.0594-22.0192-1.127821.3049
125.60792.9211-0.42872.0322-0.29281.0955-0.01220.0248-0.1155-0.01490.0068-0.1817-0.01810.2325-0.00650.0453-0.0038-0.00060.0783-0.00480.0681-5.585.090214.8297
132.28392.4713-0.23186.3351-1.2720.4544-0.02580.17920.2124-0.26440.0855-0.1898-0.15330.2919-0.0190.1226-0.04920.03770.158-0.01710.137610.940617.346525.1466
145.0042-2.0308-1.35073.86140.7292.8572-0.04140.1588-0.1232-0.13060.0467-0.07560.15760.07010.00060.0627-0.0129-0.00270.0475-0.00970.0401-2.08184.292327.2169
152.75910.9509-0.10912.79080.37052.6661-0.0043-0.08840.03710.09210.00980.33430.0217-0.20120.02230.05240.00770.00680.04820.01850.0888-12.532711.383835.8145
161.45831.4425-0.48654.74970.06061.97620.02360.07470.1774-0.19190.1035-0.0006-0.20540.0893-0.09390.0826-0.02090.02780.083-0.00230.07893.003820.081326.4834
172.06071.399-0.78962.8729-0.82271.87350.0486-0.026-0.01480.04470.0168-0.1301-0.01960.1224-0.05980.0509-0.0009-0.00410.0519-0.01290.04952.12512.876737.4018
183.1222-1.0779-1.92522.4825-3.02117.6417-0.0792-0.0323-0.04410.23020.17050.05040.2012-0.0463-0.01770.1154-0.0161-0.02010.04180.00450.0574-7.1287-1.633541.4868
194.30242.6274-0.90232.6877-0.7651.32450.07-0.0247-0.21640.13650.0005-0.41770.09480.3130.01920.06190.0178-0.01040.1117-0.02980.13078.50715.877234.8111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1083 through 1116 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1117 through 1134 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1135 through 1149 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1150 through 1167 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1168 through 1172 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1173 through 1196 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1083 through 1116 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1117 through 1134 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1135 through 1149 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1150 through 1167 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1168 through 1172 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1173 through 1196 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 1083 through 1102 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1103 through 1116 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 1117 through 1134 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 1135 through 1149 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 1150 through 1167 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 1168 through 1172 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 1173 through 1196 )C0

+
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