cellular heat acclimation / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / regulation of stem cell differentiation / NuRD complex / ESC/E(Z) complex / response to steroid hormone / positive regulation of stem cell population maintenance / ATPase complex ...cellular heat acclimation / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / regulation of stem cell differentiation / NuRD complex / ESC/E(Z) complex / response to steroid hormone / positive regulation of stem cell population maintenance / ATPase complex / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / negative regulation of cell migration / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / negative regulation of transforming growth factor beta receptor signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / brain development / negative regulation of cell growth / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA replication / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta Similarity search - Domain/homology
Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.409 / % possible all: 98
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
ADSC
Quantum
datacollection
DENZO
datareduction
HKL-2000
datascaling
PHASES
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD data phased model Resolution: 2.4→19.53 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.405 / SU ML: 0.108 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24862
935
5.1 %
RANDOM
Rwork
0.18418
-
-
-
obs
0.18745
17375
99.95 %
-
all
-
17375
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 31.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1 Å2
0 Å2
0 Å2
2-
-
1.2 Å2
0 Å2
3-
-
-
-0.19 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.268 Å
0.094 Å
Luzzati d res low
-
6 Å
Luzzati sigma a
0.229 Å
0.251 Å
Refinement step
Cycle: LAST / Resolution: 2.4→19.53 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3186
0
1
210
3397
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.003
0.021
3273
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
0.75
1.926
4458
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.663
5
395
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.463
24.845
161
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.715
15
538
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.773
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.061
0.2
485
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
2515
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.213
0.3
1397
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.319
0.5
2143
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.174
0.5
346
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.127
0.3
31
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.187
0.5
12
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
4.836
2
2030
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
6.542
3
3223
X-RAY DIFFRACTION
r_scbond_it
5.491
2
1421
X-RAY DIFFRACTION
r_scangle_it
7.295
3
1235
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.4→2.461 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.279
69
-
Rwork
0.192
1251
-
obs
-
-
99.7 %
+
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