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- PDB-6m44: 355 bp di-nucleosome harboring cohesive DNA termini (high cryopro... -

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Basic information

Entry
Database: PDB / ID: 6m44
Title355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant)
Components
  • (DNA (355-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN / Nucleosome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / 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 / Deposition of new CENPA-containing nucleosomes at the centromere ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Meiotic recombination / Metalloprotease DUBs / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / antibacterial humoral response / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / 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 / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
other sequences (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsAdhireksan, Z. / Sharma, D. / Lee, P.L. / Davey, C.A.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Nat Commun / Year: 2020
Title: Near-atomic resolution structures of interdigitated nucleosome fibres.
Authors: Adhireksan, Z. / Sharma, D. / Lee, P.L. / Davey, C.A.
History
DepositionMar 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (355-MER)
J: DNA (355-MER)
K: Histone H3.1
L: Histone H4
M: Histone H2A type 1-B/E
N: Histone H2B type 1-J
O: Histone H3.1
P: Histone H4
Q: Histone H2A type 1-B/E
R: Histone H2B type 1-J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,16022
Polymers439,00018
Non-polymers1604
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area121650 Å2
ΔGint-824 kcal/mol
Surface area160970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.038, 218.595, 115.931
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12A
22K
13A
23O
14B
24F
15B
25L
16B
26P
17C
27G
18C
28M
19C
29Q
110D
210H
111D
211N
112D
212R
113E
213K
114E
214O
115F
215L
116F
216P
117G
217M
118G
218Q
119H
219N
120H
220R
121K
221O
122L
222P
123M
223Q
124N
224R

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALAAA38 - 13539 - 136
21PROPROALAALAEE38 - 13539 - 136
12PROPROALAALAAA38 - 13539 - 136
22PROPROALAALAKK38 - 13539 - 136
13PROPROARGARGAA38 - 13439 - 135
23PROPROARGARGOO38 - 13439 - 135
14ASPASPGLYGLYBB24 - 10225 - 103
24ASPASPGLYGLYFF24 - 10225 - 103
15ASPASPGLYGLYBB24 - 10225 - 103
25ASPASPGLYGLYLL24 - 10225 - 103
16ASPASPGLYGLYBB24 - 10225 - 103
26ASPASPGLYGLYPP24 - 10225 - 103
17THRTHRLYSLYSCC16 - 11817 - 119
27THRTHRLYSLYSGG16 - 11817 - 119
18THRTHRLYSLYSCC16 - 11817 - 119
28THRTHRLYSLYSMM16 - 11817 - 119
19THRTHRPROPROCC16 - 11717 - 118
29THRTHRPROPROQQ16 - 11717 - 118
110SERSERALAALADD32 - 12433 - 125
210SERSERALAALAHH32 - 12433 - 125
111ARGARGLYSLYSDD31 - 12532 - 126
211ARGARGLYSLYSNN31 - 12532 - 126
112ARGARGALAALADD31 - 12432 - 125
212ARGARGALAALARR31 - 12432 - 125
113PROPROALAALAEE38 - 13539 - 136
213PROPROALAALAKK38 - 13539 - 136
114PROPROARGARGEE38 - 13439 - 135
214PROPROARGARGOO38 - 13439 - 135
115ASPASPGLYGLYFF24 - 10225 - 103
215ASPASPGLYGLYLL24 - 10225 - 103
116ASPASPGLYGLYFF24 - 10225 - 103
216ASPASPGLYGLYPP24 - 10225 - 103
117THRTHRLYSLYSGG16 - 11817 - 119
217THRTHRLYSLYSMM16 - 11817 - 119
118THRTHRPROPROGG16 - 11717 - 118
218THRTHRPROPROQQ16 - 11717 - 118
119SERSERALAALAHH32 - 12433 - 125
219SERSERALAALANN32 - 12433 - 125
120SERSERALAALAHH32 - 12433 - 125
220SERSERALAALARR32 - 12433 - 125
121PROPROARGARGKK38 - 13439 - 135
221PROPROARGARGOO38 - 13439 - 135
122ASPASPGLYGLYLL24 - 10225 - 103
222ASPASPGLYGLYPP24 - 10225 - 103
123THRTHRPROPROMM16 - 11717 - 118
223THRTHRPROPROQQ16 - 11717 - 118
124ARGARGALAALANN31 - 12432 - 125
224ARGARGALAALARR31 - 12432 - 125

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

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Components

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Protein , 4 types, 16 molecules AEKOBFLPCGMQDHNR

#1: Protein
Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein
Histone H4


Mass: 11394.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein
Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein
Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (355-MER)


Mass: 109450.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) other sequences (unknown) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (355-MER)


Mass: 109819.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) other sequences (unknown) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 5 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.81→48.03 Å / Num. obs: 41344 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.96 / Rpim(I) all: 0.04 / Net I/σ(I): 11.4
Reflection shellResolution: 3.81→3.96 Å / Rmerge(I) obs: 1.454 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4614 / CC1/2: 0.424 / Rpim(I) all: 0.646

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ut9

3ut9


Resolution: 3.81→48.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 64.245 / SU ML: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.889
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 861 2.1 %RANDOM
Rwork0.2077 ---
obs0.2093 40456 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 455.33 Å2 / Biso mean: 187.051 Å2 / Biso min: 77.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å2-2.03 Å2
2---0.03 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 3.81→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11934 14557 4 1 26496
Biso mean--157.25 105.53 -
Num. residues----2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01228424
X-RAY DIFFRACTIONr_bond_other_d0.0020.01820102
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.36741461
X-RAY DIFFRACTIONr_angle_other_deg1.3822.15746801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45651488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31518.661702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.062152297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.76515167
X-RAY DIFFRACTIONr_chiral_restr0.0710.23726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026346
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29670.05
12E29670.05
21A29630.05
22K29630.05
31A29700.02
32O29700.02
41B23790.05
42F23790.05
51B23880.06
52L23880.06
61B24190.02
62P24190.02
71C29400.07
72G29400.07
81C29420.07
82M29420.07
91C29490.03
92Q29490.03
101D27400.08
102H27400.08
111D27920.1
112N27920.1
121D28170.03
122R28170.03
131E30090.02
132K30090.02
141E29380.05
142O29380.05
151F24230.01
152L24230.01
161F23760.06
162P23760.06
171G29740.04
172M29740.04
181G29220.07
182Q29220.07
191H27820.04
192N27820.04
201H27370.08
202R27370.08
211K29410.05
212O29410.05
221L23820.06
222P23820.06
231M29320.07
232Q29320.07
241N27670.08
242R27670.08
LS refinement shellResolution: 3.81→3.907 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.38 71 -
Rwork0.355 2927 -
obs--97.53 %

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