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- PDB-6m3v: 355 bp di-nucleosome harboring cohesive DNA termini -

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Basic information

Entry
Database: PDB / ID: 6m3v
Title355 bp di-nucleosome harboring cohesive DNA termini
Components
  • (DNA (355-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN / Nucleosome / H2A.X / 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 / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...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 / epigenetic regulation of gene expression / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / 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. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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: 4.6 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 4, 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)439,11921
Polymers439,00018
Non-polymers1193
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area122310 Å2
ΔGint-799 kcal/mol
Surface area162400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.987, 228.970, 118.839
Angle α, β, γ (deg.)90.000, 92.680, 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: 0 / Refine code: 0

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
13PROPROALAALAAA38 - 13539 - 136
23PROPROALAALAOO38 - 13539 - 136
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
114PROPROALAALAEE38 - 13539 - 136
214PROPROALAALAOO38 - 13539 - 136
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
121PROPROALAALAKK38 - 13539 - 136
221PROPROALAALAOO38 - 13539 - 136
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 / 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, 3 molecules

#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion / 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 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.6→49.33 Å / Num. obs: 26415 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Net I/σ(I): 6.6
Reflection shellResolution: 4.6→4.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4782 / CC1/2: 0.481 / Rpim(I) all: 0.818 / % possible all: 100

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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: 4.6→49.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.957 / SU B: 149.901 / SU ML: 1.719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 526 2 %RANDOM
Rwork0.2049 ---
obs0.2061 25862 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 673.23 Å2 / Biso mean: 250.089 Å2 / Biso min: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å2-4.61 Å2
2--4.29 Å2-0 Å2
3----1.97 Å2
Refinement stepCycle: final / Resolution: 4.6→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11911 14557 3 0 26471
Biso mean--122.37 --
Num. residues----2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01228401
X-RAY DIFFRACTIONr_bond_other_d0.0020.01820072
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.36741431
X-RAY DIFFRACTIONr_angle_other_deg1.3582.15846729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1351485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07118.661702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.871152289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.39615167
X-RAY DIFFRACTIONr_chiral_restr0.0690.23723
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026344
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29940.04
12E29940.04
21A29980.04
22K29980.04
31A30190.02
32O30190.02
41B23790.06
42F23790.06
51B24000.05
52L24000.05
61B24130.04
62P24130.04
71C29090.07
72G29090.07
81C29020.07
82M29020.07
91C29060.03
92Q29060.03
101D27000.07
102H27000.07
111D27320.08
112N27320.08
121D27640.03
122R27640.03
131E30200.02
132K30200.02
141E29880.04
142O29880.04
151F24000.04
152L24000.04
161F23780.05
162P23780.05
171G29360.03
172M29360.03
181G28850.07
182Q28850.07
191H27330.03
192N27330.03
201H26950.08
202R26950.08
211K29830.04
212O29830.04
221L24060.06
222P24060.06
231M28900.07
232Q28900.07
241N27010.08
242R27010.08
LS refinement shellResolution: 4.6→4.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 36 -
Rwork0.359 1922 -
all-1958 -
obs--100 %

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