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- PDB-6la9: 349 bp di-nucleosome harboring cohesive DNA termini assembled wit... -

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Basic information

Entry
Database: PDB / ID: 6la9
Title349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant)
Components
  • (DNA (349-MER)) x 2
  • Histone H1.0
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN / Nucleosome / DNA-protein complex / DNA BINDING PROTEIN-DNA complex / Linker Histone / H1.0
Function / homology
Function and homology information


positive regulation of transcription regulatory region DNA binding / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin ...positive regulation of transcription regulatory region DNA binding / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / nucleosome binding / 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 / transcription repressor complex / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / 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 / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / chromatin DNA binding / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / actin cytoskeleton / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / nuclear body / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin / Golgi apparatus / protein-containing complex / extracellular space / DNA binding
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / 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 domain / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H1.0 / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
other sequences (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsAdhireksan, Z. / Sharma, D. / Lee, P.L. / Davey, C.A.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (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
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 (349-MER)
J: DNA (349-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
S: Histone H1.0
T: Histone H1.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,82962
Polymers477,14820
Non-polymers1,68142
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area126530 Å2
ΔGint-1113 kcal/mol
Surface area167160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.780, 172.880, 216.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
125S
225T

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
11PROPROARGARGAA38 - 13439 - 135
21PROPROARGARGEE38 - 13439 - 135
12LYSLYSALAALAAA37 - 13538 - 136
22LYSLYSALAALAKK37 - 13538 - 136
13PROPROARGARGAA38 - 13439 - 135
23PROPROARGARGOO38 - 13439 - 135
14ARGARGGLYGLYBB23 - 10124 - 102
24ARGARGGLYGLYFF23 - 10124 - 102
15ARGARGGLYGLYBB23 - 10224 - 103
25ARGARGGLYGLYLL23 - 10224 - 103
16ARGARGGLYGLYBB23 - 10224 - 103
26ARGARGGLYGLYPP23 - 10224 - 103
17LYSLYSLYSLYSCC13 - 11814 - 119
27LYSLYSLYSLYSGG13 - 11814 - 119
18LYSLYSLYSLYSCC13 - 11814 - 119
28LYSLYSLYSLYSMM13 - 11814 - 119
19LYSLYSPROPROCC15 - 11716 - 118
29LYSLYSPROPROQQ15 - 11716 - 118
110ARGARGLYSLYSDD31 - 12532 - 126
210ARGARGLYSLYSHH31 - 12532 - 126
111ARGARGLYSLYSDD31 - 12532 - 126
211ARGARGLYSLYSNN31 - 12532 - 126
112ARGARGLYSLYSDD31 - 12532 - 126
212ARGARGLYSLYSRR31 - 12532 - 126
113PROPROARGARGEE38 - 13439 - 135
213PROPROARGARGKK38 - 13439 - 135
114PROPROALAALAEE38 - 13539 - 136
214PROPROALAALAOO38 - 13539 - 136
115ARGARGGLYGLYFF23 - 10124 - 102
215ARGARGGLYGLYLL23 - 10124 - 102
116ARGARGGLYGLYFF23 - 10124 - 102
216ARGARGGLYGLYPP23 - 10124 - 102
117LYSLYSLYSLYSGG13 - 11814 - 119
217LYSLYSLYSLYSMM13 - 11814 - 119
118LYSLYSPROPROGG15 - 11716 - 118
218LYSLYSPROPROQQ15 - 11716 - 118
119ARGARGLYSLYSHH31 - 12532 - 126
219ARGARGLYSLYSNN31 - 12532 - 126
120ARGARGLYSLYSHH31 - 12532 - 126
220ARGARGLYSLYSRR31 - 12532 - 126
121PROPROARGARGKK38 - 13439 - 135
221PROPROARGARGOO38 - 13439 - 135
122ARGARGGLYGLYLL23 - 10224 - 103
222ARGARGGLYGLYPP23 - 10224 - 103
123LYSLYSPROPROMM15 - 11716 - 118
223LYSLYSPROPROQQ15 - 11716 - 118
124ARGARGLYSLYSNN31 - 12532 - 126
224ARGARGLYSLYSRR31 - 12532 - 126
125HISHISALAALASS25 - 9625 - 96
225HISHISALAALATT25 - 9625 - 96

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
25

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Components

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Protein , 5 types, 18 molecules AEKOBFLPCGMQDHNRST

#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
#7: Protein Histone H1.0 / Histone H1' / Histone H1(0)


Mass: 20927.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H1-0, H1F0, H1FV / Production host: Escherichia coli (E. coli) / References: UniProt: P07305

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (349-MER)


Mass: 107606.539 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 (349-MER)


Mass: 107957.430 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 , 3 types, 46 molecules

#8: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Calcium chloride, potassium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 98.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→99.01 Å / Num. obs: 47850 / % possible obs: 97.6 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.096 / Rrim(I) all: 0.234 / Net I/σ(I): 7.8
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 9 % / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6640 / CC1/2: 0.309 / Rpim(I) all: 0.796 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LAB, 4QLC

6lab

4qlc


Resolution: 3.7→91.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.767
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 1001 2.1 %RANDOM
Rwork0.1943 ---
obs0.1958 46780 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 739 Å2 / Biso mean: 131.204 Å2 / Biso min: 50.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2--1.5 Å2-0 Å2
3----3.5 Å2
Refinement stepCycle: final / Resolution: 3.7→91.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13203 14311 42 4 27560
Biso mean--123.25 64.37 -
Num. residues----2365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01229429
X-RAY DIFFRACTIONr_bond_other_d0.0270.01821278
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.3842736
X-RAY DIFFRACTIONr_angle_other_deg2.3912.11749519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81651649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24518.729763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.035152573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.69415180
X-RAY DIFFRACTIONr_chiral_restr0.080.23860
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223224
X-RAY DIFFRACTIONr_gen_planes_other0.0070.026555
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29510.07
12E29510.07
21A30110.06
22K30110.06
31A29660.08
32O29660.08
41B23880.07
42F23880.07
51B24460.05
52L24460.05
61B24160.09
62P24160.09
71C30000.1
72G30000.1
81C30510.06
82M30510.06
91C29550.08
92Q29550.08
101D27930.1
102H27930.1
111D28760.04
112N28760.04
121D28010.09
122R28010.09
131E29630.06
132K29630.06
141E29970.08
142O29970.08
151F23850.07
152L23850.07
161F24130.06
162P24130.06
171G30010.09
172M30010.09
181G29910.06
182Q29910.06
191H28010.1
192N28010.1
201H28590.08
202R28590.08
211K29460.08
212O29460.08
221L24160.08
222P24160.08
231M29570.08
232Q29570.08
241N28010.1
242R28010.1
251S19530.17
252T19530.17
LS refinement shellResolution: 3.7→3.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 93 -
Rwork0.37 3262 -
all-3355 -
obs--93.92 %

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