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- PDB-5b1l: The mouse nucleosome structure containing H3t -

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Basic information

Entry
Database: PDB / ID: 5b1l
TitleThe mouse nucleosome structure containing H3t
Components
  • DNA (146-MER)
  • Histone H2A type 1
  • Histone H2B type 3-A
  • Histone H3t
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / chromatin / spermatogenesis / histone-fold / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


: / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Inhibition of DNA recombination at telomere / Transcriptional regulation by small RNAs / B-WICH complex positively regulates rRNA expression / HDACs deacetylate histones / chromatin organization => GO:0006325 ...: / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Inhibition of DNA recombination at telomere / Transcriptional regulation by small RNAs / B-WICH complex positively regulates rRNA expression / HDACs deacetylate histones / chromatin organization => GO:0006325 / DNA Damage/Telomere Stress Induced Senescence / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recognition and association of DNA glycosylase with site containing an affected purine / Chromatin modifying enzymes / SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / Cleavage of the damaged purine / Condensation of Prophase Chromosomes / Interleukin-7 signaling / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Nonhomologous End-Joining (NHEJ) / Metalloprotease DUBs / UCH proteinases / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / Oxidative Stress Induced Senescence / Ub-specific processing proteases / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / 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, subunit A / Histone, subunit A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B / Histone H2A type 1-B / Histone H4 / Histone H3.1 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsUrahama, T. / Machida, S. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Taguchi, H. / Kurumizaka, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
the Japan Agency for Medical Research and Development (AMED) Japan
Ministry of Education, Culture, Sports, Science and Technology (MEXT)25116002 Japan
CitationJournal: Cell Rep / Year: 2017
Title: Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis
Authors: Ueda, J. / Harada, A. / Urahama, T. / Machida, S. / Maehara, K. / Hada, M. / Makino, Y. / Nogami, J. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tanaka, H. / Tachiwana, H. / Yao, T. / ...Authors: Ueda, J. / Harada, A. / Urahama, T. / Machida, S. / Maehara, K. / Hada, M. / Makino, Y. / Nogami, J. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tanaka, H. / Tachiwana, H. / Yao, T. / Yamada, M. / Iwamoto, T. / Isotani, A. / Ikawa, M. / Tachibana, T. / Okada, Y. / Kimura, H. / Ohkawa, Y. / Kurumizaka, H. / Yamagata, K.
History
DepositionDec 8, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3t
B: Histone H4
C: Histone H2A type 1
D: Histone H2B type 3-A
E: Histone H3t
F: Histone H4
G: Histone H2A type 1
H: Histone H2B type 3-A
I: DNA (146-MER)
J: DNA (146-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,31727
Polymers202,46110
Non-polymers85617
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59140 Å2
ΔGint-506 kcal/mol
Surface area70960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.968, 107.425, 167.332
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
11chain A
21chain E
12chain B
22chain F
13chain C
23chain G
14chain D
24chain H
15chain I
25chain J

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROCLCLchain AAA - K38 - 30142
21PROPROCLCLchain EEE - N38 - 30142
12ASNASNHOHHOHchain BBB - CA25 - 21129
22ARGARGHOHHOHchain FFF - GA19 - 22123
13ARGARGCLCLchain CCC - L11 - 30115
23LYSLYSCLCLchain GGG - O15 - 30119
14GLYGLYMNMNchain DDD - M32 - 30136
24ARGARGHOHHOHchain HHH - IA33 - 20737
15DTDTMNMNchain III - U2 - 3062
25DADAMNMNchain JJJ - AA147 - 4061

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3t


Mass: 15744.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gm12260 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68433*PLUS
#2: Protein Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62806
#3: Protein Histone H2A type 1


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag, Hist1h2ai, Hist1h2an, Hist1h2ao
Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22752, UniProt: C0HKE1*PLUS
#4: Protein Histone H2B type 3-A


Mass: 14307.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist3h2ba / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D2U9

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DNA chain , 1 types, 2 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T Easy / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha]

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Non-polymers , 3 types, 242 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE OF HISTONE H3T HAS BEEN REGISTERED IN GENBANK WITH ACCESSION ID EDL07696.1.

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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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 75240 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.94 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Χ2: 0.807 / Net I/av σ(I): 20.842 / Net I/σ(I): 5.9 / Num. measured all: 496153
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.436.70.45474330.8970.190.4930.472100
2.43-2.536.70.37274210.9230.1550.4040.5100
2.53-2.656.30.29474260.9510.1270.3210.534100
2.65-2.796.70.23674620.970.0980.2560.555100
2.79-2.966.60.17774480.9820.0750.1930.594100
2.96-3.196.90.12274930.9930.050.1320.661100
3.19-3.516.70.0875010.9970.0330.0870.827100
3.51-4.026.40.0775500.9960.030.0761.017100
4.02-5.066.60.06176060.9960.0250.0661.21100
5.06-506.30.05879000.9980.0250.0631.69899.9

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Processing

Software
NameVersionClassification
HKL-2000704ydata collection
HKL-2000704ydata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CV5

2cv5


Resolution: 2.35→41.833 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 3771 5.03 %Random selection
Rwork0.1969 71148 --
obs0.1993 74919 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.87 Å2 / Biso mean: 48.1914 Å2 / Biso min: 14.12 Å2
Refinement stepCycle: final / Resolution: 2.35→41.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 5942 17 225 12164
Biso mean--59.06 39.35 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112727
X-RAY DIFFRACTIONf_angle_d1.26118430
X-RAY DIFFRACTIONf_chiral_restr0.0562095
X-RAY DIFFRACTIONf_plane_restr0.0081327
X-RAY DIFFRACTIONf_dihedral_angle_d29.2055246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A954X-RAY DIFFRACTION7.978TORSIONAL
12E954X-RAY DIFFRACTION7.978TORSIONAL
21B740X-RAY DIFFRACTION7.978TORSIONAL
22F740X-RAY DIFFRACTION7.978TORSIONAL
31C960X-RAY DIFFRACTION7.978TORSIONAL
32G960X-RAY DIFFRACTION7.978TORSIONAL
41D836X-RAY DIFFRACTION7.978TORSIONAL
42H836X-RAY DIFFRACTION7.978TORSIONAL
51I2874X-RAY DIFFRACTION7.978TORSIONAL
52J2874X-RAY DIFFRACTION7.978TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3501-2.37980.331230.237226262749
2.3798-2.41110.33651350.245626112746
2.4111-2.44410.2821430.239226032746
2.4441-2.4790.27941410.239325862727
2.479-2.5160.34761290.225526272756
2.516-2.55540.26891330.232526132746
2.5554-2.59720.29061360.234525882724
2.5972-2.6420.28931360.238426052741
2.642-2.69010.31591410.243626092750
2.6901-2.74180.32751320.242426322764
2.7418-2.79770.27211420.242725802722
2.7977-2.85860.27431300.24826512781
2.8586-2.9250.32161280.250226322760
2.925-2.99820.28161390.254826072746
2.9982-3.07920.28481540.228426062760
3.0792-3.16980.25291450.219926092754
3.1698-3.27210.23681350.204326292764
3.2721-3.3890.25871590.202526002759
3.389-3.52460.23341460.195526352781
3.5246-3.68490.2361560.190726222778
3.6849-3.8790.23671330.192226522785
3.879-4.12190.23181510.181926412792
4.1219-4.43980.1981390.161926682807
4.4398-4.8860.20891260.16326832809
4.886-5.59160.20811500.170426792829
5.5916-7.03940.21191440.18127202864
7.0394-41.83960.18961450.149428342979

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