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- PDB-5gse: Crystal structure of unusual nucleosome -

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Basic information

Entry
Database: PDB / ID: 5gse
TitleCrystal structure of unusual nucleosome
Components
  • (DNA (250-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / histone-fold / DNA-binding / nucleus / STRUCTURAL 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 / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / 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 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / 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 / protein heterodimerization activity / Amyloid fiber formation / 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, 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/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsKato, D. / Osakabe, A. / Arimura, Y. / Park, S.Y. / Kurumizaka, H.
Funding support Japan, 5items
OrganizationGrant numberCountry
MEXT KAKENHI Grant25116002 Japan
Agency for Medical Research and Development, the Platform Project for Supporting Drug Discovery and Life Science Research Japan
the Waseda Research Institute for Science and Engineering Japan
Japan Society for the Promotion of Science15H06691 Japan
Japan Society for the Promotion of Science16J06850 Japan
CitationJournal: Science / Year: 2017
Title: Crystal structure of the overlapping dinucleosome composed of hexasome and octasome
Authors: Kato, D. / Osakabe, A. / Arimura, Y. / Mizukami, Y. / Horikoshi, N. / Saikusa, K. / Akashi, S. / Nishimura, Y. / Park, S.Y. / Nogami, J. / Maehara, K. / Ohkawa, Y. / Matsumoto, A. / Kono, H. ...Authors: Kato, D. / Osakabe, A. / Arimura, Y. / Mizukami, Y. / Horikoshi, N. / Saikusa, K. / Akashi, S. / Nishimura, Y. / Park, S.Y. / Nogami, J. / Maehara, K. / Ohkawa, Y. / Matsumoto, A. / Kono, H. / Inoue, R. / Sugiyama, M. / Kurumizaka, H.
History
DepositionAug 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 (250-MER)
J: DNA (250-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


Theoretical massNumber of molelcules
Total (without water)350,03616
Polymers350,03616
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area96730 Å2
ΔGint-664 kcal/mol
Surface area120840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.582, 101.804, 102.427
Angle α, β, γ (deg.)119.300, 106.510, 91.360
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 47:51 or resseq 54:58 or resseq...
21(chain E and (resseq 47:51 or resseq 54:58 or resseq...
31(chain K and (resseq 47:51 or resseq 54:58 or resseq...
41(chain O and (resseq 47:51 or resseq 54:58 or resseq...
12(chain B and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))
22(chain F and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))
32(chain P and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))
13(chain H and (resseq 35:45 or resseq 47:48 or (resid...
23(chain D and (resseq 35:45 or resseq 47:48 or (resid...
33(chain N and (resseq 35:45 or resseq 47:48 or (resid...
14(chain G and (resseq 16:34 or resseq 37:40 or resseq...
24(chain C and (resseq 16:34 or resseq 37:40 or resseq...
34(chain M and (resseq 16:34 or resseq 37:40 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAILEILE(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA47 - 5151 - 55
121TYRTYRTHRTHR(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA54 - 5858 - 62
131LEULEUILEILE(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA60 - 6264 - 66
141LEULEUTHRTHR(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA65 - 8069 - 84
151LEULEUALAALA(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA82 - 11486 - 118
161ARGARGPROPRO(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA116 - 121120 - 125
171ASPASPARGARG(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA123 - 128127 - 132
181ILEILEGLUGLU(chain A and (resseq 47:51 or resseq 54:58 or resseq...AA130 - 133134 - 137
211ALAALAILEILE(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE47 - 5151 - 55
221TYRTYRTHRTHR(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE54 - 5858 - 62
231LEULEUILEILE(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE60 - 6264 - 66
241LEULEUTHRTHR(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE65 - 8069 - 84
251LEULEUALAALA(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE82 - 11486 - 118
261ARGARGPROPRO(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE116 - 121120 - 125
271ASPASPARGARG(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE123 - 128127 - 132
281ILEILEGLUGLU(chain E and (resseq 47:51 or resseq 54:58 or resseq...EE130 - 133134 - 137
311ALAALAILEILE(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK47 - 5151 - 55
321TYRTYRTHRTHR(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK54 - 5858 - 62
331LEULEUILEILE(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK60 - 6264 - 66
341LEULEUTHRTHR(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK65 - 8069 - 84
351LEULEUALAALA(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK82 - 11486 - 118
361ARGARGPROPRO(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK116 - 121120 - 125
371ASPASPARGARG(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK123 - 128127 - 132
381ILEILEGLUGLU(chain K and (resseq 47:51 or resseq 54:58 or resseq...KK130 - 133134 - 137
411ALAALAILEILE(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO47 - 5151 - 55
421TYRTYRTHRTHR(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO54 - 5858 - 62
431LEULEUILEILE(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO60 - 6264 - 66
441LEULEUTHRTHR(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO65 - 8069 - 84
451LEULEUALAALA(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO82 - 11486 - 118
461ARGARGPROPRO(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO116 - 121120 - 125
471ASPASPARGARG(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO123 - 128127 - 132
481ILEILEGLUGLU(chain O and (resseq 47:51 or resseq 54:58 or resseq...OO130 - 133134 - 137
112ASNASNASNASN(chain B and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))BB2529
122GLYGLYLEULEU(chain B and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))BB28 - 5832 - 62
132VALVALTHRTHR(chain B and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))BB60 - 7364 - 77
142HISHISLEULEU(chain B and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))BB75 - 9079 - 94
152GLNGLNPHEPHE(chain B and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))BB93 - 10097 - 104
212ASNASNASNASN(chain F and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))FF2529
222GLYGLYLEULEU(chain F and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))FF28 - 5832 - 62
232VALVALTHRTHR(chain F and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))FF60 - 7364 - 77
242HISHISLEULEU(chain F and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))FF75 - 9079 - 94
252GLNGLNPHEPHE(chain F and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))FF93 - 10097 - 104
312ASNASNASNASN(chain P and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))PP2529
322GLYGLYLEULEU(chain P and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))PP28 - 5832 - 62
332VALVALTHRTHR(chain P and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))PP60 - 7364 - 77
342HISHISLEULEU(chain P and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))PP75 - 9079 - 94
352GLNGLNPHEPHE(chain P and (resseq 25 or resseq 28:58 or resseq 60:73 or resseq 75:90 or resseq 93:100))PP93 - 10097 - 104
113GLUGLULEULEU(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH35 - 4539 - 49
123GLNGLNVALVAL(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH47 - 4851 - 52
133HISHISHISHIS(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH4953
143LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
153LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
163LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
173LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
183LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
193LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
1103LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
1113LYSLYSALAALA(chain H and (resseq 35:45 or resseq 47:48 or (resid...HH34 - 12438 - 128
213GLUGLULEULEU(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD35 - 4539 - 49
223GLNGLNVALVAL(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD47 - 4851 - 52
233HISHISHISHIS(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD4953
243SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
253SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
263SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
273SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
283SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
293SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
2103SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
2113SERSERSERSER(chain D and (resseq 35:45 or resseq 47:48 or (resid...DD32 - 12336 - 127
313GLUGLULEULEU(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN35 - 4539 - 49
323GLNGLNVALVAL(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN47 - 4851 - 52
333HISHISHISHIS(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN4953
343SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
353SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
363SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
373SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
383SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
393SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
3103SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
3113SERSERALAALA(chain N and (resseq 35:45 or resseq 47:48 or (resid...NN32 - 12436 - 128
114THRTHRLEULEU(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG16 - 3420 - 38
124GLYGLYSERSER(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG37 - 4041 - 44
134ARGARGALAALA(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG42 - 7046 - 74
144ASNASNASNASN(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG7377
154LYSLYSTHRTHR(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG75 - 7679 - 80
164ILEILEASNASN(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG78 - 9482 - 98
174LEULEUGLYGLY(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG96 - 98100 - 102
184VALVALLEULEU(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG100 - 116104 - 120
194PROPROPROPRO(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG117121
1104LYSLYSPROPRO(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG9 - 11713 - 121
1114LYSLYSPROPRO(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG9 - 11713 - 121
1124LYSLYSPROPRO(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG9 - 11713 - 121
1134LYSLYSPROPRO(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG9 - 11713 - 121
1144LYSLYSPROPRO(chain G and (resseq 16:34 or resseq 37:40 or resseq...GG9 - 11713 - 121
214THRTHRLEULEU(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC16 - 3420 - 38
224GLYGLYSERSER(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC37 - 4041 - 44
234ARGARGALAALA(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC42 - 7046 - 74
244ASNASNASNASN(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC7377
254LYSLYSTHRTHR(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC75 - 7679 - 80
264ILEILEASNASN(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC78 - 9482 - 98
274LEULEUGLYGLY(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC96 - 98100 - 102
284VALVALLEULEU(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC100 - 116104 - 120
294PROPROPROPRO(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC117121
2104THRTHRPROPRO(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC16 - 11720 - 121
2114THRTHRPROPRO(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC16 - 11720 - 121
2124THRTHRPROPRO(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC16 - 11720 - 121
2134THRTHRPROPRO(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC16 - 11720 - 121
2144THRTHRPROPRO(chain C and (resseq 16:34 or resseq 37:40 or resseq...CC16 - 11720 - 121
314THRTHRLEULEU(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM16 - 3420 - 38
324GLYGLYSERSER(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM37 - 4041 - 44
334ARGARGALAALA(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM42 - 7046 - 74
344ASNASNASNASN(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM7377
354LYSLYSTHRTHR(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM75 - 7679 - 80
364ILEILEASNASN(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM78 - 9482 - 98
374LEULEUGLYGLY(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM96 - 98100 - 102
384VALVALLEULEU(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM100 - 116104 - 120
394PROPROPROPRO(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM117121
3104ALAALAPROPRO(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM12 - 11716 - 121
3114ALAALAPROPRO(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM12 - 11716 - 121
3124ALAALAPROPRO(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM12 - 11716 - 121
3134ALAALAPROPRO(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM12 - 11716 - 121
3144ALAALAPROPRO(chain M and (resseq 16:34 or resseq 37:40 or resseq...MM12 - 11716 - 121

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 14 molecules AEKOBFLPCGMDHN

#1: Protein
Histone H3.1 / Histone H3


Mass: 15719.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H3A / Plasmid: pH3.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68431
#2: Protein
Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H4A / Plasmid: pH4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB / Plasmid: pH2A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ / Plasmid: pH2B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06899

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (250-MER)


Mass: 77692.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pGEM-T Easy / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
#6: DNA chain DNA (250-MER)


Mass: 76762.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pGEM-T Easy / Production host: Escherichia coli (E. coli)

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2016
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. obs: 47834 / % possible obs: 91 % / Redundancy: 4.8 % / Biso Wilson estimate: 92.66 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.052 / Rrim(I) all: 0.117 / Χ2: 1.136 / Net I/σ(I): 6.5 / Num. measured all: 229764
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.14-3.2540.57346840.7680.3050.6520.5690
3.25-3.384.40.42147570.8780.2170.4760.6689.9
3.38-3.544.50.32746100.9210.1670.3690.81988
3.54-3.724.90.26749170.9490.1320.2980.96993.6
3.72-3.9650.21249120.9620.1040.2371.03192.8
3.96-4.264.90.15746060.9750.0770.1751.06888
4.26-4.695.10.11748700.9860.0570.1311.08892.8
4.69-5.375.10.09648890.9910.0460.1071.04992.7
5.37-6.765.10.08148080.9930.0390.0911.03691.6
6.76-504.90.06747810.9950.0340.0752.86690.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFA

3afa


Resolution: 3.14→49.659 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2359 4.95 %Ramdom selection
Rwork0.1972 45277 --
obs0.2001 47636 90.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.54 Å2 / Biso mean: 96.0751 Å2 / Biso min: 38.38 Å2
Refinement stepCycle: final / Resolution: 3.14→49.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10196 10048 0 0 20244
Num. residues----1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521596
X-RAY DIFFRACTIONf_angle_d0.90331261
X-RAY DIFFRACTIONf_chiral_restr0.0483558
X-RAY DIFFRACTIONf_plane_restr0.0062257
X-RAY DIFFRACTIONf_dihedral_angle_d28.13311301
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1384X-RAY DIFFRACTION13.69TORSIONAL
12E1384X-RAY DIFFRACTION13.69TORSIONAL
13K1384X-RAY DIFFRACTION13.69TORSIONAL
14O1384X-RAY DIFFRACTION13.69TORSIONAL
21B960X-RAY DIFFRACTION13.69TORSIONAL
22F960X-RAY DIFFRACTION13.69TORSIONAL
23P960X-RAY DIFFRACTION13.69TORSIONAL
31H1027X-RAY DIFFRACTION13.69TORSIONAL
32D1027X-RAY DIFFRACTION13.69TORSIONAL
33N1027X-RAY DIFFRACTION13.69TORSIONAL
41G1207X-RAY DIFFRACTION13.69TORSIONAL
42C1207X-RAY DIFFRACTION13.69TORSIONAL
43M1207X-RAY DIFFRACTION13.69TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.14-3.20410.42561390.37552607274689
3.2041-3.27380.3761400.30612637277791
3.2738-3.34990.31951270.28112646277390
3.3499-3.43360.30391250.26232515264086
3.4336-3.52650.2991360.24362639277590
3.5265-3.63020.29251490.23232783293294
3.6302-3.74730.28261420.23332707284993
3.7473-3.88120.27951390.22182700283993
3.8812-4.03660.26471300.20532695282591
4.0366-4.22020.26861270.19492569269688
4.2202-4.44250.2611170.18622647276489
4.4425-4.72070.2371510.18272737288894
4.7207-5.08480.22561380.18062742288093
5.0848-5.59590.24691370.19082602273989
5.5959-6.40420.23831420.21632768291093
6.4042-8.0630.25371790.17642620279992
8.063-49.66530.20741410.14082663280491

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