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- PDB-4qlc: Crystal structure of chromatosome at 3.5 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4qlc
TitleCrystal structure of chromatosome at 3.5 angstrom resolution
Components
  • (DNA (167-mer)) x 2
  • H5
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
KeywordsCHROMATIN BINDING PROTEIN/DNA / NUCLEOSOME CORE PARTICLE / HISTONE FOLD / CHROMOSOME / CHROMATIN / Global histone H5 / gH5 / NCP167 / Regulation / SEGREGATION / CHROMATOSOME / gH1 / Liker Histone H5 / Linker DNA / Protein-DNA Complexes / DNA BINDING PROTEIN-DNA complex / CHROMATIN BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / nuclear chromosome / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / chromosome / double-stranded DNA binding / protein heterodimerization activity / protein-containing complex binding / chromatin / DNA binding / nucleus
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, subunit A / Histone, subunit A / : / Histone H2B 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, 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 / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / DNA / DNA (> 10) / DNA (> 100) / Histone H5 / Histone H2B / Histone H3 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsJiang, J.S. / Zhou, B.R. / Xiao, T.S. / Bai, Y.W.
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Mechanisms of Nucleosome Recognition by Linker Histones.
Authors: Zhou, B.R. / Jiang, J. / Feng, H. / Ghirlando, R. / Xiao, T.S. / Bai, Y.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references / Derived calculations
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (167-mer)
J: DNA (167-mer)
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
U: H5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,81414
Polymers218,23711
Non-polymers5763
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61600 Å2
ΔGint-380 kcal/mol
Surface area82790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.870, 262.870, 91.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA (167-mer)


Mass: 51325.676 Da / Num. of mol.: 1 / Fragment: 167bp Widom 601 DNA
Source method: isolated from a genetically manipulated source
Details: 147 BP WIDOM 601 DNA FRAGMENT and 20 bp linker DNA fragment
Source: (gene. exp.) Homo sapiens (human) / Gene: DNA / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (167-mer)


Mass: 51783.977 Da / Num. of mol.: 1 / Fragment: 167bp Widom 601 DNA
Source method: isolated from a genetically manipulated source
Details: 147 BP WIDOM 601 DNA FRAGMENT and 20 bp linker DNA fragment
Source: (gene. exp.) Homo sapiens (human) / Gene: DNA / Production host: Escherichia coli (E. coli)

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Protein , 5 types, 9 molecules AEBFCGDHU

#3: Protein Histone H3


Mass: 15289.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: 7227
Gene: CG31613, CG33803, CG33806, CG33809, CG33812, CG33815, CG33818, CG33821, CG33824, CG33827, CG33830, CG33833, CG33836, CG33839, CG33842, CG33845, CG33848, CG33851, CG33854, CG33857, CG33860, ...Gene: CG31613, CG33803, CG33806, CG33809, CG33812, CG33815, CG33818, CG33821, CG33824, CG33827, CG33830, CG33833, CG33836, CG33839, CG33842, CG33845, CG33848, CG33851, CG33854, CG33857, CG33860, CG33863, CG33866, H3_DROME, His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Production host: Escherichia coli (E. coli) / Strain (production host): 562 / References: UniProt: P02299
#4: Protein Histone H4


Mass: 11277.257 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first residue M is replaced by I / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: 7227
Gene: CG31611, CG3379, CG33869, CG33871, CG33873, CG33875, CG33877, CG33879, CG33881, CG33883, CG33885, CG33887, CG33889, CG33891, CG33893, CG33895, CG33897, CG33899, CG33901, CG33903, CG33905, ...Gene: CG31611, CG3379, CG33869, CG33871, CG33873, CG33875, CG33877, CG33879, CG33881, CG33883, CG33885, CG33887, CG33889, CG33891, CG33893, CG33895, CG33897, CG33899, CG33901, CG33903, CG33905, CG33907, CG33909, H4, H4r, H4_DROME, His4, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909, His4r
Production host: Escherichia coli (E. coli) / Strain (production host): 562 / References: UniProt: P84040
#5: Protein Histone H2A


Mass: 13257.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EKKA are replaced by DSHKAKAK / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: 7227
Gene: CG31618, CG33808, CG33814, CG33817, CG33820, CG33823, CG33826, CG33829, CG33832, CG33835, CG33838, CG33841, CG33844, CG33847, CG33850, CG33862, CG33865, H2a, H2A_DROME, His2A, His2A:CG31618, ...Gene: CG31618, CG33808, CG33814, CG33817, CG33820, CG33823, CG33826, CG33829, CG33832, CG33835, CG33838, CG33841, CG33844, CG33847, CG33850, CG33862, CG33865, H2a, H2A_DROME, His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865
Production host: Escherichia coli (E. coli) / Strain (production host): 562 / References: UniProt: P84051
#6: Protein Histone H2B


Mass: 13595.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first residue M is replaced by I / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: 7227
Gene: CG17949, CG33868, CG33870, CG33872, CG33874, CG33876, CG33878, CG33880, CG33882, CG33884, CG33886, CG33888, CG33890, CG33892, CG33894, CG33896, CG33898, CG33900, CG33902, CG33904, CG33906, ...Gene: CG17949, CG33868, CG33870, CG33872, CG33874, CG33876, CG33878, CG33880, CG33882, CG33884, CG33886, CG33888, CG33890, CG33892, CG33894, CG33896, CG33898, CG33900, CG33902, CG33904, CG33906, CG33908, CG33910, H2B_DROME, His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Production host: Escherichia coli (E. coli) / Strain (production host): 562 / References: UniProt: P02283
#7: Protein H5


Mass: 8286.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HIS-tag at the N-term: MGSSHHHHHHSSGLVPRGSHMTE / Source: (gene. exp.) Gallus gallus (chicken) / Strain: 9031 / Gene: H5_CHICK / Production host: Escherichia coli (E. coli) / Strain (production host): 562 / References: UniProt: P02259

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Non-polymers , 1 types, 3 molecules

#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7

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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: 4.19 Å3/Da / Density % sol: 70.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.75
Details: 0.1 mM Citric acid, 0.1mM potassium chloride, and 10% MPD, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.5→45.393 Å / Num. obs: 45664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 91.5 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.2
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4INM, 1HST

4inm
PDB Unreleased entry

1hst


Resolution: 3.503→45.393 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.37 / Stereochemistry target values: TWIN_LSQ_F
Details: Zero occupancy atoms represent atoms for which no electron density observed
RfactorNum. reflection% reflection
Rfree0.2435 4443 5.06 %
Rwork0.2184 --
obs0.2196 87833 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.1 Å2
Refinement stepCycle: LAST / Resolution: 3.503→45.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 6807 39 0 13355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414280
X-RAY DIFFRACTIONf_angle_d0.75720705
X-RAY DIFFRACTIONf_dihedral_angle_d26.8235889
X-RAY DIFFRACTIONf_chiral_restr0.0332341
X-RAY DIFFRACTIONf_plane_restr0.0041471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5047-3.56510.30742130.30034128X-RAY DIFFRACTION93
3.5651-3.62990.33452250.28944191X-RAY DIFFRACTION94
3.6299-3.69970.36342160.28424201X-RAY DIFFRACTION94
3.6997-3.77520.30842180.28254193X-RAY DIFFRACTION94
3.7752-3.85720.32392230.27594218X-RAY DIFFRACTION94
3.8572-3.94690.31722160.26214150X-RAY DIFFRACTION94
3.9469-4.04550.31792250.25774220X-RAY DIFFRACTION94
4.0455-4.15480.26212250.24214223X-RAY DIFFRACTION94
4.1548-4.2770.27152200.24224171X-RAY DIFFRACTION94
4.277-4.41490.27292210.22264201X-RAY DIFFRACTION94
4.4149-4.57250.29522170.2234195X-RAY DIFFRACTION94
4.5725-4.75540.25112200.22194164X-RAY DIFFRACTION94
4.7554-4.97150.25312220.21614154X-RAY DIFFRACTION94
4.9715-5.23320.23392170.2194204X-RAY DIFFRACTION94
5.2332-5.56050.2322180.21634159X-RAY DIFFRACTION94
5.5605-5.98890.27112170.22834190X-RAY DIFFRACTION94
5.9889-6.58970.25432210.21964178X-RAY DIFFRACTION94
6.5897-7.5390.21592220.20074156X-RAY DIFFRACTION93
7.539-9.48240.16082210.15794143X-RAY DIFFRACTION93
9.4824-43.6930.13542090.14863991X-RAY DIFFRACTION90

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