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- PDB-5nl0: Crystal structure of a 197-bp palindromic 601L nucleosome in comp... -

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Basic information

Entry
Database: PDB / ID: 5nl0
TitleCrystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1
Components
  • (DNA (197-MER)) x 2
  • Histone H1.0-B
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsCHROMATIN BINDING PROTEIN / DNA / nucleosome / chromatin / linker histones / histone H1 / CHROMATIN BINDING PROTEIN - DNA complex
Function / homology
Function and homology information


chromosome condensation / nucleosome assembly / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / 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 H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...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 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H1.0-B / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.4 Å
AuthorsGarcia-Saez, I. / Petosa, C. / Dimitrov, S.
Funding support France, 6items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale. Programme Epigenetique et Stabilite du Genome France
Association pour la Recherche sur le CancerChromcomp grant France
French National Research AgencyChrome grant France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
FRISBIANR-10-INSB-05-02 France
Labex GRAL (Grenoble Alliance for Integrated Structural Cell Biology)ANR-10-LABX-49-01 France
CitationJournal: Mol Cell / Year: 2017
Title: Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
Authors: Jan Bednar / Isabel Garcia-Saez / Ramachandran Boopathi / Amber R Cutter / Gabor Papai / Anna Reymer / Sajad H Syed / Imtiaz Nisar Lone / Ognyan Tonchev / Corinne Crucifix / Hervé Menoni / ...Authors: Jan Bednar / Isabel Garcia-Saez / Ramachandran Boopathi / Amber R Cutter / Gabor Papai / Anna Reymer / Sajad H Syed / Imtiaz Nisar Lone / Ognyan Tonchev / Corinne Crucifix / Hervé Menoni / Christophe Papin / Dimitrios A Skoufias / Hitoshi Kurumizaka / Richard Lavery / Ali Hamiche / Jeffrey J Hayes / Patrick Schultz / Dimitar Angelov / Carlo Petosa / Stefan Dimitrov /
Abstract: Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp ...Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (197-MER)
J: DNA (197-MER)
K: Histone H3.2
L: Histone H4
M: Histone H2A type 1
N: Histone H2B 1.1
S: DNA (197-MER)
T: DNA (197-MER)
Z: Histone H1.0-B


Theoretical massNumber of molelcules
Total (without water)426,62117
Polymers426,62117
Non-polymers00
Water0
1
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (197-MER)
J: DNA (197-MER)
Z: Histone H1.0-B


Theoretical massNumber of molelcules
Total (without water)250,91011
Polymers250,91011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
K: Histone H3.2
L: Histone H4
M: Histone H2A type 1
N: Histone H2B 1.1
S: DNA (197-MER)
T: DNA (197-MER)


Theoretical massNumber of molelcules
Total (without water)175,7116
Polymers175,7116
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.725, 405.737, 348.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 5 types, 13 molecules AEKBFLCGMDHNZ

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as ...Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as ...Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as ...Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as ...Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Histone H1.0-B / H1-SA / H1D / Histone H1(0)-2 / Histone H5A / XlH5A


Mass: 21129.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Only the H1.0b globular domain was visible in the structure. The coordinates of this chain are those of a homology model built from chicken GH5 (pdb 1HST).
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h1f0-b / Production host: Escherichia coli (E. coli) / References: UniProt: P22844

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DNA chain , 2 types, 4 molecules ISJT

#5: DNA chain DNA (197-MER)


Mass: 60824.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: There are only 193 bp in the structure whereas there are 197 bp in the crystal; putatively this could be because two base pairs at the tip of each linker are denatured and therefore not visible.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (197-MER)


Mass: 60815.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: There are only 193 bp in the structure whereas there are 197 bp in the crystal; putatively this could be because two base pairs at the tip of each linker are denatured and therefore not visible.
Source: (gene. exp.) synthetic construct (others) / 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: 3.21 Å3/Da / Density % sol: 61.68 % / Description: Long thin rods.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 5.4→49.13 Å / Num. obs: 15641 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.072 / Net I/σ(I): 9.1
Reflection shellResolution: 5.4→6.04 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4370 / CC1/2: 0.686 / Rpim(I) all: 0.553 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(1.10_2155: ???)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UT9

3ut9


Resolution: 5.4→49.128 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.59
Details: The asymmetric unit contains a complete H1/nucleosome complex (molecule A) and half of a second complex (molecule B). Rigid-body and TLS refinement in Phenix were performed. Linker DNA was ...Details: The asymmetric unit contains a complete H1/nucleosome complex (molecule A) and half of a second complex (molecule B). Rigid-body and TLS refinement in Phenix were performed. Linker DNA was extended from the nucleosome core as B-form DNA, adjusted into density using Coot and subjected to rigid body and TLS refinement in Phenix, resulting in improved R-values. The 2Fo-Fc and Fo-Fc maps calculated using phases from the NCP and linker DNA revealed additional density corresponding to the GH1 domain in both complexes A and B. The structure of X. laevis GH1.0b was modeled by homology with the crystal structure of chicken GH5 (PDB 1HST), which shares 80% amino acid sequence identity with X. laevis GH1.0b.
RfactorNum. reflection% reflection
Rfree0.2653 1561 10.01 %
Rwork0.2397 --
obs0.2422 15602 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.4→49.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9624 11869 0 0 21493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823062
X-RAY DIFFRACTIONf_angle_d1.33433638
X-RAY DIFFRACTIONf_dihedral_angle_d27.96211841
X-RAY DIFFRACTIONf_chiral_restr0.0663825
X-RAY DIFFRACTIONf_plane_restr0.0082247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.4001-5.57410.40381410.36671271X-RAY DIFFRACTION100
5.5741-5.77310.37961350.35271217X-RAY DIFFRACTION99
5.7731-6.00380.39841410.35261255X-RAY DIFFRACTION99
6.0038-6.27650.38261400.34361271X-RAY DIFFRACTION100
6.2765-6.60670.3191390.31321249X-RAY DIFFRACTION99
6.6067-7.01950.33991410.3051268X-RAY DIFFRACTION99
7.0195-7.55970.29861410.27561266X-RAY DIFFRACTION100
7.5597-8.31720.24341410.221273X-RAY DIFFRACTION100
8.3172-9.51310.26621430.20891293X-RAY DIFFRACTION100
9.5131-11.95690.20821460.18891308X-RAY DIFFRACTION98
11.9569-49.12970.20431530.19251370X-RAY DIFFRACTION98

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