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- PDB-2xql: Fitting of the H2A-H2B histones in the electron microscopy map of... -

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Basic information

Entry
Database: PDB / ID: 2xql
TitleFitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).
DescriptorHISTONE H2A-IV, HISTONE H2B 5
KeywordsNUCLEAR PROTEIN / CHAPERONE / CHROMATIN / NUCLEAR-CHAPERONE / HISTONE-CHAPERONE
Specimen sourceGallus gallus / bird / CHICKEN / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
MethodElectron microscopy (19.5 Å resolution / Particle / Single particle)
AuthorsRamos, I. / Martin-Benito, J. / Finn, R. / Bretana, L. / Aloria, K. / Arizmendi, J.M. / Ausio, J. / Muga, A. / Valpuesta, J.M. / Prado, A.
CitationJ. Biol. Chem., 2010, 285, 33771-33778

J. Biol. Chem., 2010, 285, 33771-33778 Yorodumi Papers
Nucleoplasmin binds histone H2A-H2B dimers through its distal face.
Isbaal Ramos / Jaime Martín-Benito / Ron Finn / Laura Bretaña / Kerman Aloria / Jesús M Arizmendi / Juan Ausió / Arturo Muga / José M Valpuesta / Adelina Prado

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 2, 2010 / Release: Nov 3, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 3, 2010Structure modelrepositoryInitial release
1.1Mar 20, 2013Structure modelDerived calculations / Other / Version format compliance
1.2Aug 30, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Assembly

Deposited unit
A: HISTONE H2A-IV
B: HISTONE H2B 5
C: HISTONE H2A-IV
D: HISTONE H2B 5
E: HISTONE H2A-IV
F: HISTONE H2B 5
G: HISTONE H2A-IV
H: HISTONE H2B 5
I: HISTONE H2A-IV
J: HISTONE H2B 5


Theoretical massNumber of molelcules
Total (without water)100,06010
Polyers100,06010
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)
HISTONE H2A-IV / H2A HISTONE


Mass: 10034.639 Da / Num. of mol.: 5 / Fragment: RESIDUES 16-106
Source: (natural) Gallus gallus / bird / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
References: UniProt: P02263

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
HISTONE H2B 5 / H2B HISTONE / H2B V


Mass: 9977.441 Da / Num. of mol.: 5 / Fragment: RESIDUES 37-126
Source: (natural) Gallus gallus / bird / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
References: UniProt: P0C1H4

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: NUCLEOPLASMIN H2A-H2B HISTONES COMPLEX. / Type: COMPLEX
Buffer solutionName: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL / Details: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 1200EXII
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 5.6 mm
Specimen holderTemperature: 293 kelvins
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 14
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1SitusMODEL FITTING1
2EMANRECONSTRUCTION1
3SPIDERRECONSTRUCTION1
4XmippRECONSTRUCTION1
CTF correctionDetails: EACH PLATE
SymmetryPoint symmetry: C5
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 19.5 Å / Number of particles: 5557 / Nominal pixel size: 2.3
Details: DOCKING OF FIVE DIMERS OF H2A-H2B HISTONES IN THE NUCLEOPLASMIN H2A-H2B COMPLEX (1 5-5). THE EXTENDED REGION OF THE H2A HISTONE WAS REMOVED. THE FINAL DOCKING INCLUDES THE FRAGMENTS FROM AMINOACID 15 TO 105 OF H2A HISTONE AND 36 TO 125 OF H2B HISTONE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1777. (DEPOSITION ID: 7474).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--VOLUMETRIC CORRELATION REFINEMENT PROTOCOL--PROJECTION MATCHING
Ref protocol: OTHER / Ref space: REAL
Atomic model buildingPDB-ID: 1AOI
Least-squares processHighest resolution: 19.5 Å
Refine hist #LASTHighest resolution: 19.5 Å
Number of atoms included #LASTProtein: 7030 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7030

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