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

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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 A resolution / Single particle / Negative stain uranyl acetate)
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 StrPapers
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

DateDeposition: Sep 2, 2010 / Release: Nov 3, 2010 / Last modification: Mar 20, 2013

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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)100,06110
Polyers100,06110
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: 10034.741 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: 9977.530 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: NEGATIVE STAIN URANYL ACETATE

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Sample preparation

Assembly of specimenName: NUCLEOPLASMIN H2A-H2B HISTONES COMPLEX. / Aggregation state: PARTICLE
Buffer solutionName: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL
Sample preparationpH: 7.5
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyMicroscope model: OTHER
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 5.6 mm
Specimen holderTemperature: 293 K
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 14
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: EMAN XMIPP SPIDER / Number of particles: 5557
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 19.5 A / Nominal pixel size: 2.3 A/pix / CTF correction method: EACH PLATE
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).
Atomic model buildingMethod: VOLUMETRIC CORRELATION / Ref protocol: PROJECTION MATCHING / Ref space: REAL
Atomic model buildingPDB-ID: 1AOI
Least-squares processHighest resolution: 19.5 A
Refine hist #LASTHighest resolution: 19.5 A
Number of atoms included #LASTProtein: 7030 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7030

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