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Fitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).

by single particle reconstruction, at 19.5 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1777, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsRamos, I., Martin-Benito, J., Finn, R., Bretana, L., Aloria, K., Arizmendi, J.M., Ausio, J., Muga, A., Valpuesta, J.M., Prado, A.
DateDeposition: 2010-09-02, Release: 2010-11-03
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1777, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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EMDB-1777

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Article
Citation - primary
ArticleJ. Biol. Chem., Vol. 285, Issue 44, Page 33771-8, Year 2010
TitleNucleoplasmin binds histone H2A-H2B dimers through its distal face.
AuthorsIsbaal Ramos, Jaime Martín-Benito, Ron Finn, Laura Bretaña, Kerman Aloria, Jesús M Arizmendi, Juan Ausió, Arturo Muga, José M Valpuesta, Adelina Prado
Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, 48080 Bilbao, Spain.
KeywordsAnimals, Dimerization, Histones (chemistry), Mass Spectrometry (methods), Microscopy, Electron (methods), Nucleoplasmins (chemistry), Phosphorylation, Protein Folding, Protein Interaction Mapping, Protein Structure, Tertiary, Xenopus laevis (metabolism)
LinksDOI: 10.1074/jbc.M110.150664, PubMed: 20696766, PMC: PMC2962476
Components
ID 1 : H2A HISTONE
Image
DescriptionHISTONE H2A-IV
Typepolypeptide(L)
FragmentRESIDUES 16-106
Formula weight10034.741 Da
Number of molecules5
ID1
SourceMethod: Isolated from a natural source
Common name: CHICKEN
Cell: ERYTHROCYTE
NCBI taxonomy: ID:9031
Organism scientific: GALLUS GALLUS

LinksUniProt: P02263, Sequence view
ID 2 : H2B HISTONE, H2B V
Image
DescriptionHISTONE H2B 5
Typepolypeptide(L)
FragmentRESIDUES 37-126
Formula weight9977.530 Da
Number of molecules5
ID2
SourceMethod: Isolated from a natural source
Common name: CHICKEN
Cell: ERYTHROCYTE
NCBI taxonomy: ID:9031
Organism scientific: GALLUS GALLUS
LinksUniProt: P0C1H4, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameNUCLEOPLASMIN H2A-H2B HISTONES COMPLEX.
Buffer
Name2MM MGCL2, 240MM NACL, 25MM TRIS-HCL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeNEGATIVE STAIN URANYL ACETATE
Sample preparation
pH7.5
Sample support
DetailsCARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
Electron gun
Electron sourceTUNGSTEN HAIRPIN
Accelerating voltage100 kV
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationNominal: 60000 X
CsNominal: 5.6 mm
Nominal defocusMax: 2500 nm, Min: 1000 nm
Specimen holder
Temperature293 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images14
Processing
2D projection selection
Number of particles5557
Software nameEMAN XMIPP SPIDER
3D reconstruction
CTF correction methodEACH PLATE
DetailsDOCKING 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).
MethodPROJECTION MATCHING
Nominal pixel size2.3 A/pix
Resolution19.5 A
3D fitting
MethodVOLUMETRIC CORRELATION
Refinement ProtocolPROJECTION MATCHING
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID1AOI
Refine
Refine idELECTRON MICROSCOPY
Ls d res high19.50 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high19.50
Total atoms7030
Protein atoms7030
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Header onlypdb2xql.ent.gz
mmCIF format
mmCIF2xql.cif.gz
XML format
All2xql.xml.gz
No-atom2xql-noatom.xml.gz
Ext-atom2xql-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.6 MB