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

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2xql
Title	Fitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).
Descriptor	HISTONE H2A-IV HISTONE H2B 5
Keywords	NUCLEAR PROTEIN, CHAPERONE, CHROMATIN, NUCLEAR-CHAPERONE, HISTONE-CHAPERONE
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1777, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1777 Fit PDB-1eqz PDB-1hio PDB-1hq3 PDB-1tzy PDB-2aro PDB-2hio Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3iz2 PDB-3iz1 List of similar structure data about Omokage system

Article
Citation - primary
Article	J.Biol.Chem., Vol. 285, Page: 33771 - , Year: 2010,
Title	Nucleoplasmin Binds Histone H2A-H2B Dimers Through its Distal Face.
Authors	Ramos, I., Martin-Benito, J., Finn, R., Bretana, L., Aloria, K., Arizmendi, J.M., Ausio, J., Muga, A., Valpuesta, J.M., Prado, A.
Links	DOI: 10.1074/JBC.M110.150664

Components
ID 1 : H2A HISTONE
Image
Description	HISTONE H2A-IV
Type	polypeptide(L)
Fragment	RESIDUES 16-106
Formula weight	10034.741 Da
Number of molecules	5
ID	1
Source	Method: Isolated from a natural source Common name: CHICKEN Cell: ERYTHROCYTE NCBI taxonomy: ID:9031 Organism scientific: GALLUS GALLUS
Links	UniProt: P02263, Sequence view
ID 2 : H2B HISTONE, H2B V
Image
Description	HISTONE H2B 5
Type	polypeptide(L)
Fragment	RESIDUES 37-126
Formula weight	9977.530 Da
Number of molecules	5
ID	2
Source	Method: Isolated from a natural source Common name: CHICKEN Cell: ERYTHROCYTE NCBI taxonomy: ID:9031 Organism scientific: GALLUS GALLUS
Links	UniProt: P0C1H4, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	NUCLEOPLASMIN H2A-H2B HISTONES COMPLEX.
Buffer
Name	2MM MGCL2, 240MM NACL, 25MM TRIS-HCL
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	NEGATIVE STAIN URANYL ACETATE
Sample preparation
pH	7.5
Sample support
Details	CARBON
Experiment
Method	ELECTRON MICROSCOPY

Processing
2D projection selection
Number of particles	5557
Software name	EMAN XMIPP SPIDER
3D reconstruction
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).
Method	PROJECTION MATCHING
Nominal pixel size	2.3 A/pix
Resolution	19.5 A
3D fitting
Method	VOLUMETRIC CORRELATION
Refinement Protocol	PROJECTION MATCHING
Refinement Space	REAL
3D fitting list
3D fitting id	1
PDB entry ID	1AOI PDB-1aoi
Refine
Refine id	ELECTRON MICROSCOPY
Ls d res high	19.50 A
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
D res high	19.50
Total atoms	7030
Protein atoms	7030