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- PDB-5g2e: Structure of the Nap1 H2A H2B complex -

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Basic information

Entry
Database: PDB / ID: 5g2e
TitleStructure of the Nap1 H2A H2B complex
Components
  • HISTONE H2A TYPE 1
  • HISTONE H2B 1.1
  • NUCLEOSOME ASSEMBLY PROTEIN
KeywordsDNA BINDING PROTEIN / NUCLEOSOME ASSEMBLY PROTEIN 1 / HISTONE / H2A-H2B / CHROMATIN / NUCLEOSOME ASSEMBLY
Function / homology
Function and homology information


protein localization to cell division site after cytokinesis / Gin4 complex / cellular bud neck septin collar / budding cell bud growth / : / septin ring assembly / septum digestion after cytokinesis / nucleosome disassembly / NLS-bearing protein import into nucleus / cell division site ...protein localization to cell division site after cytokinesis / Gin4 complex / cellular bud neck septin collar / budding cell bud growth / : / septin ring assembly / septum digestion after cytokinesis / nucleosome disassembly / NLS-bearing protein import into nucleus / cell division site / enzyme activator activity / positive regulation of microtubule polymerization / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / ribosomal small subunit biogenesis / nucleosome assembly / structural constituent of chromatin / nucleosome / unfolded protein binding / histone binding / protein heterodimerization activity / chromatin binding / chromatin / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / 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 H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Nucleosome assembly protein
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
XENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.7 Å
AuthorsAguilarGurrieri, C. / Larabi, A. / Vinayachandran, V. / Patel, N.A. / Yen, K. / Reja, R. / Ebong, I.O. / Schoehn, G. / Robinson, C.V. / Pugh, B.F. / Panne, D.
CitationJournal: Embo J. / Year: 2016
Title: Structural Evidence for Nap1-Dependent H2A-H2B Deposition and Nucleosome Assembly.
Authors: Aguilar-Gurrieri, C. / Larabi, A. / Vinayachandran, V. / Patel, N.A. / Yen, K. / Reja, R. / Ebong, I. / Schoehn, G. / Robinson, C.V. / Pugh, B.F. / Panne, D.
History
DepositionApr 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSOME ASSEMBLY PROTEIN
B: NUCLEOSOME ASSEMBLY PROTEIN
C: HISTONE H2A TYPE 1
D: HISTONE H2B 1.1
E: NUCLEOSOME ASSEMBLY PROTEIN
F: NUCLEOSOME ASSEMBLY PROTEIN
G: HISTONE H2A TYPE 1
H: HISTONE H2B 1.1
I: NUCLEOSOME ASSEMBLY PROTEIN
J: NUCLEOSOME ASSEMBLY PROTEIN
K: HISTONE H2A TYPE 1
L: HISTONE H2B 1.1
M: NUCLEOSOME ASSEMBLY PROTEIN
N: NUCLEOSOME ASSEMBLY PROTEIN
O: HISTONE H2A TYPE 1
P: HISTONE H2B 1.1
Q: NUCLEOSOME ASSEMBLY PROTEIN
R: NUCLEOSOME ASSEMBLY PROTEIN
S: HISTONE H2A TYPE 1
T: HISTONE H2B 1.1
U: NUCLEOSOME ASSEMBLY PROTEIN
V: NUCLEOSOME ASSEMBLY PROTEIN
W: HISTONE H2A TYPE 1
X: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)571,41524
Polymers571,41524
Non-polymers00
Water0
1
I: NUCLEOSOME ASSEMBLY PROTEIN
J: NUCLEOSOME ASSEMBLY PROTEIN
K: HISTONE H2A TYPE 1
L: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15650 Å2
ΔGint-115.5 kcal/mol
Surface area40750 Å2
MethodPQS
2
E: NUCLEOSOME ASSEMBLY PROTEIN
F: NUCLEOSOME ASSEMBLY PROTEIN
G: HISTONE H2A TYPE 1
H: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15380 Å2
ΔGint-105.6 kcal/mol
Surface area40960 Å2
MethodPQS
3
A: NUCLEOSOME ASSEMBLY PROTEIN
B: NUCLEOSOME ASSEMBLY PROTEIN
C: HISTONE H2A TYPE 1
D: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-117.6 kcal/mol
Surface area40720 Å2
MethodPQS
4
Q: NUCLEOSOME ASSEMBLY PROTEIN
R: NUCLEOSOME ASSEMBLY PROTEIN
S: HISTONE H2A TYPE 1
T: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-114.2 kcal/mol
Surface area41130 Å2
MethodPQS
5
U: NUCLEOSOME ASSEMBLY PROTEIN
V: NUCLEOSOME ASSEMBLY PROTEIN
W: HISTONE H2A TYPE 1
X: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint-111.1 kcal/mol
Surface area40820 Å2
MethodPQS
6
M: NUCLEOSOME ASSEMBLY PROTEIN
N: NUCLEOSOME ASSEMBLY PROTEIN
O: HISTONE H2A TYPE 1
P: HISTONE H2B 1.1


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15240 Å2
ΔGint-101.9 kcal/mol
Surface area40750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)111.470, 211.130, 126.570
Angle α, β, γ (deg.)90.00, 99.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NUCLEOSOME ASSEMBLY PROTEIN / NUCLEOSOME ASSEMBLY PROTEIN 1


Mass: 36084.996 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25293
#2: Protein
HISTONE H2A TYPE 1 / HISTONE H2A


Mass: 11754.768 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06897
#3: Protein
HISTONE H2B 1.1 / H2B1.1 / HISTONE H2B


Mass: 11311.154 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02281

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 10-15% W/V PEG3350; 200 MM LICL

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-410.9749
SYNCHROTRONESRF ID23-120.9749
SYNCHROTRONESRF ID23-230.9749
Detector
TypeIDDetectorDate
ADSC CCD1CCDDec 19, 2010
DECTRIS PIXEL2PIXEL
DECTRIS PIXEL3PIXEL
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
3Mx-ray1
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 6.7→50 Å / Num. obs: 10467 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 6.7→7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z2R

2z2r


Resolution: 6.7→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: COORDINATE REFINEMENT WAS DONE USING DEFORMABLE ELASTIC NETWORK (DEN) REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.31 508 4.9 %RANDOM
Rwork0.2626 ---
obs0.2626 10150 97 %-
Solvent computationBsol: 290.909 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-58.759 Å20 Å223.489 Å2
2---40.819 Å20 Å2
3----17.94 Å2
Refinement stepCycle: LAST / Resolution: 6.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32814 0 0 0 32814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.002846
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.7527
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPARPROTEIN_REP.PARAMCNS_TOPPARPROTEIN.TOP
X-RAY DIFFRACTION2AA
X-RAY DIFFRACTION3CNS_TOPPARWATER_REP.PARAMCNS_TOPPARWATER.TOP
X-RAY DIFFRACTION4CNS_TOPPARION.PARAMCNS_TOPPARION.TOP
X-RAY DIFFRACTION5CNS_TOPPARCARBOHYDRATE.PARAMCNS_TOPPARCARBOHYDRATE.TOP

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