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- PDB-2yfw: Heterotetramer structure of Kluyveromyces lactis Cse4,H4 -

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Basic information

Entry
Database: PDB / ID: 2yfw
TitleHeterotetramer structure of Kluyveromyces lactis Cse4,H4
Components
  • HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
  • HISTONE H4
KeywordsCELL CYCLE / KINETOCHORE / CENTROMERE / HISTONE CHAPERONE / BUDDING YEAST
Function / homology
Function and homology information


CENP-A containing nucleosome / structural constituent of chromatin / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 ...Histone, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Histone H3-like centromeric protein CSE4
Similarity search - Component
Biological speciesKLUYVEROMYCES LACTIS NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCho, U.S. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Recognition of the Centromere-Specific Histone Cse4 by the Chaperone Scm3.
Authors: Cho, U.S. / Harrison, S.C.
History
DepositionApr 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: 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: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
B: HISTONE H4
C: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
D: HISTONE H4
E: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
F: HISTONE H4
G: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
H: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)88,7328
Polymers88,7328
Non-polymers00
Water25214
1
A: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
B: HISTONE H4
G: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
H: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)44,3664
Polymers44,3664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-99.4 kcal/mol
Surface area15490 Å2
MethodPISA
2
C: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
D: HISTONE H4
E: HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
F: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)44,3664
Polymers44,3664
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-93.9 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.479, 169.479, 81.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9234, 0.2429, 0.2972), (0.3676, 0.3371, 0.8667), (0.1104, 0.9096, -0.4005)89.73, -27.38, 10.52
2given(-0.9234, 0.2429, 0.2972), (0.3676, 0.3371, 0.8667), (0.1104, 0.9096, -0.4005)89.73, -27.38, 10.52
3given(0.01418, 0.4677, -0.8838), (0.5252, -0.7556, -0.3915), (-0.8509, -0.4586, -0.2563)45.74, -66.56, 17
4given(-0.09929, -0.7736, 0.6258), (-0.5608, -0.476, -0.6775), (0.822, -0.4182, -0.3866)33.38, -17.42, -51.05

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Components

#1: Protein
HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4 / CENP-A HOMOLOG / CHROMOSOME SEGREGATION PROTEIN 4 / CSE4


Mass: 10746.627 Da / Num. of mol.: 4 / Fragment: HISTONE-FOLD DOMAIN, RESIDUES 93-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLUYVEROMYCES LACTIS NRRL Y-1140 (yeast)
Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CTI2
#2: Protein
HISTONE H4 / / H4


Mass: 11436.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLUYVEROMYCES LACTIS NRRL Y-1140 (yeast)
Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CMU6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL, PH8.5, 0.2 M NACL, AND 25% PEG 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97914
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010 / Details: MIRRORS
RadiationMonochromator: CHOZU HLD8-24 MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26486 / % possible obs: 99.9 % / Observed criterion σ(I): 1.3 / Redundancy: 3.8 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQZ

1eqz


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.881 / SU B: 27.088 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 93-104, 128,184 FOR CHAIN A, RESIDUES 1-28,95-103 FOR CHAIN B, RESIDUES 93-103, 123-130, 182-184 FOR CHAIN C, RESIDUES 1-23, 95- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 93-104, 128,184 FOR CHAIN A, RESIDUES 1-28,95-103 FOR CHAIN B, RESIDUES 93-103, 123-130, 182-184 FOR CHAIN C, RESIDUES 1-23, 95-103 FOR CHAIN D, RESIDUES 126-129 FOR CHAIN E, RESIDUES 1-22, 95-103 FOR CHAIN F, RESIDUES 93-103, 182-184 FOR CHAIN G, RESIDUES 1-22,103 FOR CHAIN H ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27633 1342 5 %RANDOM
Rwork0.21828 ---
obs0.22112 25302 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.28 Å20 Å2
2--0.57 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 14 4822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9736524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98420.927205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.73215951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1061569
X-RAY DIFFRACTIONr_chiral_restr0.1010.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023463
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.52990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1124800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94731870
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4654.51724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 98 -
Rwork0.289 1829 -
obs--97.82 %

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