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- PDB-2yfv: The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4 -

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Basic information

Entry
Database: PDB / ID: 2yfv
TitleThe heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4
Components
  • HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
  • HISTONE H4
  • SCM3
KeywordsCELL CYCLE / KINETOCHORE / CENTROMERE / HISTONE CHAPERONE / BUDDING YEAST
Function / homology
Function and homology information


CENP-A containing nucleosome / structural constituent of chromatin / histone binding / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2010 / Centromere protein Scm3/HJURP / Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Histone H4, conserved site / Histone H4 signature. / Histone H4 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2010 / Centromere protein Scm3/HJURP / Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Special / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / KLLA0F05115p / 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: 2.32 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: SCM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8345
Polymers27,5803
Non-polymers2542
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-57.7 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.723, 65.530, 121.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 11692.733 Da / Num. of mol.: 1 / Fragment: RESIDUES 81-180
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: 8456.876 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-98
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: Protein SCM3 / KLLA0F05115P


Mass: 7430.433 Da / Num. of mol.: 1 / Fragment: RESIDUES 41-103
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: Q6CL77
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.59 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 4.5
Details: 0.1 M SODIUM CITRATE, PH4.5, 6% PEG 4000, AND 0.1 M SODIUM IODIDE

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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: Oct 10, 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: 2.3→50 Å / Num. obs: 11636 / % possible obs: 94.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.5 / % possible all: 55.3

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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: 2.32→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.225 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 126-130 OF CHAIN A ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25712 555 4.8 %RANDOM
Rwork0.22026 ---
obs0.22195 11073 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.054 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20 Å2
2--3.52 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 2 58 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9692215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27522.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.35915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8051520
X-RAY DIFFRACTIONr_chiral_restr0.1060.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021177
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_it0.6731.51001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35621620
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4093651
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1634.5595
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: 2.322→2.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 35 -
Rwork0.293 656 -
obs--81.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3373-0.11912.62121.4610.47716.1363-0.07330.33550.102-0.254-0.04920.0637-0.172-0.12070.12250.03730.00220.02450.05530.05630.0982-10.619710.3622-29.0981
22.1331-0.3032-1.09012.37961.9710.41280.03490.4277-0.0208-0.59940.0127-0.0813-0.386-0.2845-0.04760.0457-0.0295-0.00830.05050.04720.0984-12.26819.9319-33.9279
31.02991.28431.7021.08931.36391.2329-0.15730.0928-0.1224-0.16530.10490.0266-0.19530.08320.05240.1369-0.01390.01540.2077-0.00410.1968-4.2359-4.0081-27.0598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 120
2X-RAY DIFFRACTION1A121 - 133
3X-RAY DIFFRACTION1A134 - 168
4X-RAY DIFFRACTION1A169 - 176
5X-RAY DIFFRACTION1A177 - 180
6X-RAY DIFFRACTION2B24 - 34
7X-RAY DIFFRACTION2B35 - 40
8X-RAY DIFFRACTION2B41 - 66
9X-RAY DIFFRACTION2B67 - 78
10X-RAY DIFFRACTION2B79 - 95
11X-RAY DIFFRACTION3C44 - 57
12X-RAY DIFFRACTION3C58 - 68
13X-RAY DIFFRACTION3C69 - 76
14X-RAY DIFFRACTION3C77 - 90
15X-RAY DIFFRACTION3C91 - 104

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