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- PDB-4x23: CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE P... -

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Basic information

Entry
Database: PDB / ID: 4x23
TitleCRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE
Components
  • (DNA (147-MER)) x 2
  • CENP-C
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
Keywordsstructural protein/dna / NUCLEOSOME CORE PARTICLE / WIDOM 601 DNA FRAGMMENT / HISTONE FOLD / CENP-C COMPLEX / SEGREGATION / CHROMOSOME CENTROMERE / KINETOCHORE ASSEMBLY / CONSTITUTIVE CENTROMERE-ASSOCIATED NETWORK (CCAN) PROTEINS / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / spindle attachment to meiosis I kinetochore / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / centromeric DNA binding / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / inner kinetochore / nucleosomal DNA binding / nuclear chromosome / pericentric heterochromatin / chromosome segregation / kinetochore / structural constituent of chromatin / nucleosome / heterochromatin formation / mitotic cell cycle / nucleosome assembly / chromosome / chromatin organization / protein heterodimerization activity / chromatin / protein-containing complex binding / DNA binding / identical protein binding / nucleus
Similarity search - Function
CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Histone, subunit A / Histone, subunit A / RmlC-like cupin domain superfamily ...CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Histone, subunit A / Histone, subunit A / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 1. / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3 / Histone H4 / Histone H2A / CENP-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJiang, J.S.
CitationJournal: Science / Year: 2013
Title: A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C.
Authors: Kato, H. / Jiang, J.S. / Zhou, B.R. / Rozendaal, M. / Feng, H. / Ghirlando, R. / Xiao, T.S. / Straight, A.F. / Bai, Y.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionDec 10, 2014ID: 4INM
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Derived calculations
Revision 1.2Jul 13, 2016Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (147-MER)
J: DNA (147-MER)
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
V: CENP-C
U: CENP-C
S: DNA (147-MER)
T: DNA (147-MER)
K: Histone H3
L: Histone H4
M: Histone H2A
N: Histone H2B
O: Histone H3
P: Histone H4
Q: Histone H2A
R: Histone H2B
X: CENP-C
W: CENP-C


Theoretical massNumber of molelcules
Total (without water)359,94424
Polymers359,94424
Non-polymers00
Water00
1
I: DNA (147-MER)
J: DNA (147-MER)
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
V: CENP-C
U: CENP-C


Theoretical massNumber of molelcules
Total (without water)179,97212
Polymers179,97212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
S: DNA (147-MER)
T: DNA (147-MER)
K: Histone H3
L: Histone H4
M: Histone H2A
N: Histone H2B
O: Histone H3
P: Histone H4
Q: Histone H2A
R: Histone H2B
X: CENP-C
W: CENP-C


Theoretical massNumber of molelcules
Total (without water)179,97212
Polymers179,97212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.994, 176.102, 208.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 4 molecules ISJT

#1: DNA chain DNA (147-MER)


Mass: 45138.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 147 BP WIDOM 601 DNA FRAGMENT (+ STRAND) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (147-MER)


Mass: 45610.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 147 BP WIDOM 601 DNA FRAGMENT (- STRAND) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein , 4 types, 16 molecules AEKOBFLPCGMQDHNR

#3: Protein
Histone H3


Mass: 11365.296 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 41-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02299
#4: Protein
Histone H4


Mass: 8910.394 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 25-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His4 / Production host: Escherichia coli (E. coli) / References: UniProt: P84040
#5: Protein
Histone H2A


Mass: 11093.877 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 16-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2A / Production host: Escherichia coli (E. coli) / References: UniProt: P84051
#6: Protein
Histone H2B


Mass: 10019.455 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 33-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2B / Production host: Escherichia coli (E. coli) / References: UniProt: P02283

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Protein/peptide , 1 types, 4 molecules VUXW

#7: Protein/peptide
CENP-C


Mass: 3222.686 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 710-734 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q66LH7

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Details

Sequence detailsTHE DISCREPANCY AT THE C-TERM OF H3 SEQUENCES (CHAINS A,E,K,O) IS A RESULT OF CHIMERIC CENP-A, I.E. ...THE DISCREPANCY AT THE C-TERM OF H3 SEQUENCES (CHAINS A,E,K,O) IS A RESULT OF CHIMERIC CENP-A, I.E. THE LAST THREE RESIDUES OF H3 (-ERA) TO THE LAST SIX RESIDUES OF CENP-A (-IEGGLG)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% MPD, 40MM SODIUM CACODYLATE, 24MM SPERMINE TETRA-HCL, 80MM SODIUM CHLORIDE, 20MM MAGNESIUM CHLORIDE; RESERVIOR 35% MPD. PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
PH range: 7.4 - 7.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12741
22741
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONNSLS X29A21.075
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 13, 2012
ADSC QUANTUM 3152CCDJun 22, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.0751
ReflectionResolution: 3.5→50 Å / Num. obs: 48623 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 122.9 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.5 / % possible all: 78.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata scaling
Blu-Icedata collection
CBASSdata collection
HKL-2000data scaling
CNS1.3refinement
PHASERphasing
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PYO, 3MVD

2pyo

3mvd


Resolution: 3.5→49.543 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.82 / Stereochemistry target values: ML / Details: CNS 1.3 WAS USED FOR LOW RESOLUTION REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 1838 3.78 %Random
Rwork0.2362 ---
obs0.2382 48623 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 157.6 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12002 11972 0 0 23974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325588
X-RAY DIFFRACTIONf_angle_d0.55937074
X-RAY DIFFRACTIONf_dihedral_angle_d26.07110504
X-RAY DIFFRACTIONf_chiral_restr0.0224220
X-RAY DIFFRACTIONf_plane_restr0.0022672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.59460.42491380.353537X-RAY DIFFRACTION100
3.5946-3.70030.36361400.33133545X-RAY DIFFRACTION100
3.7003-3.81970.38771400.31593554X-RAY DIFFRACTION100
3.8197-3.95620.40041390.30383540X-RAY DIFFRACTION100
3.9562-4.11450.32691400.29043572X-RAY DIFFRACTION100
4.1145-4.30170.35221400.2713564X-RAY DIFFRACTION100
4.3017-4.52830.27841410.24493574X-RAY DIFFRACTION100
4.5283-4.81180.24861400.24033564X-RAY DIFFRACTION100
4.8118-5.1830.26051420.24483618X-RAY DIFFRACTION100
5.183-5.70390.34261410.27713595X-RAY DIFFRACTION100
5.7039-6.52770.35331420.26713638X-RAY DIFFRACTION100
6.5277-8.21810.27181450.22553651X-RAY DIFFRACTION100
8.2181-49.54820.20191500.15933833X-RAY DIFFRACTION100

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