[English] 日本語
Yorodumi
- PDB-4x23: CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE P... -

+
Open data


ID or keywords:

Loading...

-
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


pericentric heterochromatin => GO:0005721 / condensed chromosome, centromeric region => GO:0000779 / kinetochore => GO:0000776 / Interleukin-7 signaling / Chromatin modifying enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Ub-specific processing proteases ...pericentric heterochromatin => GO:0005721 / condensed chromosome, centromeric region => GO:0000779 / kinetochore => GO:0000776 / Interleukin-7 signaling / Chromatin modifying enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Ub-specific processing proteases / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / polytene chromosome band / monopolar spindle attachment to meiosis I kinetochore / polytene chromosome / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / chromatin assembly or disassembly / nucleosomal DNA binding / heterochromatin assembly => GO:0031507 / pericentric heterochromatin / nuclear chromosome / kinetochore / chromosome segregation / DNA-templated transcription, initiation / nucleosome assembly / nucleosome / chromatin organization / mitotic cell cycle / chromosome / protein heterodimerization activity / chromatin / protein-containing complex binding / DNA binding / identical protein binding / nucleus
Similarity search - Function
Centromere assembly component CENP-C middle DNMT3B-binding region / CENP-C, middle DNMT3B-binding domain / Kinetochore assembly subunit CENP-C N-terminal / Kinetochore assembly subunit CENP-C, N-terminal domain / Mif2/CENP-C cupin domain / Mif2/CENP-C like / Centromere protein C/Mif2/cnp3 / Histone, subunit A / Histone, subunit A / RmlC-like cupin domain superfamily ...Centromere assembly component CENP-C middle DNMT3B-binding region / CENP-C, middle DNMT3B-binding domain / Kinetochore assembly subunit CENP-C N-terminal / Kinetochore assembly subunit CENP-C, N-terminal domain / Mif2/CENP-C cupin domain / Mif2/CENP-C like / Centromere protein C/Mif2/cnp3 / Histone, subunit A / Histone, subunit A / RmlC-like cupin domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / RmlC-like jelly roll fold / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA (> 100) / DNA (> 10) / DNA / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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
γ
α
β
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

-
Components

-
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)

-
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

-
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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
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

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more