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- EMDB-7318: Cryo-EM structure of CENP-A nucleosome complexed with CENP-LN -

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Basic information

Entry
Database: EMDB / ID: EMD-7318
TitleCryo-EM structure of CENP-A nucleosome complexed with CENP-LN
Map dataCryo-EM structure of CENP-A nucleosome complexed with CENP-LN
Sample
  • Complex: CENP-A NCP/CENP-LN complex
    • Complex: CENP-A NCP
      • Protein or peptide: Histone H3-like centromeric protein A (CENP-A)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
    • Complex: CENP-NL complex
      • Protein or peptide: Centromere protein N (CENP-N)
      • Protein or peptide: Centromere protein L (CENP-L)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsLi XR / Wang CL / Tian T / Zang JY / Zhou ZH
CitationJournal: Cell Res / Year: 2018
Title: Molecular basis for CENP-N recognition of CENP-A nucleosome on the human kinetochore.
Authors: Tian Tian / Xiaorun Li / Yingying Liu / Chengliang Wang / Xing Liu / Guoqiang Bi / Xuan Zhang / Xuebiao Yao / Z Hong Zhou / Jianye Zang /
History
DepositionDec 25, 2017-
Header (metadata) releaseJan 24, 2018-
Map releaseJan 31, 2018-
UpdateMar 14, 2018-
Current statusMar 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7318.png

Downloads & links

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Map

FileDownload / File: emd_7318.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of CENP-A nucleosome complexed with CENP-LN
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 168 pix.
= 179.76 Å		1.07 Å/pix.
x 168 pix.
= 179.76 Å		1.07 Å/pix.
x 168 pix.
= 179.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.060965627 - 0.12632711
Average (Standard dev.)0.0014361275 (±0.008412439)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 179.76001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z179.760179.760179.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0610.1260.001

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Supplemental data

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Sample components

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Entire : CENP-A NCP/CENP-LN complex

EntireName: CENP-A NCP/CENP-LN complex
Components
  • Complex: CENP-A NCP/CENP-LN complex
    • Complex: CENP-A NCP
      • Protein or peptide: Histone H3-like centromeric protein A (CENP-A)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
    • Complex: CENP-NL complex
      • Protein or peptide: Centromere protein N (CENP-N)
      • Protein or peptide: Centromere protein L (CENP-L)

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Supramolecule #1: CENP-A NCP/CENP-LN complex

SupramoleculeName: CENP-A NCP/CENP-LN complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: CENP-A nucleosome complexed with CENP-LN
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: CENP-A NCP

SupramoleculeName: CENP-A NCP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #13-#14
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)

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Supramolecule #3: CENP-NL complex

SupramoleculeName: CENP-NL complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#12
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Histone H3-like centromeric protein A (CENP-A)

MacromoleculeName: Histone H3-like centromeric protein A (CENP-A) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

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Macromolecule #11: Centromere protein N (CENP-N)

MacromoleculeName: Centromere protein N (CENP-N) / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWDVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR ...String:
MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWDVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQALT IASKHHQIVK MDLRSRYLDS LKAIVFKQYN QTFETHNSTT PLQERSLGLD INMDSRIIHE NIVEKERVQR ITQETFGDYP QPQLEFAQYK LETKFKSGLN GSILAEREEP LRCLIKFSSP HLLEALKSLA PAGIADAPLS PLLTCIPNKR MNYFKIRDK

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Macromolecule #12: Centromere protein L (CENP-L)

MacromoleculeName: Centromere protein L (CENP-L) / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSYSAPEST PSASSRPEDY FIGATPLQKR LESVRKQSSF ILTPPRRKIP QCSQLQEDVD PQKVAFLLHK QWTLYSLTPL YKFSYSNLKE YSRLLNAFIV AEKQKGLAVE VGEDFNIKVI FSTLLGMKGT QRDPEAFLVQ IVSKSQLPSE NREGKVLWTG WFCCVFGDSL ...String:
MDSYSAPEST PSASSRPEDY FIGATPLQKR LESVRKQSSF ILTPPRRKIP QCSQLQEDVD PQKVAFLLHK QWTLYSLTPL YKFSYSNLKE YSRLLNAFIV AEKQKGLAVE VGEDFNIKVI FSTLLGMKGT QRDPEAFLVQ IVSKSQLPSE NREGKVLWTG WFCCVFGDSL LETVSEDFTC LPLFLANGAE SNTAIIGTWF QKTFDCYFSP LAINAFNLSW MAAMWTACKM DHYVATTEFL WSVPCSPQSL DISFAIHPED AKALWDSVHK TPGEVTQEEV DLFMDCLYSH FHRHFKIHLS ATRLVRVSTS VASAHTDGKI KILCHKYLIG VLAYLTELAI FQIE

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Macromolecule #13: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 13 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC ACATATATAC ATCCGAT

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Macromolecule #14: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 14 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
ATCGGATGTA TATATGTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTTA AGCGGTGCTA GAGCTGTCTA CGACCAATTG AGCGGCCTCG GCACCGGGAT TCTCGAT

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TECNAI 20
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Image recording ID1
CTF correctionSoftware: (Name: Gctf (ver. 1.06), CTFFIND (ver. 4.1.5)) / Details: Gctf & CTFFIND4
Startup modelType of model: OTHER
Details: The H2B-K34-ubiquitylation nucleosome single particle reconstruction density achieved in the lab was low-pass filtered and served as the initial model.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 130598
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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