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- EMDB-3765: Structure of nucleosome-Chd1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3765
TitleStructure of nucleosome-Chd1 complex
Map data
Sample
  • Complex: Protein-Nucleic Acid complex
    • Complex: Protein-Nucleic Acid complex
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H2B 1.1
    • Complex: Protein-Nucleic Acid complex
      • DNA: DNA (162-MER)
      • DNA: DNA (162-MER)
    • Complex: Protein-Nucleic Acid complex
      • Protein or peptide: Chromo domain-containing protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsATPase / Complex / Nucleosome / DNA / DNA BINDING PROTEIN / Chromatin Remodeling
Function / homology
Function and homology information


nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / 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-like fold domain / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Chromo domain-containing protein 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsFarnung L / Vos SM
CitationJournal: Nature / Year: 2017
Title: Nucleosome-Chd1 structure and implications for chromatin remodelling.
Authors: Lucas Farnung / Seychelle M Vos / Christoph Wigge / Patrick Cramer /
Abstract: Chromatin-remodelling factors change nucleosome positioning and facilitate DNA transcription, replication, and repair. The conserved remodelling factor chromodomain-helicase-DNA binding protein ...Chromatin-remodelling factors change nucleosome positioning and facilitate DNA transcription, replication, and repair. The conserved remodelling factor chromodomain-helicase-DNA binding protein 1(Chd1) can shift nucleosomes and induce regular nucleosome spacing. Chd1 is required for the passage of RNA polymerase IIthrough nucleosomes and for cellular pluripotency. Chd1 contains the DNA-binding domains SANT and SLIDE, a bilobal motor domain that hydrolyses ATP, and a regulatory double chromodomain. Here we report the cryo-electron microscopy structure of Chd1 from the yeast Saccharomyces cerevisiae bound to a nucleosome at a resolution of 4.8 Å. Chd1 detaches two turns of DNA from the histone octamer and binds between the two DNA gyres in a state poised for catalysis. The SANT and SLIDE domains contact detached DNA around superhelical location (SHL) -7 of the first DNA gyre. The ATPase motor binds the second DNA gyre at SHL +2 and is anchored to the N-terminal tail of histone H4, as seen in a recent nucleosome-Snf2 ATPase structure. Comparisons with published results reveal that the double chromodomain swings towards nucleosomal DNA at SHL +1, resulting in ATPase closure. The ATPase can then promote translocation of DNA towards the nucleosome dyad, thereby loosening the first DNA gyre and remodelling the nucleosome. Translocation may involve ratcheting of the two lobes of the ATPase, which is trapped in a pre- or post-translocation state in the absence or presence, respectively, of transition state-mimicking compounds.
History
DepositionJun 19, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseOct 11, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o9g
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3765.png

Downloads & links

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Map

FileDownload / File: emd_3765.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0317 / Movie #1: 0.0317
Minimum - Maximum-0.06631131 - 0.14244908
Average (Standard dev.)0.0005557438 (±0.005116877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 328.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z328.800328.800328.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0660.1420.001

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Supplemental data

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Mask #1

Fileemd_3765_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_3765_half_map_1.map
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Half map: #2

Fileemd_3765_half_map_2.map
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Sample components

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Entire : Protein-Nucleic Acid complex

EntireName: Protein-Nucleic Acid complex
Components
  • Complex: Protein-Nucleic Acid complex
    • Complex: Protein-Nucleic Acid complex
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H2B 1.1
    • Complex: Protein-Nucleic Acid complex
      • DNA: DNA (162-MER)
      • DNA: DNA (162-MER)
    • Complex: Protein-Nucleic Acid complex
      • Protein or peptide: Chromo domain-containing protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Protein-Nucleic Acid complex

SupramoleculeName: Protein-Nucleic Acid complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: Protein-Nucleic Acid complex

SupramoleculeName: Protein-Nucleic Acid complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: Protein-Nucleic Acid complex

SupramoleculeName: Protein-Nucleic Acid complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: Protein-Nucleic Acid complex

SupramoleculeName: Protein-Nucleic Acid complex / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.526769 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSA

UniProtKB: Histone H2B 1.1

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Macromolecule #8: Chromo domain-containing protein 1

MacromoleculeName: Chromo domain-containing protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 168.496609 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE DEFEDEEGEE DSGEDEDEED FEEDDDYYG SPIKQNRSKP KSRTKSKSKS KPKSQSEKQS TVKIPTRFSN RQNKTVNYNI DYSDDDLLES EDDYGSEEAL S EENVHEAS ...String:
MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE DEFEDEEGEE DSGEDEDEED FEEDDDYYG SPIKQNRSKP KSRTKSKSKS KPKSQSEKQS TVKIPTRFSN RQNKTVNYNI DYSDDDLLES EDDYGSEEAL S EENVHEAS ANPQPEDFHG IDIVINHRLK TSLEEGKVLE KTVPDLNNCK ENYEFLIKWT DESHLHNTWE TYESIGQVRG LK RLDNYCK QFIIEDQQVR LDPYVTAEDI EIMDMERERR LDEFEEFHVP ERIIDSQRAS LEDGTSQLQY LVKWRRLNYD EAT WENATD IVKLAPEQVK HFQNRENSKI LPQYSSNYTS QRPRFEKLSV QPPFIKGGEL RDFQLTGINW MAFLWSKGDN GILA DEMGL GKTVQTVAFI SWLIFARRQN GPHIIVVPLS TMPAWLDTFE KWAPDLNCIC YMGNQKSRDT IREYEFYTNP RAKGK KTMK FNVLLTTYEY ILKDRAELGS IKWQFMAVDE AHRLKNAESS LYESLNSFKV ANRMLITGTP LQNNIKELAA LVNFLM PGR FTIDQEIDFE NQDEEQEEYI HDLHRRIQPF ILRRLKKDVE KSLPSKTERI LRVELSDVQT EYYKNILTKN YSALTAG AK GGHFSLLNIM NELKKASNHP YLFDNAEERV LQKFGDGKMT RENVLRGLIM SSGKMVLLDQ LLTRLKKDGH RVLIFSQM V RMLDILGDYL SIKGINFQRL DGTVPSAQRR ISIDHFNSPD SNDFVFLLST RAGGLGINLM TADTVVIFDS DWNPQADLQ AMARAHRIGQ KNHVMVYRLV SKDTVEEEVL ERARKKMILE YAIISLGVTD GNKYTKKNEP NAGELSAILK FGAGNMFTAT DNQKKLEDL NLDDVLNHAE DHVTTPDLGE SHLGGEEFLK QFEVTDYKAD IDWDDIIPEE ELKKLQDEEQ KRKDEEYVKE Q LEMMNRRD NALKKIKNSV NGDGTAANSD SDDDSTSRSS RRRARANDMD SIGESEVRAL YKAILKFGNL KEILDELIAD GT LPVKSFE KYGETYDEMM EAAKDCVHEE EKNRKEILEK LEKHATAYRA KLKSGEIKAE NQPKDNPLTR LSLKKREKKA VLF NFKGVK SLNAESLLSR VEDLKYLKNL INSNYKDDPL KFSLGNNTPK PVQNWSSNWT KEEDEKLLIG VFKYGYGSWT QIRD DPFLG ITDKIFLNEV HNPVAKKSAS SSDTTPTPSK KGKGITGSSK KVPGAIHLGR RVDYLLSFLR GGLNTKSPSA DIGSK KLPT GPSKKRQRKP ANHSKSMTPE ITSSEPANGP PSKRMKALPK GPAALINNTR LSPNSPTPPL KSKVSRDNGT RQSSNP SSG SAHEKEYDSM DEEDCRHTMS AIRTSLKRLR RGGKSLDRKE WAKILKTELT TIGNHIESQK GSSRKASPEK YRKHLWS YS ANFWPADVKS TKLMAMYDKI TESQKK

UniProtKB: Chromo domain-containing protein 1

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Macromolecule #6: DNA (162-MER)

MacromoleculeName: DNA (162-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 64.143914 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)(DT)(DA)(DA)(DC)(DG)(DA)(DT)(DG) (DC)(DT)(DG)(DG)(DG)(DC)(DA) (DT)(DA) (DA)(DG)(DC)(DG)(DT)(DG)(DG)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DC)(DC)(DG)(DG) (DC) (DG)(DC)(DA)(DT)(DA)(DA)(DA)(DG)(DG)(DG) (DT)(DA)(DA)(DA)(DT)(DT)(DC)(DG)(DA) (DA)(DA)(DA)(DC)(DA)(DG)(DC)(DG)

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Macromolecule #7: DNA (162-MER)

MacromoleculeName: DNA (162-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 64.293945 KDa
SequenceString: (DC)(DG)(DC)(DT)(DG)(DT)(DT)(DT)(DT)(DC) (DG)(DA)(DA)(DT)(DT)(DT)(DA)(DC)(DC)(DC) (DT)(DT)(DT)(DA)(DT)(DG)(DC)(DG)(DC) (DC)(DG)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA) (DC) (DC)(DA)(DC)(DG)(DC)(DT) ...String:
(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DT)(DT)(DC) (DG)(DA)(DA)(DT)(DT)(DT)(DA)(DC)(DC)(DC) (DT)(DT)(DT)(DA)(DT)(DG)(DC)(DG)(DC) (DC)(DG)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA) (DC) (DC)(DA)(DC)(DG)(DC)(DT)(DT)(DA) (DT)(DG)(DC)(DC)(DC)(DA)(DG)(DC)(DA)(DT) (DC)(DG) (DT)(DT)(DA)(DA)(DT)(DC)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC)(DT)(DG) (DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG)(DT)(DT) (DA)(DA)(DA)(DA) (DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC) (DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT)(DG)(DC) (DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT)

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #10: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number real images: 3802 / Average exposure time: 10.0 sec. / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 990000
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.4) / Number images used: 67032
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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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

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