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- EMDB-11585: Cryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11585
TitleCryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex
Map data
Sample
  • Complex: Complex of cohesin, Scc2, ATP and DNA
    • Complex: Complex of cohesin and Scc2
      • Protein or peptide: Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1
      • Protein or peptide: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
      • Protein or peptide: Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1
      • Protein or peptide: Sister chromatid cohesion protein 2
    • Complex: double strand DNA
      • DNA: DNA (34-MER)
      • DNA: DNA (34-MER)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin loader activity / tRNA gene clustering / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion ...SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin loader activity / tRNA gene clustering / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / DNA secondary structure binding / cohesin complex / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / reciprocal meiotic recombination / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / chromosome, centromeric region / protein localization to chromatin / condensed nuclear chromosome / double-strand break repair / double-stranded DNA binding / regulation of gene expression / sequence-specific DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / chromatin / protein kinase binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic ...Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Armadillo-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 1 / Structural maintenance of chromosomes protein 3 / Sister chromatid cohesion protein 2 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLee B-G / Gonzalez Llamazares A / Collier J / Nasmyth KA / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
CitationJournal: Elife / Year: 2020
Title: Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3.
Authors: James E Collier / Byung-Gil Lee / Maurici Brunet Roig / Stanislav Yatskevich / Naomi J Petela / Jean Metson / Menelaos Voulgaris / Andres Gonzalez Llamazares / Jan Löwe / Kim A Nasmyth /
Abstract: In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped ...In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are 'clamped' in a sub-compartment created by Scc2's association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.
History
DepositionAug 4, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-6zz6
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11585.png

Downloads & links

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Map

FileDownload / File: emd_11585.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.02
Minimum - Maximum-0.087005906 - 0.17313385
Average (Standard dev.)0.0001588921 (±0.0025428992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z342.400342.400342.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0870.1730.000

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Supplemental data

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Mask #1

Fileemd_11585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11585_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11585_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of cohesin, Scc2, ATP and DNA

EntireName: Complex of cohesin, Scc2, ATP and DNA
Components
  • Complex: Complex of cohesin, Scc2, ATP and DNA
    • Complex: Complex of cohesin and Scc2
      • Protein or peptide: Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1
      • Protein or peptide: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
      • Protein or peptide: Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1
      • Protein or peptide: Sister chromatid cohesion protein 2
    • Complex: double strand DNA
      • DNA: DNA (34-MER)
      • DNA: DNA (34-MER)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of cohesin, Scc2, ATP and DNA

SupramoleculeName: Complex of cohesin, Scc2, ATP and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightExperimental: 485 KDa

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Supramolecule #2: Complex of cohesin and Scc2

SupramoleculeName: Complex of cohesin and Scc2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: double strand DNA

SupramoleculeName: double strand DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: Structural maintenance of chromosomes protein 1,Structural mainte...

MacromoleculeName: Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1
type: protein_or_peptide / ID: 1
Details: 2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044- ...Details: 2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 40.8545 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GRLVGLELSN FKSYRGVTKV GFGESNFTSI IGPNGSGKSN MMDAISFVLG VRSNHLRSNI LKDLIYRGVL SNPQSAYVKA FYQKGNKLV ELMRIISRNG DTSYKIDGKT VSYKDYSIFL ENENILIKAK NFLVFQGDVE QIAAQSPVEL SRMFEEVSGS I QYKKEYEE ...String:
GRLVGLELSN FKSYRGVTKV GFGESNFTSI IGPNGSGKSN MMDAISFVLG VRSNHLRSNI LKDLIYRGVL SNPQSAYVKA FYQKGNKLV ELMRIISRNG DTSYKIDGKT VSYKDYSIFL ENENILIKAK NFLVFQGDVE QIAAQSPVEL SRMFEEVSGS I QYKKEYEE LKEKIEKLSK SAEEKKILNQ FLKIKKKRKE LFEKTFDYVS DHLDAIYREL TKNPNSNVEL AGGNASLTIE DE DEPFNAG IKYHATPPLK RFKDMEYLSG GEKTVAALAL LFAINSYQPS PFFVLDQVDA ALDITNVQRI AAYIRRHRNP DLQ FIVISL KNTMFEKSDA LVGVYRQQQE NSSKIITLDL SNYA

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Macromolecule #2: Structural maintenance of chromosomes protein 3,Structural mainte...

MacromoleculeName: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
type: protein_or_peptide / ID: 2
Details: 0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, ...Details: 0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 48.295016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPYIKRVIIK GFKTYRNETI IDNFSPHQNV IIGSNGSGKS NFFAAIRFVL SDDYSNLKRE ERQGLIHQGS GGSVMSASVE IVFHDPDHS MILPSGVLSR GDDEVTIRRT VGLKKDDYQL NDRNVTKGDI VRMLETAGFS MNNPYNIVPQ GKIVALTNAK D KERLQLLE ...String:
GPYIKRVIIK GFKTYRNETI IDNFSPHQNV IIGSNGSGKS NFFAAIRFVL SDDYSNLKRE ERQGLIHQGS GGSVMSASVE IVFHDPDHS MILPSGVLSR GDDEVTIRRT VGLKKDDYQL NDRNVTKGDI VRMLETAGFS MNNPYNIVPQ GKIVALTNAK D KERLQLLE DVVGAKSFEV KLKASLKKME ETEQKKIQIN KEMGELNSKL SEMEQERKEL EKYNELERNR KRAFENFKKF NE RRKDLAE RASELDESKD SIQDLIVKLK QQKVNAVDST FQKVSENFEA VFERLVPRGT AKLIIHRYTG VSISVSFNSK QNE QLHVEQ LSGGQKTVCA IALILAIQMV DPASFYLFDQ IDAALDKQYR TAVATLLKEL SKNAQFICTT FRTDMLQVAD KFFR VKYEN KISTVIEVNR EEAIGFIR

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Macromolecule #3: Sister chromatid cohesion protein 1,Sister chromatid cohesion pro...

MacromoleculeName: Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1
type: protein_or_peptide / ID: 3
Details: 67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502- ...Details: 67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 9.123593 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
TLRTSGELLQ GIVRVYSKQA TFLLTDIKDT LTKISMLVIF TDVLKSITKR EASRGFFDIL SLATEGCIGL SQTEAFGNIK IDA

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Macromolecule #4: Sister chromatid cohesion protein 2

MacromoleculeName: Sister chromatid cohesion protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 171.310625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYPGKDKNI PGRIIEALED LPLSYLVPKD GLAALVNAPM RVSLPFDKTI FTSADDGRDV NINVLGTANS TTSSIKNEAE KERLVFKRP SNFTSSANSV DYVPTNFLEG LSPLAQSVLS THKGLNDSIN IEKKSEIVSR PEAKHKLESV TSNAGNLSFN D NSSNKKTK ...String:
MSYPGKDKNI PGRIIEALED LPLSYLVPKD GLAALVNAPM RVSLPFDKTI FTSADDGRDV NINVLGTANS TTSSIKNEAE KERLVFKRP SNFTSSANSV DYVPTNFLEG LSPLAQSVLS THKGLNDSIN IEKKSEIVSR PEAKHKLESV TSNAGNLSFN D NSSNKKTK TSTGVTMTQA NLAEQYLNDL KNILDIVGFD QNSAEIGNIE YWLQLPNKKF VLTTNCLTKL QMTIKNITDN PQ LSNSIEI TWLLRLLDVM VCNIKFSKSS LKMGLDDSML RYIALLSTIV LFNIFLLGKN DSNLHRESYI MEPVNFLSDL IES LKILTI EYGSLKIEFD TFQEALELLP KYIRNGPFLD DNVTAKLVYI FSDLLMNNDI EATTNIQFQS FWDNVKRISS DILV SLFGS FDQQRGFIIE ELLSHIEKLP TKRIQKKLRK VGNQNIYITD FTFTLMSMLE NINCYSFCNQ MKDIAPENID LLKNE YKKQ EEFLFNIVEH INDTILERFF KNPSALRYVI DNFVQDLLLL ISSPQWPVTE KILSSLLKRL LSVYSPSMQV SANIET ICL QLIGNIGSTI FDIKCSTRDH EDNNLIKMIN YPETLPHFFK SFEECIAYNE TIKCRRSATR FLWNLRLGTI LILEEYT KD AKEQIITVDN ELKKILEQIK DGGLGPELEN READFSTIKL DYFSILHAFE LLNLYDPYLK LILSLLAKDK IKLRSTAI K CLSMLASKDK VILSNPMVKE TIHRRLNDSS ASVKDAILDL VSINSSYFEF YQQINNNYND DSIMVRKHVL RINEKMYDE TNDIVTKVYV IARILMKIED EEDNIIDMAR LILLNRWILK VHEVLDQPEK LKEISSSVLL VMSRVAIMNE KCSQLFDLFL NFYLLNKEA HSKEAYDKIT HVLTILTDFL VQKIVELNSD DTNEKNSIVD KQNFLNLLAK FADSTVSFLT KDHITALYPY M VSDEKSDF HYYILQVFRC TFEKLANFKQ KFLYDLETTL LSRLPKMNVR EIDEAMPLIW SVATHRHDTA RVAKACSSCL SH LHPYINK ANNEEAAIVV DGKLQRLIYL STGFARFCFP KPSNDKIAFL QEGETLYEHI TKCLLVLSKD KITHVIRRVA VKN LTKLCG NHPKLFNSRH VLHLLDKEFQ SDQLDIKLVI LESLYDLFLL EERKSVRNTG VNSTLSSNSI LKKKLLKTNR VEFA NDGVC SALATRFLDN ILQLCLLRDL KNSLVAIRLL KLILKFGYTN PSHSIPTVIA LFASTSQYIR HVAYELLEDL FEKYE TLVF SSLSRGVTKA IHYSIHTDEK YYYKHDHFLS LLEKLCGTGK KNGPKFFKVL KRIMQSYLDD ITDLTSTNSS VQKSIF VLC TNISNITFVS QYDLVSLLKT IDLTTDRLKE VIMDEIGDNV SSLSVSEEKL SGIILIQLSL QDLGTYLLHL YGLRDDV LL LDIVEESELK NKQLPAKKPD ISKFSAQLEN IEQYSSNGKL LTYFRKHVKD T

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Macromolecule #5: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.604072 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)

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Macromolecule #6: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.297598 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 588164

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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

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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

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