[English] 日本語
Yorodumi
- EMDB-22360: Structure of Drosophila ORC bound to GC-rich DNA and Cdc6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22360
TitleStructure of Drosophila ORC bound to GC-rich DNA and Cdc6
Map dataunsharpened cryo-EM map
Sample
  • Complex: Drosophila ORC bound to GC-rich DNA and Cdc6
    • Protein or peptide: x 7 types
    • DNA: x 2 types
  • Ligand: x 2 types
Keywordsorigin recognition complex / DNA replication initiation / REPLICATION / REPLICATION-DNA complex
Function / homology
Function and homology information


alpha-heterochromatin / larval feeding behavior / CDC6 association with the ORC:origin complex / septin cytoskeleton / CDK-mediated phosphorylation and removal of Cdc6 / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin ...alpha-heterochromatin / larval feeding behavior / CDC6 association with the ORC:origin complex / septin cytoskeleton / CDK-mediated phosphorylation and removal of Cdc6 / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / positive regulation of border follicle cell migration / origin recognition complex / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / olfactory learning / nuclear pre-replicative complex / DNA replication preinitiation complex / mitotic chromosome condensation / mitotic DNA replication checkpoint signaling / chromosome condensation / DNA replication origin binding / DNA replication initiation / nuclear pore / ribonucleoprotein complex binding / heterochromatin / GTPase activator activity / mitotic spindle organization / learning / DNA-templated DNA replication / mitotic cell cycle / learning or memory / DNA replication / cell division / chromatin binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex, subunit 6 ...Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cdc6, C-terminal / CDC6, C terminal winged helix domain / : / AAA domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 3, N-terminal / : / : / Origin recognition complex (ORC) subunit 3 N-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex winged helix C-terminal / ORC5, lid domain / Orc1-like, AAA ATPase domain / : / : / Origin recognition complex subunit 2 RecA-like domain / ORC2 WHD / AAA ATPase domain / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / Origin recognition complex subunit 5 / Origin recognition complex subunit 3 / Cell division control protein / Origin recognition complex subunit 4 / Origin recognition complex subunit 6
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSchmidt JM / Bleichert F
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-STG-757909 Switzerland
CitationJournal: Nat Commun / Year: 2020
Title: Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6.
Authors: Schmidt JM / Bleichert F
History
DepositionJul 27, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jk3
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

-
Map

FileDownload / File: emd_22360.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened cryo-EM map
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.013212696 - 0.046966515
Average (Standard dev.)0.000014122947 (±0.0016594775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0130.0470.000

-
Supplemental data

-
Sample components

+
Entire : Drosophila ORC bound to GC-rich DNA and Cdc6

EntireName: Drosophila ORC bound to GC-rich DNA and Cdc6
Components
  • Complex: Drosophila ORC bound to GC-rich DNA and Cdc6
    • Protein or peptide: Origin recognition complex subunit 2
    • Protein or peptide: Origin recognition complex subunit 3
    • Protein or peptide: Origin recognition complex subunit 4
    • Protein or peptide: Origin recognition complex subunit 5
    • Protein or peptide: Origin recognition complex subunit 6
    • Protein or peptide: Origin recognition complex subunit 1
    • Protein or peptide: Cell division control protein
    • DNA: DNA (33-MER)
    • DNA: DNA (33-MER)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: Drosophila ORC bound to GC-rich DNA and Cdc6

SupramoleculeName: Drosophila ORC bound to GC-rich DNA and Cdc6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Drosophila melanogaster (fruit fly)

+
Macromolecule #1: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 69.086445 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSASNKGGYK TPRKENLMSI ENLTNSEEES EDLNTAMVGN AVESQPKVTS RRSTRRPSPT KKYQAYQKES NGKGQEERIV VNYVEMSDE RSSDAEDQEE EESIEESENA ARPAAKDLHL IQSEYNVAGT SMFGFNTPKK RDAMALAALN ATPCTPKTPK T PRLGVKTP ...String:
MSASNKGGYK TPRKENLMSI ENLTNSEEES EDLNTAMVGN AVESQPKVTS RRSTRRPSPT KKYQAYQKES NGKGQEERIV VNYVEMSDE RSSDAEDQEE EESIEESENA ARPAAKDLHL IQSEYNVAGT SMFGFNTPKK RDAMALAALN ATPCTPKTPK T PRLGVKTP DTKRKKSMDQ PKTPAHVRTR VKKQIAKIVA DSDEDFSGDE SDFRPSDEES SSSSSSSDAG NSSDNDAADD EP KTPSRAR RAIVVPVLPK TPSAARLRQS ARAKKSNEFV PESDGYFHSH ASSKILTSDH TLDRLKNPRL AADRVFSLLS EIK TSAEHE GSINAIMEEY RSYFPKWMCI LNEGFNILLY GLGSKHQLLQ SFHREVLHKQ TVLVVNGFFP SLTIKDMLDS ITSD ILDAG ISPANPHEAV DMIEEEFALI PETHLFLIVH NLDGAMLRNV KAQAILSRLA RIPNIHLLAS IDHINTPLLW DQGKL CSFN FSWWDCTTML PYTNETAFEN SLLVQNSGEL ALSSMRSVFS SLTTNSRGIY MLIVKYQLKN KGNATYQGMP FRDLYS SCR EAFLVSSDLA LRAQLTEFLD HKLVKSKRSV DGSEQLTIPI DGALLQQFLE EQEKK

UniProtKB: Origin recognition complex subunit 2

+
Macromolecule #2: Origin recognition complex subunit 3

MacromoleculeName: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 82.364523 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDPTISVSKG CFVYKNGATR AGKKAASKRK RPAAESSSLL GKEVVQQPFY EEYRKAWNQI NDHIADLQHR SYARTLEQLV DFVVGQAER DTPDEVLPTA ALLTGINQPD HLSQFTALTQ RLHAQRAAMV CVLQSRDCAT LKAAVETLVF GLVEDNAEVE Q MEDEDEDE ...String:
MDPTISVSKG CFVYKNGATR AGKKAASKRK RPAAESSSLL GKEVVQQPFY EEYRKAWNQI NDHIADLQHR SYARTLEQLV DFVVGQAER DTPDEVLPTA ALLTGINQPD HLSQFTALTQ RLHAQRAAMV CVLQSRDCAT LKAAVETLVF GLVEDNAEVE Q MEDEDEDE DGAERDRKRL RRSQCTMKQL KSWYTNNFDS EQKRRQLVVI LPDFECFNAS VLQDLILILS AHCGSLPFVL VL GVATAMT AVHGTLPYHV SSKIRLRVFQ TQAAPTGLNE VLDKVLLSPK YAFHLSGKTF KFLTHIFLYY DFSIHGFIQG FKY CLMEHF FGGNAFALCT DYSKALGRIK QLTHEDMETI RRLPSFRPYV EQINDCKRII AVLTDDDYLK KKLPQLLRDC LLHF LLFRC SLEFLTELVG DLPRCPLGKL RRELYVNCLN RAIISTPEYK ECLQMLSFLS KDEFVAKVNR ALERTEQFLV EEIAP LELG EACTAVLRPK LEAIRLAVDE VVKATMATIT TTSPNETRQA TDHLTPVASR QELKDQLLQR SKEDKMRHQL NTPTTQ FGR ALQKTLQLIE TQIVQDHLRA LQDAPPIHEL FVFSDIATVR RNIIGAPRAA LHTALNNPHF YMQCKCCELQ DQSLLVG TL PDLSVVYKLH LECGRMINLF DWLQAFRSVV SDSDHEEVAQ EQIDPQIQAR FTRAVAELQF LGYIKMSKRK TDHATRLT W

UniProtKB: Origin recognition complex subunit 3

+
Macromolecule #3: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 52.277109 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMPEADRE LVSIRRFLKE RLQRDYTTLR GYAKERSNVR LLLQRTAEMG ESNSLLLLGP RGSGKTTLIN SVLADLLPNK SFGENTLIV HLDGNLHTDD RVALKSITVQ MQLENAADGK VFGSFAENLA FLLQCLKAGG KHSKSVIFIL EEFDLFCAHH N QTLLYNLF ...String:
SNAMPEADRE LVSIRRFLKE RLQRDYTTLR GYAKERSNVR LLLQRTAEMG ESNSLLLLGP RGSGKTTLIN SVLADLLPNK SFGENTLIV HLDGNLHTDD RVALKSITVQ MQLENAADGK VFGSFAENLA FLLQCLKAGG KHSKSVIFIL EEFDLFCAHH N QTLLYNLF DVSQSAQAPI CVLGVTCRLD VIELLEKRVK SRFSHRQVFL FPSLRRFEDY VDLCRDLLSL PTGNSLLLAA EK IYNLQNI QSGALYFSRN HFDPGEYGFS PRLRDAWNKQ ICKVLATQQA RSTLQALHDF DISEAYLKNF LFRLVAHLRP QSP HITAEK MAAVGSQFEG DDKIELLCGL SVLELCLIIA IKHHSQIYDR DSFNFEIIYA RFSKFAKVST TMQAVERSIV LKAF EHLRI AELIMPLTGG AGGGVGKVQK EFEMHKLALT YSQIHHCMQR YQALPTEVAQ WAQSSLI

UniProtKB: Origin recognition complex subunit 4

+
Macromolecule #4: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 52.175066 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEAICSSLEP LFPCREAAIE TLGELIGDSS ETYPSAIYLF GHSGTGKTAL TRAFLKECGK RQNVRTAHLN AIECYTTKIM LEILLDSLA PDQGDALKVD NMLDFVEQLR RQAATRVEDQ GFLIAVDNAE RLRDMDANVL PVLLRLQELT NLNLCVILLS Q LPFEKFYN ...String:
MEAICSSLEP LFPCREAAIE TLGELIGDSS ETYPSAIYLF GHSGTGKTAL TRAFLKECGK RQNVRTAHLN AIECYTTKIM LEILLDSLA PDQGDALKVD NMLDFVEQLR RQAATRVEDQ GFLIAVDNAE RLRDMDANVL PVLLRLQELT NLNLCVILLS Q LPFEKFYN KTGLSEIVCL HLAQYNKAET QRILGSDFQQ VRNQLLEQFA QDKKRLEICQ EAVTEDFYNN YLNLFLSVFY KA CRDVPEL QLTARKCLST YLEPVLDGTV DATDISRLWR HIAGPLRSAL TQIYMRIEKP AEEVEDFTAI EDQSVRKLAQ SLE LPYYAK FLLIAAFLAS HNAAKQDKRL FVKHHGKQRK RMQTVNARAK TTEKMSTTLG PKSFSIDRLL AIFYAILEEK VGLT CNLLS QISTLVHLNL LSFVSGEQNI MEGSARLQCT IGLEFVLQIG KVVGFNVRQY LCDFM

UniProtKB: Origin recognition complex subunit 5

+
Macromolecule #5: Origin recognition complex subunit 6

MacromoleculeName: Origin recognition complex subunit 6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 29.284129 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTTLIEQLIT KMGLREEPNV LEKTTELVRL LELRSTNVPL QINEYGKIVL CADLASCMIG IAFDKEQALK LSGLRKSQYL NNKRMFEKL LDLNKLASVN DICVQLGLNE VARKAEELMT LFKGVAATED MGTDTSHPQY ATMAVFQACR LLKKKVSKSK L MPFSNLRP ...String:
MTTLIEQLIT KMGLREEPNV LEKTTELVRL LELRSTNVPL QINEYGKIVL CADLASCMIG IAFDKEQALK LSGLRKSQYL NNKRMFEKL LDLNKLASVN DICVQLGLNE VARKAEELMT LFKGVAATED MGTDTSHPQY ATMAVFQACR LLKKKVSKSK L MPFSNLRP SQFQLLEQQW ERMIAKHHKE SKVPSSTDME GKLKENQNEN IKGHEAKKAH KPPPEDYEIW KARMLAKAQA KL KELEASQ SHMDSQLLEA

UniProtKB: Origin recognition complex subunit 6

+
Macromolecule #6: Origin recognition complex subunit 1

MacromoleculeName: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 54.485633 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAPRRSIHL SNIVEQRVFE DDEIISTPKR GRSKKTVQDN DEDYSPKKSV QKTPTRTRRS STTTKTATTP SKGITTATAT PMTPSQKMK KIRAGELSPS MQQRTDLPAK DSSKSELQLA REQLHVSVVP KSLPCREREF ENIYAFLEGK IQDQCGGCMY V SGVPGTGK ...String:
SNAPRRSIHL SNIVEQRVFE DDEIISTPKR GRSKKTVQDN DEDYSPKKSV QKTPTRTRRS STTTKTATTP SKGITTATAT PMTPSQKMK KIRAGELSPS MQQRTDLPAK DSSKSELQLA REQLHVSVVP KSLPCREREF ENIYAFLEGK IQDQCGGCMY V SGVPGTGK TATVTGVIRT LQRMAKQNEL PAFEYLEING MRLTEPRQAY VQIYKQLTGK TVSWEQAHAL LEKRFTTPAP RR VTTVLLV DELDILCNRR QDVVYNLLDW PTKSAAKLVV VTIANTMDLP ERLLMGKVTS RLGLTRLTFQ PYSHKQLQEI VTA RLGGSE TFKGEAVQLV ARKVAAVSGD ARRALDICRR ATEIADTAAV KCVTMLHVQQ ALAEMIASAK VQAIRNCSRM EQIF LQAIA AEVTRTGVEE TTFMGVYQQV ETIAAFMGVT FPPPGRALRL CSKLGAERLI ISEHSRNDLF QKILLNVSAD DIHYA LRVE EMVN

UniProtKB: Origin recognition complex subunit 1

+
Macromolecule #7: Cell division control protein

MacromoleculeName: Cell division control protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 48.049465 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNANNLPSPS RNKYQNARRV LNSAETQNLP GRESQLQELR EFFSNHLESQ TSGSLYVSGQ PGTGKTACLS LLLRDPDFSK RLQRVYINC TSIASVGAVY KKLCTELQLK VSGRTERDHL EAIQRHLKTA KRMLLLVLDE IDQLCTSRQE VLYTIFEWPA L PGSRILLV ...String:
SNANNLPSPS RNKYQNARRV LNSAETQNLP GRESQLQELR EFFSNHLESQ TSGSLYVSGQ PGTGKTACLS LLLRDPDFSK RLQRVYINC TSIASVGAVY KKLCTELQLK VSGRTERDHL EAIQRHLKTA KRMLLLVLDE IDQLCTSRQE VLYTIFEWPA L PGSRILLV GIANSLDLTD RALMRLNARC ELKPRLMHFP PYSKQQIVEI FKSRLAEAEV LDVFPPVTLQ LLAAKVSAIS GD VRRALDI GRRVVEIAEQ QKRDGEKEFN MKALQLEGKD AVEAKEKQDT LKPVQVTQVA AVLNKVYGAS QNLEEDIEAS FPL QQKLML CTLVLMLRNE RNKDISMGRL HEVYRRVCAK RNILALDQAE FTGTVDLVET RGILRIMRKK EPRLHKVLLQ WDEE EVHAA LSDKQLIASI LSDTACLSK

UniProtKB: Cell division control protein

+
Macromolecule #8: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.679869 KDa
SequenceString: (DG)(DG)(DG)(DG)(DC)(DT)(DC)(DG)(DA)(DC) (DT)(DC)(DC)(DA)(DA)(DG)(DT)(DG)(DC)(DG) (DG)(DG)(DG)(DC)(DA)(DC)(DT)(DC)(DG) (DT)(DC)(DT)(DG)(DT)(DG)(DA)(DG)(DG)(DG) (DG) (DG)(DC)(DT)(DC)(DA)(DG) ...String:
(DG)(DG)(DG)(DG)(DC)(DT)(DC)(DG)(DA)(DC) (DT)(DC)(DC)(DA)(DA)(DG)(DT)(DG)(DC)(DG) (DG)(DG)(DG)(DC)(DA)(DC)(DT)(DC)(DG) (DT)(DC)(DT)(DG)(DT)(DG)(DA)(DG)(DG)(DG) (DG) (DG)(DC)(DT)(DC)(DA)(DG)(DT)(DT) (DC)(DG)(DC)(DA)(DC)(DT)(DG)(DC)(DG)(DG) (DG)(DG)

+
Macromolecule #9: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.315686 KDa
SequenceString: (DC)(DC)(DC)(DC)(DG)(DC)(DA)(DG)(DT)(DG) (DC)(DG)(DA)(DA)(DC)(DT)(DG)(DA)(DG)(DC) (DC)(DC)(DC)(DC)(DT)(DC)(DA)(DC)(DA) (DG)(DA)(DC)(DG)(DA)(DG)(DT)(DG)(DC)(DC) (DC) (DC)(DG)(DC)(DA)(DC)(DT) ...String:
(DC)(DC)(DC)(DC)(DG)(DC)(DA)(DG)(DT)(DG) (DC)(DG)(DA)(DA)(DC)(DT)(DG)(DA)(DG)(DC) (DC)(DC)(DC)(DC)(DT)(DC)(DA)(DC)(DA) (DG)(DA)(DC)(DG)(DA)(DG)(DT)(DG)(DC)(DC) (DC) (DC)(DG)(DC)(DA)(DC)(DT)(DT)(DG) (DG)(DA)(DG)(DT)(DC)(DG)(DA)(DG)(DC)(DC) (DC)(DC)

+
Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Component:
ConcentrationName
25.0 mMHEPES-KOH
250.0 mMpotassium acetate
10.0 mMmagnesium acetate
1.0 mMDTT
1.0 mMATP
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsRecombinantly expressed and purified Drosophila ORC and Cdc6 were mixed with DNA and the DNA-bound ternary complex purified by size exclusion chromatography.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 40.0 e/Å2
#0 - Details: Two different datasets were recorded for this sample.
#1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Average electron dose: 50.0 e/Å2
#1 - Details: Two different datasets were recorded for this sample.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 174891
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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