[English] 日本語
Yorodumi
- EMDB-51441: OCCM maturation intermediate stalled with an Arginine Finger muta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51441
TitleOCCM maturation intermediate stalled with an Arginine Finger mutation in Mcm5: Conformer 1
Map dataconsensus map unmodified
Sample
  • Complex: ORC-Cdt1-MCM complex
    • Protein or peptide: x 13 types
    • DNA: x 1 types
  • Ligand: x 3 types
KeywordsAAA+ ATPase / DNA translocase / ATPase switch / DNA replication / REPLICATION
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / nuclear DNA replication / Assembly of the ORC complex at the origin of replication / premeiotic DNA replication ...CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / nuclear DNA replication / Assembly of the ORC complex at the origin of replication / premeiotic DNA replication / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / nucleosome organization / Activation of ATR in response to replication stress / DNA replication preinitiation complex / MCM complex / replication fork protection complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / single-stranded DNA helicase activity / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / silent mating-type cassette heterochromatin formation / DNA strand elongation involved in DNA replication / Orc1 removal from chromatin / nuclear replication fork / regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / nucleosome binding / helicase activity / transcription elongation by RNA polymerase II / heterochromatin formation / single-stranded DNA binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / DNA replication / cell division / DNA damage response / chromatin binding / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Origin recognition complex, subunit 6, fungi / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 ...DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Origin recognition complex, subunit 6, fungi / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / 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 / AAA ATPase domain / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / : / : / MCM3 winged helix domain / MCM4, winged helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor Mcm5 / MCM3-like, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / EF-Hand 1, calcium-binding site / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / Origin recognition complex subunit 2 / DNA replication licensing factor MCM7 / Origin recognition complex subunit 6 / Cell division cycle protein CDT1 / Origin recognition complex subunit 5 / DNA replication licensing factor MCM6 ...DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / Origin recognition complex subunit 2 / DNA replication licensing factor MCM7 / Origin recognition complex subunit 6 / Cell division cycle protein CDT1 / Origin recognition complex subunit 5 / DNA replication licensing factor MCM6 / Origin recognition complex subunit 1 / Origin recognition complex subunit 3 / Origin recognition complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsButryn A / Costa A
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)820102European Union
The Francis Crick InstituteCC2009 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Unidirectional MCM translocation away from ORC drives origin licensing.
Authors: Agata Butryn / Julia F Greiwe / Alessandro Costa /
Abstract: The MCM motor of the eukaryotic replicative helicase is loaded as a double hexamer onto DNA by the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ATP binding supports formation of the ORC-Cdc6- ...The MCM motor of the eukaryotic replicative helicase is loaded as a double hexamer onto DNA by the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ATP binding supports formation of the ORC-Cdc6-Cdt1-MCM (OCCM) helicase-recruitment complex where ORC-Cdc6 and one MCM hexamer form two juxtaposed rings around duplex DNA. ATP hydrolysis by MCM completes MCM loading but the mechanism is unknown. Here, we used cryo-EM to characterise helicase loading with ATPase-dead Arginine Finger variants of the six MCM subunits. We report the structure of two MCM complexes with different DNA grips, stalled as they mature to loaded MCM. The Mcm2 Arginine Finger-variant stabilises DNA binding by Mcm2 away from ORC/Cdc6. The Arginine Finger-variant of the neighbouring Mcm5 subunit stabilises DNA engagement by Mcm5 downstream of the Mcm2 binding site. Cdc6 and Orc1 progressively disengage from ORC as MCM translocates along DNA. We observe that duplex DNA translocation by MCM involves a set of leading-strand contacts by the pre-sensor 1 ATPase hairpins and lagging-strand contacts by the helix-2-insert hairpins. Mutating any of the MCM residues involved impairs high-salt resistant DNA binding in vitro and double-hexamer formation assessed by electron microscopy. Thus, ATPase-powered duplex DNA translocation away from ORC underlies MCM loading.
History
DepositionAug 28, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51441.png

Downloads & links

-
Map

FileDownload / File: emd_51441.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map unmodified
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 440 pix.
= 418. Å		0.95 Å/pix.
x 440 pix.
= 418. Å		0.95 Å/pix.
x 440 pix.
= 418. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.34597987 - 0.6740292
Average (Standard dev.)0.0017075957 (±0.022718603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 418.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: consensus map density-modified with EMReady

Fileemd_51441_additional_1.map
Annotationconsensus map density-modified with EMReady
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: consensus map density-modified with DeepEMhancer

Fileemd_51441_additional_2.map
Annotationconsensus map density-modified with DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_51441_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_51441_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : ORC-Cdt1-MCM complex

EntireName: ORC-Cdt1-MCM complex
Components
  • Complex: ORC-Cdt1-MCM complex
    • Protein or peptide: DNA replication licensing factor MCM2
    • Protein or peptide: DNA replication licensing factor MCM3
    • Protein or peptide: DNA replication licensing factor MCM4
    • Protein or peptide: Minichromosome maintenance protein 5
    • Protein or peptide: DNA replication licensing factor MCM6
    • Protein or peptide: DNA replication licensing factor MCM7
    • Protein or peptide: Cell division cycle protein CDT1
    • Protein or peptide: Origin recognition complex subunit 1
    • 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
    • DNA: DNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

+
Supramolecule #1: ORC-Cdt1-MCM complex

SupramoleculeName: ORC-Cdt1-MCM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.1 MDa

+
Macromolecule #1: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 98.911539 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDNRRRRRE EDDSDSENEL PPSSPQQHFR GGMNPVSSPI GSPDMINPEG DDNEVDDVPD IDEVEEQMNE VDLMDDNMYE DYAADHNRD RYDPDQVDDR EQQELSLSER RRIDAQLNER DRLLRNVAYI DDEDEEQEGA AQLDEMGLPV QRRRRRRQYE D LENSDDDL ...String:
MSDNRRRRRE EDDSDSENEL PPSSPQQHFR GGMNPVSSPI GSPDMINPEG DDNEVDDVPD IDEVEEQMNE VDLMDDNMYE DYAADHNRD RYDPDQVDDR EQQELSLSER RRIDAQLNER DRLLRNVAYI DDEDEEQEGA AQLDEMGLPV QRRRRRRQYE D LENSDDDL LSDMDIDPLR EELTLESLSN VKANSYSEWI TQPNVSRTIA RELKSFLLEY TDETGRSVYG ARIRTLGEMN SE SLEVNYR HLAESKAILA LFLAKCPEEM LKIFDLVAME ATELHYPDYA RIHSEIHVRI SDFPTIYSLR ELRESNLSSL VRV TGVVTR RTGVFPQLKY VKFNCLKCGS ILGPFFQDSN EEIRISFCTN CKSKGPFRVN GEKTVYRNYQ RVTLQEAPGT VPPG RLPRH REVILLADLV DVSKPGEEVE VTGIYKNNYD GNLNAKNGFP VFATIIEANS IKRREGNTAN EGEEGLDVFS WTEEE EREF RKISRDRGII DKIISSMAPS IYGHRDIKTA VACSLFGGVP KNVNGKHSIR GDINVLLLGD PGTAKSQILK YVEKTA HRA VFATGQGASA VGLTASVRKD PITKEWTLEG GALVLADKGV CLIDEFDKMN DQDRTSIHEA MEQQSISISK AGIVTTL QA RCSIIAAANP NGGRYNSTLP LAQNVSLTEP ILSRFDILCV VRDLVDEEAD ERLATFVVDS HVRSHPENDE DREGEELK N NGESAIEQGE DEINEQLNAR QRRLQRQRKK EEEISPIPQE LLMKYIHYAR TKIYPKLHQM DMDKVSRVYA DLRRESIST GSFPITVRHL ESILRIAESF AKMRLSEFVS SYDLDRAIKV VVDSFVDAQK VSVRRQLRRS FAIYTLGH

UniProtKB: DNA replication licensing factor MCM2

+
Macromolecule #2: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 111.720242 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKRRWKKNFI AVSAANRFKK ISSSGALENL YFQGEMEGST GFDGDATTFF APDAVFGDRV RRFQEFLDTF TSYRDSVRSI QVYNSNNAA NYNDDQDDAD ERDLLGDDDG DDLEKEKKAA SSTSLNILPH RIIISLDDLR EFDRSFWSGI LVEPAYFIPP A EKALTDLA ...String:
MKRRWKKNFI AVSAANRFKK ISSSGALENL YFQGEMEGST GFDGDATTFF APDAVFGDRV RRFQEFLDTF TSYRDSVRSI QVYNSNNAA NYNDDQDDAD ERDLLGDDDG DDLEKEKKAA SSTSLNILPH RIIISLDDLR EFDRSFWSGI LVEPAYFIPP A EKALTDLA DSMDDVPHPN ASAVSSRHPW KLSFKGSFGA HALSPRTLTA QHLNKLVSVE GIVTKTSLVR PKLIRSVHYA AK TGRFHYR DYTDATTTLT TRIPTPAIYP TEDTEGNKLT TEYGYSTFID HQRITVQEMP EMAPAGQLPR SIDVILDDDL VDK TKPGDR VNVVGVFKSL GAGGMNQSNS NTLIGFKTLI LGNTVYPLHA RSTGVAARQM LTDFDIRNIN KLSKKKDIFD ILSQ SLAPS IYGHDHIKKA ILLMLMGGVE KNLENGSHLR GDINILMVGD PSTAKSQLLR FVLNTASLAI ATTGRGSSGV GLTAA VTTD RETGERRLEA GAMVLADRGV VCIDEFDKMT DVDRVAIHEV MEQQTVTIAK AGIHTTLNAR CSVIAAANPV FGQYDV NRD PHQNIALPDS LLSRFDLLFV VTDDINEIRD RSISEHVLRT HRYLPPGYLE GEPVRERLNL SLAVGEDADI NPEEHSN SG AGVENEGEDD EDHVFEKFNP LLQAGAKLAK NKGNYNGTEI PKLVTIPFLR KYVQYAKERV IPQLTQEAIN VIVKNYTD L RNDDNTKKSP ITARTLETLI RLATAHAKVR LSKTVNKVDA KVAANLLRFA LLGEDIGNDI DEEESEYEEA LSKRSPQKS PKKRQRVRQP ASNSGSPIKS TPRRSTASSV NATPSSARRI LRFQDDEQNA GEDDNDIMSP LPADEEAELQ RRLQLGLRVS PRRREHLHA PEEGSSGPLT EVGTPRLPNV SSAGQDDEQQ QSVISFDNVE PGTISTGRLS LISGIIARLM QTEIFEEESY P VASLFERI NEELPEEEKF SAQEYLAGLK IMSDRNNLMV ADDKVWRV

UniProtKB: DNA replication licensing factor MCM3

+
Macromolecule #3: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 105.138375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSQQSSSPTK EDNNSSSPVV PNPDSVPPQL SSPALFYSSS SSQGDIYGRN NSQNLSQGEG NIRAAIGSSP LNFPSSSQRQ NSDVFQSQG RQGRIRSSAS ASGRSRYHSD LRSDRALPTS SSSLGRNGQN RVHMRRNDIH TSDLSSPRRI VDFDTRSGVN T LDTSSSSA ...String:
MSQQSSSPTK EDNNSSSPVV PNPDSVPPQL SSPALFYSSS SSQGDIYGRN NSQNLSQGEG NIRAAIGSSP LNFPSSSQRQ NSDVFQSQG RQGRIRSSAS ASGRSRYHSD LRSDRALPTS SSSLGRNGQN RVHMRRNDIH TSDLSSPRRI VDFDTRSGVN T LDTSSSSA PPSEASEPLR IIWGTNVSIQ ECTTNFRNFL MSFKYKFRKI LDEREEFINN TTDEELYYIK QLNEMRELGT SN LNLDARN LLAYKQTEDL YHQLLNYPQE VISIMDQTIK DCMVSLIVDN NLDYDLDEIE TKFYKVRPYN VGSCKGMREL NPN DIDKLI NLKGLVLRST PVIPDMKVAF FKCNVCDHTM AVEIDRGVIQ EPARCERIDC NEPNSMSLIH NRCSFADKQV IKLQ ETPDF VPDGQTPHSI SLCVYDELVD SCRAGDRIEV TGTFRSIPIR ANSRQRVLKS LYKTYVDVVH VKKVSDKRLD VDTST IEQE LMQNKVDHNE VEEVRQITDQ DLAKIREVAA REDLYSLLAR SIAPSIYELE DVKKGILLQL FGGTNKTFTK GGRYRG DIN ILLCGDPSTS KSQILQYVHK ITPRGVYTSG KGSSAVGLTA YITRDVDTKQ LVLESGALVL SDGGVCCIDE FDKMSDS TR SVLHEVMEQQ TISIAKAGII TTLNARSSIL ASANPIGSRY NPNLPVTENI DLPPPLLSRF DLVYLVLDKV DEKNDREL A KHLTNLYLED KPEHISQDDV LPVEFLTMYI SYAKEHIHPI ITEAAKTELV RAYVGMRKMG DDSRSDEKRI TATTRQLES MIRLAEAHAK MKLKNVVELE DVQEAVRLIR SAIKDYATDP KTGKIDMNLV QTGKSVIQRK LQEDLSREIM NVLKDQASDS MSFNELIKQ INEHSQDRVE SSDIQEALSR LQQEDKVIVL GEGVRRSVRL NNRV

UniProtKB: DNA replication licensing factor MCM4

+
Macromolecule #4: Minichromosome maintenance protein 5

MacromoleculeName: Minichromosome maintenance protein 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 86.419617 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSFDRPEIYS APVLQGESPN DDDNTEIIKS FKNFILEFRL DSQFIYRDQL RNNILVKNYS LTVNMEHLIG YNEDIYKKLS DEPSDIIPL FETAITQVAK RISILSRAQS ANNNDKDPEN TSMDTDSLLL NSLPTFQLIL NSNANQIPLR DLDSEHVSKI V RLSGIIIS ...String:
MSFDRPEIYS APVLQGESPN DDDNTEIIKS FKNFILEFRL DSQFIYRDQL RNNILVKNYS LTVNMEHLIG YNEDIYKKLS DEPSDIIPL FETAITQVAK RISILSRAQS ANNNDKDPEN TSMDTDSLLL NSLPTFQLIL NSNANQIPLR DLDSEHVSKI V RLSGIIIS TSVLSSRATY LSIMCRNCRH TTSITINNFN SITGNTVSLP RSCLSTIESE SSMANESNIG DESTKKNCGP DP YIIIHES SKFIDQQFLK LQEIPELVPV GEMPRNLTMT CDRYLTNKVI PGTRVTIVGI YSIYNSKNGA GSGRSGGGNG GSG VAIRTP YIKILGIQSD VETSSIWNSV TMFTEEEEEE FLQLSRNPKL YEILTNSIAP SIFGNEDIKK AIVCLLMGGS KKIL PDGMR LRGDINVLLL GDPGTAKSQL LKFVEKVSPI AVYTSGKGSS AAGLTASVQR DPMTREFYLE GGAMVLADGG VVCID EFDK MRDEDRVAIH EAMEQQTISI AKAGITTVLN SRTSVLAAAN PIYGRYDDLK SPGDNIDFQT TILSAFDMIF IVKDDH NEE RDISIANHVI NIHTGNANAM QNQQEENGSE ISIEKMKRYI TYCRLKCAPR LSPQAAEKLS SNFVTIRKQL LINELES TE RSSIPITIRQ LEAIIRITES LAKLELSPIA QERHVDEAIR LFQASTMDAA SQDPIGGLNQ ASGTSLSEIR RFEQELKR R LPIGWSTSYQ TLRREFVDTH RFSQLALDKA LYALEKHETI QLRHQGQNIY RSGV

UniProtKB: Minichromosome maintenance protein 5

+
Macromolecule #5: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 113.110211 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSPFPADTP SSNRPSNSSP PPSSIGAGFG SSSGLDSQIG SRLHFPSSSQ PHVSNSQTGP FVNDSTQFSS QRLQTDGSAT NDMEGNEPA RSFKSRALNH VKKVDDVTGE KVREAFEQFL EDFSVQSTDT GEVEKVYRAQ IEFMKIYDLN TIYIDYQHLS M RENGALAM ...String:
MSSPFPADTP SSNRPSNSSP PPSSIGAGFG SSSGLDSQIG SRLHFPSSSQ PHVSNSQTGP FVNDSTQFSS QRLQTDGSAT NDMEGNEPA RSFKSRALNH VKKVDDVTGE KVREAFEQFL EDFSVQSTDT GEVEKVYRAQ IEFMKIYDLN TIYIDYQHLS M RENGALAM AISEQYYRFL PFLQKGLRRV VRKYAPELLN TSDSLKRSEG DEGQADEDEQ QDDDMNGSSL PRDSGSSAAP GN GTSAMAT RSITTSTSPE QTERVFQISF FNLPTVHRIR DIRSEKIGSL LSISGTVTRT SEVRPELYKA SFTCDMCRAI VDN VEQSFK YTEPTFCPNP SCENRAFWTL NVTRSRFLDW QKVRIQENAN EIPTGSMPRT LDVILRGDSV ERAKPGDRCK FTGV EIVVP DVTQLGLPGV KPSSTLDTRG ISKTTEGLNS GVTGLRSLGV RDLTYKISFL ACHVISIGSN IGASSPDANS NNRET ELQM AANLQANNVY QDNERDQEVF LNSLSSDEIN ELKEMVKDEH IYDKLVRSIA PAVFGHEAVK KGILLQMLGG VHKSTV EGI KLRGDINICV VGDPSTSKSQ FLKYVVGFAP RSVYTSGKAS SAAGLTAAVV RDEEGGDYTI EAGALMLADN GICCIDE FD KMDISDQVAI HEAMEQQTIS IAKAGIHATL NARTSILAAA NPVGGRYNRK LSLRGNLNMT APIMSRFDLF FVILDDCN E KIDTELASHI VDLHMKRDEA IEPPFSAEQL RRYIKYARTF KPILTKEARS YLVEKYKELR KDDAQGFSRS SYRITVRQL ESMIRLSEAI ARANCVDEIT PSFIAEAYDL LRQSIIRVDV DDVEMDEEFD NIESQSHAAS GNNDDNDDGT GSGVITSEPP ADIEEGQSE ATARPGTSEK KKTTVTYDKY VSMMNMIVRK IAEVDREGAE ELTAVDIVDW YLLQKENDLG SLAEYWEERR L AFKVIKRL VKDRILMEIH GTRHNLRDLE NEENENNKTV YVIHPNCEVL DQLEPQDSS

UniProtKB: DNA replication licensing factor MCM6

+
Macromolecule #6: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 95.049875 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSAALPSIQL PVDYNNLFNE ITDFLVTFKQ DTLSSDATRN ENEDENLDAE NIEQHLLEKG PKYMAMLQKV ANRELNSVII DLDDILQYQ NEKFLQGTQA DDLVSAIQQN ANHFTELFCR AIDNNMPLPT KEIDYKDDVL DVILNQRRLR NERMLSDRTN E IRSENLMD ...String:
MSAALPSIQL PVDYNNLFNE ITDFLVTFKQ DTLSSDATRN ENEDENLDAE NIEQHLLEKG PKYMAMLQKV ANRELNSVII DLDDILQYQ NEKFLQGTQA DDLVSAIQQN ANHFTELFCR AIDNNMPLPT KEIDYKDDVL DVILNQRRLR NERMLSDRTN E IRSENLMD TTMDPPSSMN DALREVVEDE TELFPPNLTR RYFLYFKPLS QNCARRYRKK AISSKPLSVR QIKGDFLGQL IT VRGIITR VSDVKPAVEV IAYTCDQCGY EVFQEVNSRT FTPLSECTSE ECSQNQTKGQ LFMSTRASKF SAFQECKIQE LSQ QVPVGH IPRSLNIHVN GTLVRSLSPG DIVDVTGIFL PAPYTGFKAL KAGLLTETYL EAQFVRQHKK KFASFSLTSD VEER VMELI TSGDVYNRLA KSIAPEIYGN LDVKKALLLL LVGGVDKRVG DGMKIRGDIN VCLMGDPGVA KSQLLKAICK ISPRG VYTT GKGSSGVGLT AAVMKDPVTD EMILEGGALV LADNGICCID EFDKMDESDR TAIHEVMEQQ TISISKAGIN TTLNAR TSI LAAANPLYGR YNPRLSPLDN INLPAALLSR FDILFLMLDI PSRDDDEKLA EHVTYVHMHN KQPDLDFTPV EPSKMRE YI AYAKTKRPVM SEAVNDYVVQ AYIRLRQDSK REMDSKFSFG QATPRTLLGI IRLSQALAKL RLADMVDIDD VEEALRLV R VSKESLYQET NKSKEDESPT TKIFTIIKKM LQETGKNTLS YENIVKTVRL RGFTMLQLSN CIQEYSYLNV WHLINEGNT LKFVDDGTMD TDQEDSLVST PKLAPQTTAS ANVSAQDSDI DLQDA

UniProtKB: DNA replication licensing factor MCM7

+
Macromolecule #7: Cell division cycle protein CDT1

MacromoleculeName: Cell division cycle protein CDT1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 68.486055 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSGTANSRRK EVLRVPVIDL NRVSDEEQLL PVVRAILLQH DTFLLKNYAN KAVLDALLAG LTTKDLPDTS QGFDANFTGT LPLEDDVWL EQYIFDTDPQ LRFDRKCRNE SLCSIYSRLF KLGLFFAQLC VKSVVSSAEL QDCISTSHYA TKLTRYFNDN G STHDGADA ...String:
MSGTANSRRK EVLRVPVIDL NRVSDEEQLL PVVRAILLQH DTFLLKNYAN KAVLDALLAG LTTKDLPDTS QGFDANFTGT LPLEDDVWL EQYIFDTDPQ LRFDRKCRNE SLCSIYSRLF KLGLFFAQLC VKSVVSSAEL QDCISTSHYA TKLTRYFNDN G STHDGADA GATVLPTGDD FQYLFERDYV TFLPTGVLTI FPCAKAIRYK PSTMATTDNS WVSIDEPDCL LFHTGTLLAR WS QGMHTTS PLQIDPRANI VSLTIWPPLT TPISSKGEGT IANHLLEQQI KAFPKVAQQY YPRELSILRL QDAMKFVKEL FTV CETVLS LNALSRSTGV PPELHVLLPQ ISSMMKRKIV QDDILKLLTI WSDAYVVELN SRGELTMNLP KRDNLTTLTN KSRT LAFVE RAESWYQQVI ASKDEIMTDV PAFKINKRRS SSNSKTVLSS KVQTKSSNAN ALNNSRYLAN SKENFMYKEK MPDSQ ANLM DRLRERERRS AALLSQRQKR YQQFLAMKMT QVFDILFSLT RGQPYTETYL SSLIVDSLQD SNNPIGTKEA SEILAG LQG ILPMDISVHQ VDGGLKVYRW NSLDKNRFSK LLQIHKSKQQ D

UniProtKB: Cell division cycle protein CDT1

+
Macromolecule #8: Origin recognition complex subunit 1

MacromoleculeName: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 108.612922 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKRRWKKNFI AVSAANRFKK ISSSGALENL YFQGEMAKTL KDLQGWEIIT TDEQGNIIDG GQKRLRRRGA KTEHYLKRSS DGIKLGRGD SVVMHNEAAG TYSVYMIQEL RLNTLNNVVE LWALTYLRWF EVNPLAHYRQ FNPDANILNR PLNYYNKLFS E TANKNELY ...String:
MKRRWKKNFI AVSAANRFKK ISSSGALENL YFQGEMAKTL KDLQGWEIIT TDEQGNIIDG GQKRLRRRGA KTEHYLKRSS DGIKLGRGD SVVMHNEAAG TYSVYMIQEL RLNTLNNVVE LWALTYLRWF EVNPLAHYRQ FNPDANILNR PLNYYNKLFS E TANKNELY LTAELAELQL FNFIRVANVM DGSKWEVLKG NVDPERDFTV RYICEPTGEK FVDINIEDVK AYIKKVEPRE AQ EYLKDLT LPSKKKEIKR GPQKKDKATQ TAQISDAETR ATDITDNEDG NEDESSDYES PSDIDVSEDM DSGEISADEL EEE EDEEED EDEEEKEARH TNSPRKRGRK IKLGKDDIDA SVQPPPKKRG RKPKDPSKPR QMLLISSCRA NNTPVIRKFT KKNV ARAKK KYTPFSKRFK SIAAIPDLTS LPEFYGNSSE LMASRFENKL KTTQKHQIVE TIFSKVKKQL NSSYVKEEIL KSANF QDYL PARENEFASI YLSAYSAIES DSATTIYVAG TPGVGKTLTV REVVKELLSS SAQREIPDFL YVEINGLKMV KPTDCY ETL WNKVSGERLT WAASMESLEF YFKRVPKNKK KTIVVLLDEL DAMVTKSQDI MYNFFNWTTY ENAKLIVIAV ANTMDLP ER QLGNKITSRI GFTRIMFTGY THEELKNIID LRLKGLNDSF FYVDTKTGNA ILIDAAGNDT TVKQTLPEDV RKVRLRMS A DAIEIASRKV ASVSGDARRA LKVCKRAAEI AEKHYMAKHG YGYDGKTVIE DENEEQIYDD EDKDLIESNK AKDDNDDDD DNDGVQTVHI THVMKALNET LNSHVITFMT RLSFTAKLFI YALLNLMKKN GSQEQELGDI VDEIKLLIEV NGSNKFVMEI AKTLFQQGS DNISEQLRII SWDFVLNQLL DAGILFKQTM KNDRICCVKL NISVEEAKRA MNEDETLRNL

UniProtKB: Origin recognition complex subunit 1

+
Macromolecule #9: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 64.426324 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: SPDPALKPKT PSKAPRKRGR PRKIQEELTD RIKKDEKDTI SSKKKRKLDK DTSGNVNEES KTSNNKQVME KTGIKEKRER EKIQVATTT YEDNVTPQTD DNFVSNSPEP PEPATPSKKS LTTNHDFTSP LKQIIMNNLK EYKDSTSPGK LTLSRNFTPT P VPKNKKLY ...String:
SPDPALKPKT PSKAPRKRGR PRKIQEELTD RIKKDEKDTI SSKKKRKLDK DTSGNVNEES KTSNNKQVME KTGIKEKRER EKIQVATTT YEDNVTPQTD DNFVSNSPEP PEPATPSKKS LTTNHDFTSP LKQIIMNNLK EYKDSTSPGK LTLSRNFTPT P VPKNKKLY QTSETKSASS FLDTFEGYFD QRKIVRTNAK SRHTMSMAPD VTREEFSLVS NFFNENFQKR PRQKLFEIQK KM FPQYWFE LTQGFSLLFY GVGSKRNFLE EFAIDYLSPK IAYSQLAYEN ELQQNKPVNS IPCLILNGYN PSCNYRDVFK EIT DLLVPA ELTRSETKYW GNHVILQIQK MIDFYKNQPL DIKLILVVHN LDGPSIRKNT FQTMLSFLSV IRQIAIVAST DHIY APLLW DNMKAQNYNF VFHDISNFEP STVESTFQDV MKMGKSDTSS GAEGAKYVLQ SLTVNSKKMY KLLIETQMQN MGNLS ANTG PKRGTQRTGV ELKLFNHLCA ADFIASNEIA LRSMLREFIE HKMANITKNN SGMEIIWVPY TYAELEKLLK TVLNTL

UniProtKB: Origin recognition complex subunit 2

+
Macromolecule #10: Origin recognition complex subunit 3

MacromoleculeName: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 72.161766 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDLNQSKKM NVSEFADAQR SHYTVYPSLP QSNKNDKHIP FVKLLSGKES EVNVEKRWEL YHQLHSHFHD QVDHIIDNIE ADLKAEISD LLYSETTQKR RCFNTIFLLG SDSTTKIELK DESSRYNVLI ELTPKESPNV RMMLRRSMYK LYSAADAEEH P TIKYEDIN ...String:
MSDLNQSKKM NVSEFADAQR SHYTVYPSLP QSNKNDKHIP FVKLLSGKES EVNVEKRWEL YHQLHSHFHD QVDHIIDNIE ADLKAEISD LLYSETTQKR RCFNTIFLLG SDSTTKIELK DESSRYNVLI ELTPKESPNV RMMLRRSMYK LYSAADAEEH P TIKYEDIN DEDGDFTEQN NDVSYDLSLV ENFKRLFGKD LAMVFNFKDV DSINFNTLDN FIILLKSAFK YDHVKISLIF NI NTNLSNI EKNLRQSTIR LLKRNYHKLD VSSNKGFKYG NQIFQSFLDT VDGKLNLSDR FVEFILSKMA NNTNHNLQLL TKM LDYSLM SYFFQNAFSV FIDPVNVDFL NDDYLKILSR CPTFMFFVEG LIKQHAPADE ILSLLTNKNR GLEEFFVEFL VREN PINGH AKFVARFLEE ELNITNFNLI ELYHNLLIGK LDSYLDRWSA CKEYKDRLHF EPIDTIFQEL FTLDNRSGLL TQSIF PSYK SNIEDNLLSW EQVLPSLDKE NYDTLSGDLD KIMAPVLGQL FKLYREANMT INIYDFYIAF RETLPKEEIL NFIRKD PSN TKLLELAETP DAFDKVALIL FMQAIFAFEN MGLIKFQSTK SYDLVEKCVW RGI

UniProtKB: Origin recognition complex subunit 3

+
Macromolecule #11: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 60.772152 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTISEARLSP QVNLLPIKRH SNEEVEETAA ILKKRTIDNE KCKDSDPGFG SLQRRLLQQL YGTLPTDEKI IFTYLQDCQQ EIDRIIKQS IIQKESHSVI LVGPRQSYKT YLLDYELSLL QQSYKEQFIT IRLNGFIHSE QTAINGIATQ LEQQLQKIHG S EEKIDDTS ...String:
MTISEARLSP QVNLLPIKRH SNEEVEETAA ILKKRTIDNE KCKDSDPGFG SLQRRLLQQL YGTLPTDEKI IFTYLQDCQQ EIDRIIKQS IIQKESHSVI LVGPRQSYKT YLLDYELSLL QQSYKEQFIT IRLNGFIHSE QTAINGIATQ LEQQLQKIHG S EEKIDDTS LETISSGSLT EVFEKILLLL DSTTKTRNED SGEVDRESIT KITVVFIFDE IDTFAGPVRQ TLLYNLFDMV EH SRVPVCI FGCTTKLNIL EYLEKRVKSR FSQRVIYMPQ IQNLDDMVDA VRNLLTVRSE ISPWVSQWNE TLEKELSDPR SNL NRHIRM NFETFRSLPT LKNSIIPLVA TSKNFGSLCT AIKSCSFLDI YNKNQLSNNL TGRLQSLSDL ELAILISAAR VALR AKDGS FNFNLAYAEY EKMIKAINSR IPTVAPTTNV GTGQSTFSID NTIKLWLKKD VKNVWENLVQ LDFFTEKSAV GLRDN ATAA FYASNYQFQG TMIPFDLRSY QMQIILQELR RIIPKSNMYY SWTQL

UniProtKB: Origin recognition complex subunit 4

+
Macromolecule #12: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 55.347168 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNVTTPEVAF REYQTNCLAS YISADPDITP SNLILQGYSG TGKTYTLKKY FNANPNLHAV WLEPVELVSW KPLLQAIART VQYKLKTLY PNIPTTDYDP LQVEEPFLLV KTLHNIFVQY ESLQEKTCLF LILDGFDSLQ DLDAALFNKY IKLNELLPKD S KINIKFIY ...String:
MNVTTPEVAF REYQTNCLAS YISADPDITP SNLILQGYSG TGKTYTLKKY FNANPNLHAV WLEPVELVSW KPLLQAIART VQYKLKTLY PNIPTTDYDP LQVEEPFLLV KTLHNIFVQY ESLQEKTCLF LILDGFDSLQ DLDAALFNKY IKLNELLPKD S KINIKFIY TMLETSFLQR YSTHCIPTVM FPRYNVDEVS TILVMSRCGE LMEDSCLRKR IIEEQITDCT DDQFQNVAAN FI HLIVQAF HSYTGNDIFA LNDLIDFKWP KYVSRITKEN IFEPLALYKS AIKLFLSTDD NLSENGQGES AITTNRDDLE NSQ TYDLSI ISKYLLIASY ICSYLEPRYD ASIFSRKTRI IQGRAAYGRR KKKEVNPRYL QPSLFAIERL LAIFQAIFPI QGKA ESGSL SALREESLMK ANIEVFQNLS ELHTLKLIAT TMNKNIDYLS PKVRWKVNVP WEIIKEISES VHFNISDYFS DIHE

UniProtKB: Origin recognition complex subunit 5

+
Macromolecule #13: Origin recognition complex subunit 6

MacromoleculeName: Origin recognition complex subunit 6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.369531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSMQQVQHCV AEVLRLDPQE KPDWSSGYLK KLTNATSILY NTSLNKVMLK QDEEVARCHI CAYIASQKMN EKHMPDLCYY IDSIPLEPK KAKHLMNLFR QSLSNSSPMK QFAWTPSPKK NKRSPVKNGG RFTSSDPKEL RNQLFGTPTK VRKSQNNDSF V IPELPPMQ ...String:
MSMQQVQHCV AEVLRLDPQE KPDWSSGYLK KLTNATSILY NTSLNKVMLK QDEEVARCHI CAYIASQKMN EKHMPDLCYY IDSIPLEPK KAKHLMNLFR QSLSNSSPMK QFAWTPSPKK NKRSPVKNGG RFTSSDPKEL RNQLFGTPTK VRKSQNNDSF V IPELPPMQ TNESPSITRR KLAFEEDEDE DEEEPGNDGL SLKSHSNKSI TGTRNVDSDE YENHESDPTS EEEPLGVQES RS GRTKQNK AVGKPQSELK TAKALRKRGR IPNSLLVKKY CKMTTEEIIR LCNDFELPRE VAYKIVDEYN INASRLVCPW QLV CGLVLN CTFIVFNERR RKDPRIDHFI VSKMCSLMLT SKVDDVIECV KLVKELIIGE KWFRDLQIRY DDFDGIRYDE IIFR KLGSM LQTTNILVTD DQYNIWKKRI EMDLALTEPL

UniProtKB: Origin recognition complex subunit 6

+
Macromolecule #14: DNA

MacromoleculeName: DNA / type: dna / ID: 14 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.931301 KDa
SequenceString:
(DC)(DG)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DG) (DA)(DT)(DC)(DG)(DA)(DT)(DC)(DG)(DA)(DT) (DC)(DG)(DA)(DT)(DC)(DG)(DA)(DT)(DC) (DG)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DG)(DA) (DT) (DC)(DG)

+
Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

+
Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #17: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.34 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49788
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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