[English] 日本語
Yorodumi
- EMDB-19566: Human OCCM DNA licensing intermediate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19566
TitleHuman OCCM DNA licensing intermediate
Map data
Sample
  • Complex: hOCCM
    • Protein or peptide: x 12 types
    • DNA: x 2 types
KeywordsDNA Replication / MCM2-7 / DNA licensing / human / origin / ORC / pre-RC / Cdc6 / Cdt1 / REPLICATION
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of chromosome segregation / positive regulation of chromatin binding / cellular response to vasopressin / polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / positive regulation of DNA-templated DNA replication / regulation of nuclear cell cycle DNA replication ...DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of chromosome segregation / positive regulation of chromatin binding / cellular response to vasopressin / polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / positive regulation of DNA-templated DNA replication / regulation of nuclear cell cycle DNA replication / E2F-enabled inhibition of pre-replication complex formation / Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of DNA-templated DNA replication / nuclear origin of replication recognition complex / traversing start control point of mitotic cell cycle / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / alpha DNA polymerase:primase complex / mitotic DNA replication / regulation of phosphorylation / DNA replication checkpoint signaling / attachment of mitotic spindle microtubules to kinetochore / CMG complex / inner kinetochore / nuclear pre-replicative complex / DNA replication preinitiation complex / MCM complex / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / Transcription of E2F targets under negative control by DREAM complex / neural precursor cell proliferation / regulation of mitotic metaphase/anaphase transition / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / positive regulation of cytokinesis / negative regulation of DNA replication / spindle midzone / G1/S-Specific Transcription / negative regulation of cell cycle / regulation of DNA replication / cellular response to angiotensin / DNA replication origin binding / cochlea development / protein polymerization / Activation of the pre-replicative complex / DNA replication initiation / glial cell proliferation / Activation of ATR in response to replication stress / heterochromatin / intercellular bridge / DNA polymerase binding / cellular response to interleukin-4 / DNA helicase activity / Assembly of the ORC complex at the origin of replication / protein serine/threonine kinase binding / cellular response to epidermal growth factor stimulus / Assembly of the pre-replicative complex / positive regulation of DNA replication / CDK-mediated phosphorylation and removal of Cdc6 / helicase activity / kinetochore / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation / spindle pole / mitotic spindle / mitotic cell cycle / nucleosome assembly / single-stranded DNA binding / histone binding / DNA helicase / chromosome, telomeric region / DNA replication / cell population proliferation / nuclear body / cilium / negative regulation of cell population proliferation / cell division / nucleotide binding / intracellular membrane-bounded organelle / apoptotic process / centrosome / DNA damage response / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane
Similarity search - Function
CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain ...CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal 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 / Cdc6, C-terminal / CDC6, C terminal winged helix 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 / DNA replication licensing factor MCM2-like, winged-helix domain / AAA lid domain / AAA lid domain / : / DNA replication licensing factor MCM7, winged helix / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain / 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 / Winged helix DNA-binding domain superfamily / 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
Origin recognition complex subunit 5 / Origin recognition complex subunit 4 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM2 / Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / DNA replication licensing factor MCM6 / Cell division control protein 6 homolog ...Origin recognition complex subunit 5 / Origin recognition complex subunit 4 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM2 / Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / DNA replication licensing factor MCM6 / Cell division control protein 6 homolog / DNA replication factor Cdt1 / Origin recognition complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.68 Å
AuthorsWells JN / Leber V / Edwards LV / Allyjaun S / Peach M / Tomkins J / Kefala-Stavridi A / Faull SV / Aramayo R / Pestana CM ...Wells JN / Leber V / Edwards LV / Allyjaun S / Peach M / Tomkins J / Kefala-Stavridi A / Faull SV / Aramayo R / Pestana CM / Ranjha L / Speck C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UK100006 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Reconstitution of human DNA licensing and the structural and functional analysis of key intermediates.
Authors: Jennifer N Wells / Lucy V Edwardes / Vera Leber / Shenaz Allyjaun / Matthew Peach / Joshua Tomkins / Antonia Kefala-Stavridi / Sarah V Faull / Ricardo Aramayo / Carolina M Pestana / Lepakshi ...Authors: Jennifer N Wells / Lucy V Edwardes / Vera Leber / Shenaz Allyjaun / Matthew Peach / Joshua Tomkins / Antonia Kefala-Stavridi / Sarah V Faull / Ricardo Aramayo / Carolina M Pestana / Lepakshi Ranjha / Christian Speck /
Abstract: Human DNA licensing initiates replication fork assembly and DNA replication. This reaction promotes the loading of the hMCM2-7 complex on DNA, which represents the core of the replicative helicase ...Human DNA licensing initiates replication fork assembly and DNA replication. This reaction promotes the loading of the hMCM2-7 complex on DNA, which represents the core of the replicative helicase that unwinds DNA during S-phase. Here, we report the reconstitution of human DNA licensing using purified proteins. We showed that the in vitro reaction is specific and results in the assembly of high-salt resistant hMCM2-7 double-hexamers. With ATPγS, an hORC1-5-hCDC6-hCDT1-hMCM2-7 (hOCCM) assembles independent of hORC6, but hORC6 enhances double-hexamer formation. We determined the hOCCM structure, which showed that hORC-hCDC6 recruits hMCM2-7 via five hMCM winged-helix domains. The structure highlights how hORC1 activates the hCDC6 ATPase and uncovered an unexpected role for hCDC6 ATPase in complex disassembly. We identified that hCDC6 binding to hORC1-5 stabilises hORC2-DNA interactions and supports hMCM3-dependent recruitment of hMCM2-7. Finally, the structure allowed us to locate cancer-associated mutations at the hCDC6-hMCM3 interface, which showed specific helicase loading defects.
History
DepositionFeb 5, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19566.png

Downloads & links

-
Map

FileDownload / File: emd_19566.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.43658993 - 1.0455133
Average (Standard dev.)0.0060549886 (±0.05182058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19566_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19566_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19566_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : hOCCM

EntireName: hOCCM
Components
  • Complex: hOCCM
    • Protein or peptide: DNA replication licensing factor MCM2
    • Protein or peptide: Isoform 2 of DNA replication licensing factor MCM3
    • Protein or peptide: DNA replication licensing factor MCM4
    • Protein or peptide: DNA replication licensing factor MCM6
    • Protein or peptide: DNA replication licensing factor MCM7
    • Protein or peptide: Origin recognition complex subunit 1
    • Protein or peptide: Origin recognition complex subunit 2
    • Protein or peptide: Isoform 2 of Origin recognition complex subunit 3
    • Protein or peptide: Origin recognition complex subunit 4
    • Protein or peptide: Origin recognition complex subunit 5
    • Protein or peptide: Cell division control protein 6 homolog
    • Protein or peptide: DNA replication factor Cdt1
    • DNA: DNA
    • DNA: DNA

+
Supramolecule #1: hOCCM

SupramoleculeName: hOCCM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.01 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: Homo sapiens (human)
Molecular weightTheoretical: 106.435773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGAG SATMAESSES FTMASSPAQR RRGNDPLTSS PGRSSRRTDA LTSSPGRDL PPFEDESEGL LGTEGPLEEE EDGEELIGDG MERDYRAIPE LDAYEAEGLA LDDEDVEELT ASQREAAERA M RQRDREAG ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGAG SATMAESSES FTMASSPAQR RRGNDPLTSS PGRSSRRTDA LTSSPGRDL PPFEDESEGL LGTEGPLEEE EDGEELIGDG MERDYRAIPE LDAYEAEGLA LDDEDVEELT ASQREAAERA M RQRDREAG RGLGRMRRGL LYDSDEEDEE RPARKRRQVE RATEDGEEDE EMIESIENLE DLKGHSVREW VSMAGPRLEI HH RFKNFLR THVDSHGHNV FKERISDMCK ENRESLVVNY EDLAAREHVL AYFLPEAPAE LLQIFDEAAL EVVLAMYPKY DRI TNHIHV RISHLPLVEE LRSLRQLHLN QLIRTSGVVT SCTGVLPQLS MVKYNCNKCN FVLGPFCQSQ NQEVKPGSCP ECQS AGPFE VNMEETIYQN YQRIRIQESP GKVAAGRLPR SKDAILLADL VDSCKPGDEI ELTGIYHNNY DGSLNTANGF PVFAT VILA NHVAKKDNKV AVGELTDEDV KMITSLSKDQ QIGEKIFASI APSIYGHEDI KRGLALALFG GEPKNPGGKH KVRGDI NVL LCGDPGTAKS QFLKYIEKVS SRAIFTTGQG ASAVGLTAYV QRHPVSREWT LEAGALVLAD RGVCLIDEFD KMNDQDR TS IHEAMEQQSI SISKAGIVTS LQARCTVIAA ANPIGGRYDP SLTFSENVDL TEPIISRFDI LCVVRDTVDP VQDEMLAR F VVGSHVRHHP SNKEEEGLAN GSAAEPAMPN TYGVEPLPQE VLKKYIIYAK ERVHPKLNQM DQDKVAKMYS DLRKESMAT GSIPITVRHI ESMIRMAEAH ARIHLRDYVI EDDVNMAIRV MLESFIDTQK FSVMRSMRKT FARYLSFRRD NNELLLFILK QLVAEQVTY QRNRFGAQQD TIEVPEKDLV DKARQINIHN LSAFYDSELF RMNKFSHDLK RKMILQQF

UniProtKB: DNA replication licensing factor MCM2

+
Macromolecule #2: Isoform 2 of DNA replication licensing factor MCM3

MacromoleculeName: Isoform 2 of DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.04332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLPRSPPLPR GNLWWREEFG SFRAGVESSW EPPRDFGGGS SLAAGMAGTV VLDDVELREA QRDYLDFLDD EEDQGIYQSK VRELISDNQ YRLIVNVNDL RRKNEKRANR LLNNAFEELV AFQRALKDFV ASIDATYAKQ YEEFYVGLEG SFGSKHVSPR T LTSCFLSC ...String:
MLPRSPPLPR GNLWWREEFG SFRAGVESSW EPPRDFGGGS SLAAGMAGTV VLDDVELREA QRDYLDFLDD EEDQGIYQSK VRELISDNQ YRLIVNVNDL RRKNEKRANR LLNNAFEELV AFQRALKDFV ASIDATYAKQ YEEFYVGLEG SFGSKHVSPR T LTSCFLSC VVCVEGIVTK CSLVRPKVVR SVHYCPATKK TIERRYSDLT TLVAFPSSSV YPTKDEENNP LETEYGLSVY KD HQTITIQ EMPEKAPAGQ LPRSVDVILD DDLVDKAKPG DRVQVVGTYR CLPGKKGGYT SGTFRTVLIA CNVKQMSKDA QPS FSAEDI AKIKKFSKTR SKDIFDQLAK SLAPSIHGHD YVKKAILCLL LGGVERDLEN GSHIRGDINI LLIGDPSVAK SQLL RYVLC TAPRAIPTTG RGSSGVGLTA AVTTDQETGE RRLEAGAMVL ADRGVVCIDE FDKMSDMDRT AIHEVMEQGR VTIAK AGIH ARLNARCSVL AAANPVYGRY DQYKTPMENI GLQDSLLSRF DLLFIMLDQM DPEQDREISD HVLRMHRYRA PGEQDG DAM PLGSAVDILA TDDPNFSQED QQDTQIYEKH DNLLHGTKKK KEKMVSAAFM KKYIHVAKII KPVLTQESAT YIAEEYS RL RSQDSMSSDT ARTSPVTART LETLIRLATA HAKARMSKTV DLQDAEEAVE LVQYAYFKKV LEKEKKRKKR SEDESETE D EEEKSQEDQE QKRKRRKTRQ PDAKDGDSYD PYDFSDTEEE MPQVHTPKTA DSQETKESQK VELSESRLKA FKVALLDVF REAHAQSIGM NRLTESINRD SEEPFSSVEI QAALSKMQDD NQVMVSEGII FLI

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: Homo sapiens (human)
Molecular weightTheoretical: 99.119461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHE NLYFQGSSAT MSSPASTPSR RGSRRGRATP AQTPRSEDAR SSPSQRRRGE DSTSTGELQP MPTSPGVDLQ SPAAQDVLF SSPPQMHSSA IPLDFDVSSP LTYGTPSSRV EGTPRSGVRG TPVRQRPDLG SAQKGLQVDL QSDGAAAEDI V ASEQSLGQ ...String:
MHHHHHHHHE NLYFQGSSAT MSSPASTPSR RGSRRGRATP AQTPRSEDAR SSPSQRRRGE DSTSTGELQP MPTSPGVDLQ SPAAQDVLF SSPPQMHSSA IPLDFDVSSP LTYGTPSSRV EGTPRSGVRG TPVRQRPDLG SAQKGLQVDL QSDGAAAEDI V ASEQSLGQ KLVIWGTDVN VAACKENFQR FLQRFIDPLA KEEENVGIDI TEPLYMQRLG EINVIGEPFL NVNCEHIKSF DK NLYRQLI SYPQEVIPTF DMAVNEIFFD RYPDSILEHQ IQVRPFNALK TKNMRNLNPE DIDQLITISG MVIRTSQLIP EMQ EAFFQC QVCAHTTRVE MDRGRIAEPS VCGRCHTTHS MALIHNRSLF SDKQMIKLQE SPEDMPAGQT PHTVILFAHN DLVD KVQPG DRVNVTGIYR AVPIRVNPRV SNVKSVYKTH IDVIHYRKTD AKRLHGLDEE AEQKLFSEKR VELLKELSRK PDIYE RLAS ALAPSIYEHE DIKKGILLQL FGGTRKDFSH TGRGKFRAEI NILLCGDPGT SKSQLLQYVY NLVPRGQYTS GKGSSA VGL TAYVMKDPET RQLVLQTGAL VLSDNGICCI DEFDKMNEST RSVLHEVMEQ QTLSIAKAGI ICQLNARTSV LAAANPI ES QWNPKKTTIE NIQLPHTLLS RFDLIFLLLD PQDEAYDRRL AHHLVALYYQ SEEQAEEELL DMAVLKDYIA YAHSTIMP R LSEEASQALI EAYVDMRKIG SSRGMVSAYP RQLESLIRLA EAHAKVRLSN KVEAIDVEEA KRLHREALKQ SATDPRTGI VDISILTTGM SATSRKRKEE LAEALKKLIL SKGKTPALKY QQLFEDIRGQ SDIAITKDMF EEALRALADD DFLTVTGKTV RLL

UniProtKB: DNA replication licensing factor MCM4

+
Macromolecule #4: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.010273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDLAAAAEPG AGSQHLEVRD EVAEKCQKLF LDFLEEFQSS DGEIKYLQLA EELIRPERNT LVVSFVDLEQ FNQQLSTTIQ EEFYRVYPY LCRALKTFVK DRKEIPLAKD FYVAFQDLPT RHKIRELTSS RIGLLTRISG QVVRTHPVHP ELVSGTFLCL D CQTVIRDV ...String:
MDLAAAAEPG AGSQHLEVRD EVAEKCQKLF LDFLEEFQSS DGEIKYLQLA EELIRPERNT LVVSFVDLEQ FNQQLSTTIQ EEFYRVYPY LCRALKTFVK DRKEIPLAKD FYVAFQDLPT RHKIRELTSS RIGLLTRISG QVVRTHPVHP ELVSGTFLCL D CQTVIRDV EQQFKYTQPN ICRNPVCANR RRFLLDTNKS RFVDFQKVRI QETQAELPRG SIPRSLEVIL RAEAVESAQA GD KCDFTGT LIVVPDVSKL STPGARAETN SRVSGVDGYE TEGIRGLRAL GVRDLSYRLV FLACCVAPTN PRFGGKELRD EEQ TAESIK NQMTVKEWEK VFEMSQDKNL YHNLCTSLFP TIHGNDEVKR GVLLMLFGGV PKTTGEGTSL RGDINVCIVG DPST AKSQF LKHVEEFSPR AVYTSGKASS AAGLTAAVVR DEESHEFVIE AGALMLADNG VCCIDEFDKM DVRDQVAIHE AMEQQ TISI TKAGVKATLN ARTSILAAAN PISGHYDRSK SLKQNINLSA PIMSRFDLFF ILVDECNEVT DYAIARRIVD LHSRIE ESI DRVYSLDDIR RYLLFARQFK PKISKESEDF IVEQYKHLRQ RDGSGVTKSS WRITVRQLES MIRLSEAMAR MHCCDEV QP KHVKEAFRLL NKSIIRVETP DVNLDQEEEI QMEVDEGAGG INGHADSPAP VNGINGYNED INQESAPKAS LRLGFSEY C RISNLIVLHL RKVEEEEDES ALKRSELVNW YLKEIESEID SEEELINKKR IIEKVIHRLT HYDHVLIELT QAGLKGSTE GSESYEEDPY LVVNPNYLLE D

UniProtKB: DNA replication licensing factor MCM6

+
Macromolecule #5: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.411875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALKDYALEK EKVKKFLQEF YQDDELGKKQ FKYGNQLVRL AHREQVALYV DLDDVAEDDP ELVDSICENA RRYAKLFADA VQELLPQYK EREVVNKDVL DVYIEHRLMM EQRSRDPGMV RSPQNQYPAE LMRRFELYFQ GPSSNKPRVI REVRADSVGK L VTVRGIVT ...String:
MALKDYALEK EKVKKFLQEF YQDDELGKKQ FKYGNQLVRL AHREQVALYV DLDDVAEDDP ELVDSICENA RRYAKLFADA VQELLPQYK EREVVNKDVL DVYIEHRLMM EQRSRDPGMV RSPQNQYPAE LMRRFELYFQ GPSSNKPRVI REVRADSVGK L VTVRGIVT RVSEVKPKMV VATYTCDQCG AETYQPIQSP TFMPLIMCPS QECQTNRSGG RLYLQTRGSR FIKFQEMKMQ EH SDQVPVG NIPRSITVLV EGENTRIAQP GDHVSVTGIF LPILRTGFRQ VVQGLLSETY LEAHRIVKMN KSEDDESGAG ELT REELRQ IAEEDFYEKL AASIAPEIYG HEDVKKALLL LLVGGVDQSP RGMKIRGNIN ICLMGDPGVA KSQLLSYIDR LAPR SQYTT GRGSSGVGLT AAVLRDSVSG ELTLEGGALV LADQGVCCID EFDKMAEADR TAIHEVMEQQ TISIAKAGIL TTLNA RCSI LAAANPAYGR YNPRRSLEQN IQLPAALLSR FDLLWLIQDR PDRDNDLRLA QHITYVHQHS RQPPSQFEPL DMKLMR RYI AMCREKQPMV PESLADYITA AYVEMRREAW ASKDATYTSA RTLLAILRLS TALARLRMVD VVEKEDVNEA IRLMEMS KD SLLGDKGQTA RTQRPADVIF ATVRELVSGG RSVRFSEAEQ RCVSRGFTPA QFQAALDEYE ELNVWQVNAS RTRITFV

UniProtKB: DNA replication licensing factor MCM7

+
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: Homo sapiens (human)
Molecular weightTheoretical: 108.813562 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MGSLQDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLTFLY DGIEIQADQA PEDLDMEDN DIIEAHREQI GGAHYPTRLK TRKTYSWVGR PLLDRKLHYQ TYREMCVKTE GCSTEIHIQI GQFVLIEGDD D ENPYVAKL ...String:
MGSLQDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLTFLY DGIEIQADQA PEDLDMEDN DIIEAHREQI GGAHYPTRLK TRKTYSWVGR PLLDRKLHYQ TYREMCVKTE GCSTEIHIQI GQFVLIEGDD D ENPYVAKL LELFEDDSDP PPKKRARVQW FVRFCEVPAC KRHLLGRKPG AQEIFWYDYP ACDSNINAET IIGLVRVIPL AP KDVVPTN LKNEKTLFVK LSWNEKKFRP LSSELFAELN KPQESAAKCQ KPVRAKSKSA ESPSWTPAEH VAKRIESRHS ASK SRQTPT HPLTPRARKR LELGNLGNPQ MSQQTSCASL DSPGRIKRKV AFSEITSPSK RSQPDKLQTL SPALKAPEKT RETG LSYTE DDKKASPEHR IILRTRIAAS KTIDIREERT LTPISGGQRS SVVPSVILKP ENIKKRDAKE AKAQNEATST PHRIR RKSS VLTMNRIRQQ LRFLGNSKSD QEEKEILPAA EISDSSSDEE EASTPPLPRR APRTVSRNLR SSLKSSLHTL TKVPKK SLK PRTPRCAAPQ IRSRSLAAQE PASVLEEARL RLHVSAVPES LPCREQEFQD IYNFVESKLL DHTGGCMYIS GVPGTGK TA TVHEVIRCLQ QAAQANDVPP FQYIEVNGMK LTEPHQVYVQ ILQKLTGQKA TANHAAELLA KQFCTRGSPQ ETTVLLVD E LDLLWTHKQD IMYNLFDWPT HKEARLVVLA IANTMDLPER IMMNRVSSRL GLTRMCFQPY TYSQLQQILR SRLKHLKAF EDDAIQLVAR KVAALSGDAR RCLDICRRAT EICEFSQQKP DSPGLVTIAH SMEAVDEMFS SSYITAIKNS SVLEQSFLRA ILAEFRRSG LEEATFQQIY SQHVALCRME GLPYPTMSET MAVCSHLGSC RLLLVEPSRN DLLLRVRLNV SQDDVLYALK D E

UniProtKB: Origin recognition complex subunit 1

+
Macromolecule #7: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.063375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSKPELKEDK MLEVHFVGDD DVLNHILDRE GGAKLKKERA QLLVNPKKII KKPEYDLEED DQEVLKDQNY VEIMGRDVQE SLKNGSATG GGNKVYSFQN RKHSEKMAKL ASELAKTPQK SVSFSLKNDP EITINVPQSS KGHSASDKVQ PKNNDKSEFL S TAPRSLRK ...String:
MSKPELKEDK MLEVHFVGDD DVLNHILDRE GGAKLKKERA QLLVNPKKII KKPEYDLEED DQEVLKDQNY VEIMGRDVQE SLKNGSATG GGNKVYSFQN RKHSEKMAKL ASELAKTPQK SVSFSLKNDP EITINVPQSS KGHSASDKVQ PKNNDKSEFL S TAPRSLRK RLIVPRSHSD SESEYSASNS EDDEGVAQEH EEDTNAVIFS QKIQAQNRVV SAPVGKETPS KRMKRDKTSD LV EEYFEAH SSSKVLTSDR TLQKLKRAKL DQQTLRNLLS KVSPSFSAEL KQLNQQYEKL FHKWMLQLHL GFNIVLYGLG SKR DLLERF RTTMLQDSIH VVINGFFPGI SVKSVLNSIT EEVLDHMGTF RSILDQLDWI VNKFKEDSSL ELFLLIHNLD SQML RGEKS QQIIGQLSSL HNIYLIASID HLNAPLMWDH AKQSLFNWLW YETTTYSPYT EETSYENSLL VKQSGSLPLS SLTHV LRSL TPNARGIFRL LIKYQLDNQD NPSYIGLSFQ DFYQQCREAF LVNSDLTLRA QLTEFRDHKL IRTKKGTDGV EYLLIP VDN GTLTDFLEKE EEEA

UniProtKB: Origin recognition complex subunit 2

+
Macromolecule #8: Isoform 2 of Origin recognition complex subunit 3

MacromoleculeName: Isoform 2 of Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.436133 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MATSSMSKGC FVFKPNSKKR KISLPIEDYF NKGKNEPEDS KLRFETYQLI WQQMKSENER LQEELNKNLF DNLIEFLQKS HSGFQKNSR DLGGQIKLRE IPTAALVLGV NVTDHDLTFG SLTEALQNNV TPYVVSLQAK DCPDMKHFLQ KLISQLMDCC V DIKSKEEE ...String:
MATSSMSKGC FVFKPNSKKR KISLPIEDYF NKGKNEPEDS KLRFETYQLI WQQMKSENER LQEELNKNLF DNLIEFLQKS HSGFQKNSR DLGGQIKLRE IPTAALVLGV NVTDHDLTFG SLTEALQNNV TPYVVSLQAK DCPDMKHFLQ KLISQLMDCC V DIKSKEEE SVHVTQRKTH YSMDSLSSWY MTVTQKTDPK MLSKKRTTSS QWQSPPVVVI LKDMESFATK VLQDFIIISS QH LHEFPLI LIFGIATSPI IIHRLLPHAV SSLLCIELFQ SLSCKEHLTT VLDKLLLTTQ FPFKINEKVL QVLTNIFLYH DFS VQNFIK GLQLSLLEHF YSQPLSVLCC NLPEAKRRIN FLSNNQCENI RRLPSFRRYV EKQASEKQVA LLTNERYLKE ETQL LLENL HVYHMNYFLV LRCLHKFTSS LPKYPLGRQI RELYCTCLEK NIWDSEEYAS VLQLLRMLAK DELMTILEKC FKVFK SYCE NHLGSTAKRI EEFLAQFQSL DAETKEEEDA SGSQPKGLQK TDLYHLQKSL LEMKELRRSK KQTKFEVLRE NVVNFI DCL VREYLLPPET QPLHEVVYFS AAHALREHLN AAPRIALHTA LNNPYYYLKN EALKSEEGCI PNIAPDICIA YKLHLEC SR LINLVDWSEA FATVVTAAEK MDANSATSEE MNEIIHARFI RAVSELELLG FIKPTKQKTD HVARLTWGGC

UniProtKB: Origin recognition complex subunit 3

+
Macromolecule #9: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.443266 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSSRKSKSNS LIHTECLSQV QRILRERFCR QSPHSNLFGV QVQYKHLSEL LKRTALHGES NSVLIIGPRG SGKTMLINHA LKELMEIEE VSENVLQVHL NGLLQINDKI ALKEITRQLN LENVVGDKVF GSFAENLSFL LEALKKGDRT SSCPVIFILD E FDLFAHHK ...String:
MSSRKSKSNS LIHTECLSQV QRILRERFCR QSPHSNLFGV QVQYKHLSEL LKRTALHGES NSVLIIGPRG SGKTMLINHA LKELMEIEE VSENVLQVHL NGLLQINDKI ALKEITRQLN LENVVGDKVF GSFAENLSFL LEALKKGDRT SSCPVIFILD E FDLFAHHK NQTLLYNLFD ISQSAQTPIA VIGLTCRLDI LELLEKRVKS RFSHRQIHLM NSFGFPQYVK IFKEQLSLPA EF PDKVFAE KWNENVQYLS EDRSVQEVLQ KHFNISKNLR SLHMLLMLAL NRVTASHPFM TAVDLMEASQ LCSMDSKANI VHG LSVLEI CLIIAMKHLN DIYEEEPFNF QMVYNEFQKF VQRKAHSVYN FEKPVVMKAF EHLQQLELIK PMERTSGNSQ REYQ LMKLL LDNTQIMNAL QKYPNCPTDV RQWATSSLSW L

UniProtKB: Origin recognition complex subunit 4

+
Macromolecule #10: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.349934 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MPHLENVVLC RESQVSILQS LFGERHHFSF PSIFIYGHTA SGKTYVTQTL LKTLELPHVF VNCVECFTLR LLLEQILNKL NHLSSSEDG CSTEITCETF NDFVRLFKQV TTAENLKDQT VYIVLDKAEY LRDMEANLLP GFLRLQELAD RNVTVLFLSE I VWEKFRPN ...String:
MPHLENVVLC RESQVSILQS LFGERHHFSF PSIFIYGHTA SGKTYVTQTL LKTLELPHVF VNCVECFTLR LLLEQILNKL NHLSSSEDG CSTEITCETF NDFVRLFKQV TTAENLKDQT VYIVLDKAEY LRDMEANLLP GFLRLQELAD RNVTVLFLSE I VWEKFRPN TGCFEPFVLY FPDYSIGNLQ KILSHDHPPE YSADFYAAYI NILLGVFYTV CRDLKELRHL AVLNFPKYCE PV VKGEASE RDTRKLWRNI EPHLKKAMQT VYLREISSSQ WEKLQKDDTD PGQLKGLSAH THVELPYYSK FILIAAYLAS YNP ARTDKR FFLKHHGKIK KTNFLKKHEK TSNHLLGPKP FPLDRLLAIL YSIVDSRVAP TANIFSQITS LVTLQLLTLV GHDD QLDGP KYKCTVSLDF IRAIARTVNF DIIKYLYDFL

UniProtKB: Origin recognition complex subunit 5

+
Macromolecule #11: Cell division control protein 6 homolog

MacromoleculeName: Cell division control protein 6 homolog / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.834379 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPQTRSQAQA TISFPKRKLS RALNKAKNSS DAKLEPTNVQ TVTCSPRVKA LPLSPRKRLG DDNLCNTPHL PPCSPPKQGK KENGPPHSH TLKGRRLVFD NQLTIKSPSK RELAKVHQNK ILSSVRKSQE ITTNSEQRCP LKKESACVRL FKQEGTCYQQ A KLVLNTAV ...String:
MPQTRSQAQA TISFPKRKLS RALNKAKNSS DAKLEPTNVQ TVTCSPRVKA LPLSPRKRLG DDNLCNTPHL PPCSPPKQGK KENGPPHSH TLKGRRLVFD NQLTIKSPSK RELAKVHQNK ILSSVRKSQE ITTNSEQRCP LKKESACVRL FKQEGTCYQQ A KLVLNTAV PDRLPARERE MDVIRNFLRE HICGKKAGSL YLSGAPGTGK TACLSRILQD LKKELKGFKT IMLNCMSLRT AQ AVFPAIA QEICQEEVSR PAGKDMMRKL EKHMTAEKGP MIVLVLDEMD QLDSKGQDVL YTLFEWPWLS NSHLVLIGIA NTL DLTDRI LPRLQAREKC KPQLLNFPPY TRNQIVTILQ DRLNQVSRDQ VLDNAAVQFC ARKVSAVSGD VRKALDVCRR AIEI VESDV KSQTILKPLS ECKSPSEPLI PKRVGLIHIS QVISEIDGNR MTLSQEGAQD SFPLQQKILV CSLMLLIRQL KIKEV TLGK LYEAYSKVCR KQQVAAVDQS ECLSLSGLLE ARGILGLKRN KETRLTKVFF KIEEKEIEHA LKDKALIGNI LATGLP

UniProtKB: Cell division control protein 6 homolog

+
Macromolecule #12: DNA replication factor Cdt1

MacromoleculeName: DNA replication factor Cdt1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.09902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLEVLFQG PRPEEPCGEK APAYQRFHAL AQPGLPGLVL PYKYQVLAEM FRSMDTIVGM LHNRSETPTF AKVQRGVQD MMRRRFEECN VGQIKTVYPA SYRFRQERSV PTFKDGTRRS DYQLTIEPLL EQEADGAAPQ LTASRLLQRR Q IFSQKLVE ...String:
MGSSHHHHHH SSGLEVLFQG PRPEEPCGEK APAYQRFHAL AQPGLPGLVL PYKYQVLAEM FRSMDTIVGM LHNRSETPTF AKVQRGVQD MMRRRFEECN VGQIKTVYPA SYRFRQERSV PTFKDGTRRS DYQLTIEPLL EQEADGAAPQ LTASRLLQRR Q IFSQKLVE HVKEHHKAFL ASLSPAMVVP EDQLTRWHPR FNVDEVPDIE PAALPQPPAT EKLTTAQEVL ARARNLISPR ME KALSQLA LRSAAPSSPG SPRPALPATP PATPPAASPS ALKGVSQDLL ERIRAKEAQK QLAQMTRCPE QEQRLQRLER LPE LARVLR SVFVSERKPA LSMEVACARM VGSCCTIMSP GEMEKHLLLL SELLPDWLSL HRIRTDTYVK LDKAADLAHI TARL AHQTR AEEGL

UniProtKB: DNA replication factor Cdt1

+
Macromolecule #13: DNA

MacromoleculeName: DNA / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.933735 KDa
SequenceString:
(DA)(DT)(DG)(DA)(DC)(DT)(DG)(DG)(DA)(DA) (DA)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DT) (DA)(DC)(DA)(DA)(DC)(DA)(DC)(DT)(DC) (DC)(DA)(DA)(DT)(DA)(DA)(DA)(DC)(DA)(DT)

+
Macromolecule #14: DNA

MacromoleculeName: DNA / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.379996 KDa
SequenceString:
(DA)(DA)(DT)(DG)(DT)(DT)(DT)(DA)(DT)(DT) (DG)(DG)(DA)(DG)(DT)(DG)(DT)(DT)(DG)(DT) (DA)(DC)(DA)(DA)(DA)(DA)(DA)(DA)(DG) (DT)(DT)(DT)(DC)(DC)(DA)(DG)(DT)(DC)(DA) (DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 18022 / Average exposure time: 3.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1598732
Startup modelType of model: OTHER
Details: AlphaFold models from each individual subunit were rigid body docked into the experimental map before model building in COOT.
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8730
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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