+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30467 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | HsORC2-5 with the local density of ORC2-WHD improved | |||||||||
Map data | HsORC2-5 Orc2-WHD density enhanced | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / neural precursor cell proliferation / regulation of DNA replication ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / neural precursor cell proliferation / regulation of DNA replication / DNA replication origin binding / protein polymerization / DNA replication initiation / Activation of the pre-replicative complex / glial cell proliferation / heterochromatin / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / DNA replication / chromosome, telomeric region / nuclear body / nucleotide binding / centrosome / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Cheng J / Li N / Wang X / Hu J / Zhai Y / Gao N | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Cell Discov / Year: 2020 Title: Structural insight into the assembly and conformational activation of human origin recognition complex. Authors: Jiaxuan Cheng / Ningning Li / Xiaohan Wang / Jiazhi Hu / Yuanliang Zhai / Ning Gao / Abstract: The function of the origin recognition complex (ORC) in DNA replication is highly conserved in recognizing and marking the initiation sites. The detailed molecular mechanisms by which human ORC is ...The function of the origin recognition complex (ORC) in DNA replication is highly conserved in recognizing and marking the initiation sites. The detailed molecular mechanisms by which human ORC is reconfigured into a state competent for origin association remain largely unknown. Here, we present structural characterizations of human ORC1-5 and ORC2-5 assemblies. ORC2-5 exhibits a tightly autoinhibited conformation with the winged-helix domain of ORC2 completely blocking the central DNA-binding channel. The binding of ORC1 partially relieves the autoinhibitory effect of ORC2-5 through remodeling ORC2-WHD, which makes ORC2-WHD away from the central channel creating a still autoinhibited but more dynamic structure. In particular, the AAA+ domain of ORC1 is highly flexible to sample a variety of conformations from inactive to potentially active states. These results provide insights into the detailed mechanisms regulating the autoinhibition of human ORC and its subsequent activation for DNA binding. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30467.map.gz | 6.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30467-v30.xml emd-30467.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_30467.png | 153.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30467 | HTTPS FTP |
-Validation report
Summary document | emd_30467_validation.pdf.gz | 305.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30467_full_validation.pdf.gz | 305.5 KB | Display | |
Data in XML | emd_30467_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30467 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30467 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30467.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | HsORC2-5 Orc2-WHD density enhanced | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8286 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human Origin Recognition Complex 2-5
Entire | Name: Human Origin Recognition Complex 2-5 |
---|---|
Components |
|
-Supramolecule #1: Human Origin Recognition Complex 2-5
Supramolecule | Name: Human Origin Recognition Complex 2-5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Human Origin Recognition Complex
Macromolecule | Name: Human Origin Recognition Complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAHYPTRLKT RKTYSWVGRP LLDRKLHYQT YREMCVKTEG CSTEIHIQIG QFVLIEGDDD ENPYVAKLL ELFEDDSDPP PKKRARVQWF VRFCEVPACK RHLLGRKPGA QEIFWYDYPA C DSNINAET IIGLVRVIPL APKDVVPTNL KNEKTLFVKL SWNEKKFRPL ...String: MAHYPTRLKT RKTYSWVGRP LLDRKLHYQT YREMCVKTEG CSTEIHIQIG QFVLIEGDDD ENPYVAKLL ELFEDDSDPP PKKRARVQWF VRFCEVPACK RHLLGRKPGA QEIFWYDYPA C DSNINAET IIGLVRVIPL APKDVVPTNL KNEKTLFVKL SWNEKKFRPL SSELFAELNK PQ ESAAKCQ KPVRAKSKSA ESPSWTPAEH VAKRIESRHS ASKSRQTPTH PLTPRARKRL ELG NLGNPQ MSQQTSCASL DSPGRIKRKV AFSEITSPSK RSQPDKLQTL SPALKAPEKT RETG LSYTE DDKKASPEHR IILRTRIAAS KTIDIREERT LTPISGGQRS SVVPSVILKP ENIKK RDAK EAKAQNEATS TPHRIRRKSS VLTMNRIRQQ LRFLGNSKSD QEEKEILPAA EISDSS SDE EEASTPPLPR RAPRTVSRNL RSSLKSSLHT LTKVPKKSLK PRTPRCAAPQ IRSRSLA AQ EPASVLEEAR LRLHVSAVPE SLPCREQEFQ DIYNFVESKL LDHTGGCMYI SGVPGTGK T ATVHEVIRCL QQAAQANDVP PFQYIEVNGM KLTEPHQVYV QILQKLTGQK ATANHAAEL LAKQFCTRGS PQETTVLLVD ELDLLWTHKQ DIMYNLFDWP THKEARLVVL AIANTMDLPE RIMMNRVSS RLGLTRMCFQ PYTYSQLQQI LRSRLKHLKA FEDDAIQLVA RKVAALSGDA R RCLDICRR ATEICEFSQQ KPDSPGLVTI AHSMEAVDEM FSSSYITAIK NSSVLEQSFL RA ILAEFRR SGLEEATFQQ IYSQHVALCR MEGLPYPTMS ETMAVCSHLG SCRLLLVEPS RND LLLRVR LNVSQDDVLY ALKDEMSKPE LKEDKMLEVH FVGDDDVLNH ILDREGGAKL KKERAQLLVN PKKIIKKPEY DLEED DQEV LKDQNYVEIM GRDVQESLKN GSATGGGNKV YSFQNRKHSE KMAKLASELA KTPQKS VSF SLKNDPEITI NVPQSSKGHS ASDKVQPKNN DKSEFLSTAP RSLRKRLIVP RSHSDSE SE YSASNSEDDE GVAQEHEEDT NAVIFSQKIQ AQNRVVSAPV GKETPSKRMK RDKTSDLV E EYFEAHSSSK VLTSDRTLQK LKRAKLDQQT LRNLLSKVSP SFSAELKQLN QQYEKLFHK WMLQLHLGFN IVLYGLGSKR DLLERFRTTM LQDSIHVVIN GFFPGISVKS VLNSITEEVL DHMGTFRSI LDQLDWIVNK FKEDSSLELF LLIHNLDSQM LRGEKSQQII GQLSSLHNIY L IASIDHLN APLMWDHAKQ SLFNWLWYET TTYSPYTEET SYENSLLVKQ SGSLPLSSLT HV LRSLTPN ARGIFRLLIK YQLDNQDNPS YIGLSFQDFY QQCREAFLVN SDLTLRAQLT EFR DHKLIR TKKGTDGVEY LLIPVDNGTL TDFLEKEEEE AMATSSMSKG CFVFKPNSKK RKISLPIEDY FNKGKNEPED SKLRFETYQL IWQQMKSENE R LQEELNKN LFDNLIEFLQ KSHSGFQKNS RDLGGQIKLR EIPTAALVLG VNVTDHDLTF GS LTEALQN NVTPYVVSLQ AKDCPDMKHF LQKLISQLMD CCVDIKSKEE ESVHVTQRKT HYS MDSLSS WYMTVTQKTD PKMLSKKRTT SSQWQSPPVV VILKDMESFA TKVLQDFIII SSQH LHEFP LILIFGIATS PIIIHRLLPH AVSSLLCIEL FQSLSCKEHL TTVLDKLLLT TQFPF KINE KVLQVLTNIF LYHDFSVQNF IKGLQLSLLE HFYSQPLSVL CCNLPEAKRR INFLSN NQC ENIRRLPSFR RYVEKQASEK QVALLTNERY LKEETQLLLE NLHVYHMNYF LVLRCLH KF TSSLPKYPLG RQIRELYCTC LEKNIWDSEE YASVLQLLRM LAKDELMTIL EKCFKVFK S YCENHLGSTA KRIEEFLAQF QSLDETKEEE DASGSQPKGL QKTDLYHLQK SLLEMKELR RSKKQTKFEV LRENVVNFID CLVREYLLPP ETQPLHEVVY FSAAHALREH LNAAPRIALH TALNNPYYY LKNEALKSEE GCIPNIAPDI CIAYKLHLEC SRLINLVDWS EAFATVVTAA E KMDANSAT SEEMNEIIHA RFIRAVSELE LLGFIKPTKQ KTDHVARLTW GGCMSSRKSK SNSLIHTECL SQVQRILRER FCRQSPHSNL FGVQVQYKHL SELLKRTALH GES NSVLII GPRGSGKTML INHALKELME IEEVSENVLQ VHLNGLLQIN DKIALKEITR QLNL ENVVG DKVFGSFAEN LSFLLEALKK GDRTSSCPVI FILDEFDLFA HHKNQTLLYN LFDIS QSAQ TPIAVIGLTC RLDILELLEK RVKSRFSHRQ IHLMNSFGFP QYVKIFKEQL SLPAEF PDK VFAEKWNENV QYLSEDRSVQ EVLQKHFNIS KNLRSLHMLL MLALNRVTAS HPFMTAV DL MEASQLCSMD SKANIVHGLS VLEICLIIAM KHLNDIYEEE PFNFQMVYNE FQKFVQRK A HSVYNFEKPV VMKAFEHLQQ LELIKPMERT SGNSQREYQL MKLLLDNTQI MNALQKYPN CPTDVRQWAT SSLSWLMPHL ENVVLCRESQ VSILQSLFGE RHHFSFPSIF IYGHTASGKT YVTQTLLKTL ELPHVF VNC VECFTLRLLL EQILNKLNHL SSSEDGCSTE ITCETFNDFV RLFKQVTTAE NLKDQTV YI VLDKAEYLRD MEANLLPGFL RLQELADRNV TVLFLSEIVW EKFRPNTGCF EPFVLYFP D YSIGNLQKIL SHDHPPEYSA DFYAAYINIL LGVFYTVCRD LKELRHLAVL NFPKYCEPV VKGEASERDT RKLWRNIEPH LKKAMQTVYL REISSSQWEK LQKDDTDPGQ LKGLSAHTHV ELPYYSKFI LIAAYLASYN PARTDKRFFL KHHGKIKKTN FLKKHEKTSN HLLGPKPFPL D RLLAILYS IVDSRVAPTA NIFSQITSLV TLQLLTLVGH DDQLDGPKYK CTVSLDFIRA IA RTVNFDI IKYLYDFL |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52000 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |