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- EMDB-30467: HsORC2-5 with the local density of ORC2-WHD improved -

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Basic information

Entry
Database: EMDB / ID: EMD-30467
TitleHsORC2-5 with the local density of ORC2-WHD improved
Map dataHsORC2-5 Orc2-WHD density enhanced
Sample
  • Complex: Human Origin Recognition Complex 2-5
    • Protein or peptide: Human Origin Recognition Complex
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 / DNA replication initiation / protein polymerization / 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
Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion 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 subunit 3, insertion domain / Origin recognition complex subunit 3 insertion 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 / AAA ATPase domain / Origin recognition complex, subunit 2 / 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 / Origin recognition complex subunit 2 / Origin recognition complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCheng J / Li N / Wang X / Hu J / Zhai Y / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508904 China
CitationJournal: 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
DepositionAug 19, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30467.png

Downloads & links

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Map

FileDownload / File: emd_30467.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsORC2-5 Orc2-WHD density enhanced
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.58 Å		0.83 Å/pix.
x 300 pix.
= 248.58 Å		0.83 Å/pix.
x 300 pix.
= 248.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8286 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.3745054 - 2.4662082
Average (Standard dev.)0.006335459 (±0.070105225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.58 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.82860.82860.8286
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z248.580248.580248.580
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.3752.4660.006

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Supplemental data

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Sample components

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Entire : Human Origin Recognition Complex 2-5

EntireName: Human Origin Recognition Complex 2-5
Components
  • Complex: Human Origin Recognition Complex 2-5
    • Protein or peptide: Human Origin Recognition Complex

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Supramolecule #1: Human Origin Recognition Complex 2-5

SupramoleculeName: Human Origin Recognition Complex 2-5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Human Origin Recognition Complex

MacromoleculeName: Human Origin Recognition Complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 65.0 e/Å2
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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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