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- EMDB-30462: Human Origin Recognition Complex, ORC2-5 -

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Basic information

Entry
Database: EMDB / ID: EMD-30462
TitleHuman Origin Recognition Complex, ORC2-5
Map data
Sample
  • Complex: Human Origin Recognition Complex 2-5
    • 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
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDNA replication initiation / Origin Recognition Complex (ORC) / cryo-EM / autoinhibition conformation / REPLICATION
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
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: 3.8 Å
AuthorsCheng J / Li 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 18, 2020-
Header (metadata) releaseJan 6, 2021-
Map releaseJan 6, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing 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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  • Surface view with fitted model
  • Atomic models: PDB-7cte
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30462.png

Downloads & links

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Map

FileDownload / File: emd_30462.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.)
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-0.7193612 - 1.2465053
Average (Standard dev.)0.0013956324 (±0.046095796)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.7191.2470.001

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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: 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
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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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: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.063375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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Macromolecule #2: Origin recognition complex subunit 3

MacromoleculeName: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.365055 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 DETKEEEDAS GSQPKGLQKT DLYHLQKSLL EMKELRRSKK QTKFEVLREN VVNFID CLV REYLLPPETQ PLHEVVYFSA AHALREHLNA APRIALHTAL NNPYYYLKNE ALKSEEGCIP NIAPDICIAY KLHLECS RL INLVDWSEAF ATVVTAAEKM DANSATSEEM NEIIHARFIR AVSELELLGF IKPTKQKTDH VARLTWGGC

UniProtKB: Origin recognition complex subunit 3

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Macromolecule #3: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.44425 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 PMERTSGNSE REYQ LMKLL LDNTQIMNAL QKYPNCPTDV RQWATSSLSW L

UniProtKB: Origin recognition complex subunit 4

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Macromolecule #4: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.349934 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

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

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

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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) / 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

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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