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- EMDB-22421: ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in... -

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Basic information

Entry
Database: EMDB / ID: EMD-22421
TitleORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
Map dataORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
Sample
  • Complex: ORC-DNA
    • 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
    • DNA: DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3')
    • DNA: DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium
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 / inner kinetochore / nuclear origin of replication recognition complex / nuclear pre-replicative complex / DNA replication preinitiation complex / neural precursor cell proliferation / mitotic DNA replication checkpoint signaling ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / inner kinetochore / nuclear origin of replication recognition complex / nuclear pre-replicative complex / DNA replication preinitiation complex / neural precursor cell proliferation / mitotic DNA replication checkpoint signaling / G1/S-Specific Transcription / DNA replication origin binding / regulation of DNA replication / 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 binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3, N-terminal / Origin recognition complex (ORC) subunit 3 N-terminus / 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 3, insertion domain / Origin recognition complex subunit 3, N-terminal / Origin recognition complex (ORC) subunit 3 N-terminus / 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 (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 / AAA ATPase domain / Origin recognition complex subunit 2 / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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 1 / Origin recognition complex subunit 2 / Origin recognition complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Spodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsJaremko MJ / Joshua-Tor L
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM129923 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM45436 United States
CitationJournal: Elife / Year: 2020
Title: The dynamic nature of the human origin recognition complex revealed through five cryoEM structures.
Authors: Matt J Jaremko / Kin Fan On / Dennis R Thomas / Bruce Stillman / Leemor Joshua-Tor /
Abstract: Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to ...Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·ORC3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.
History
DepositionAug 9, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00915
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.00915
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jps
  • Surface level: 0.00915
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22421.png

Downloads & links

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Map

FileDownload / File: emd_22421.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.00915 / Movie #1: 0.00915
Minimum - Maximum-0.014827838 - 0.040291328
Average (Standard dev.)-4.1742962e-05 (±0.0013930497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z342.400342.400342.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0150.040-0.000

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Supplemental data

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Sample components

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Entire : ORC-DNA

EntireName: ORC-DNA
Components
  • Complex: ORC-DNA
    • 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
    • DNA: DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3')
    • DNA: DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: ORC-DNA

SupramoleculeName: ORC-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / Details: 5 subunit ORC complex with DNA bound in the core
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 296.53 KDa

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Macromolecule #1: Origin recognition complex subunit 1

MacromoleculeName: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.310887 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPQIRSRSL AAQEPASVLE EARLRLHVSA VPESLPCREQ EFQDIYNFVE SKLLDHTGGC MYISGVPGTG KTATVHEVIR CLQQAAQAN DVPPFQYIEV NGMKLTEPHQ VYVQILQKLT GQKATANHAA ELLAKQFCTR GSPQETTVLL VDELDLLWTH K QDIMYNLF ...String:
MAPQIRSRSL AAQEPASVLE EARLRLHVSA VPESLPCREQ EFQDIYNFVE SKLLDHTGGC MYISGVPGTG KTATVHEVIR CLQQAAQAN DVPPFQYIEV NGMKLTEPHQ VYVQILQKLT GQKATANHAA ELLAKQFCTR GSPQETTVLL VDELDLLWTH K QDIMYNLF DWPTHKEARL VVLAIANTMD LPERIMMNRV SSRLGLTRMC FQPYTYSQLQ QILRSRLKHL KAFEDDAIQL VA RKVAALS GDARRCLDIC RRATEICEFS QQKPDSPGLV TIAHSMEAVD EMFSSSYITA IKNSSVLEQS FLRAILAEFR RSG LEEATF QQIYSQHVAL CRMEGLPYPT MSETMAVCSH LGSCRLLLVE PSRNDLLLRV RLNVSQDDVL YALKDE

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Macromolecule #2: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Origin recognition complex subunit 3

MacromoleculeName: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.436133 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 DAETKEEEDA SGSQPKGLQK TDLYHLQKSL LEMKELRRSK KQTKFEVLRE NVVNFI DCL VREYLLPPET QPLHEVVYFS AAHALREHLN AAPRIALHTA LNNPYYYLKN EALKSEEGCI PNIAPDICIA YKLHLEC SR LINLVDWSEA FATVVTAAEK MDANSATSEE MNEIIHARFI RAVSELELLG FIKPTKQKTD HVARLTWGGC

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Macromolecule #4: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.443266 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 PMERTSGNSQ REYQ LMKLL LDNTQIMNAL QKYPNCPTDV RQWATSSLSW L

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Macromolecule #5: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3')

MacromoleculeName: DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3') / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 3.972647 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DA)(DT)

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Macromolecule #7: DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')

MacromoleculeName: DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3') / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 3.963633 KDa
SequenceString:
(DA)(DT)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
80.0 mMNaClSodium chloridesodium chloride
3.3 mMC4H10O2S2DTT
0.8 mMC10H16N5O13P3ATPAdenosine triphosphate
0.05 % w/vC47H88O22Lauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.4 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 9068 / Average exposure time: 6.0 sec. / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2097508
CTF correctionSoftware - Name: RELION (ver. 3.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ujm

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2)
Details: Utilized Cryosparc to generate initial model, then 3D classification in Relion using the Cryosparc initial m
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 37734

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Atomic model buiding 1

Initial model
PDB IDChain

5ujm

chain_id: A

5ujm

chain_id: B

5ujm

chain_id: C

5ujm

chain_id: D

5ujm

chain_id: E
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 231 / Target criteria: Correlation Coefficient
Output model

PDB-7jps:
ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core

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Atomic model buiding 2

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-7jps:
ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core

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