[English] 日本語
Yorodumi
- EMDB-13020: CryoEM structure of DNA Polymerase alpha - primase bound to SARS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13020
TitleCryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1
Map data3D refinement map
Sample
  • Complex: Complex of DNA polymerase alpha - primase bound to SARS COV-2 nsp1
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Protein or peptide: DNA polymerase alpha subunit B
    • Protein or peptide: DNA primase small subunit
    • Protein or peptide: DNA primase large subunit
    • Protein or peptide: Non-structural protein 1
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTER
KeywordsDNA polymerase / Primase / viral protein / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / alpha DNA polymerase:primase complex ...positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / alpha DNA polymerase:primase complex / Processive synthesis on the lagging strand / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / DNA primase activity / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / primosome complex / DNA replication, synthesis of primer / lagging strand elongation / mitotic DNA replication initiation / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / DNA strand elongation involved in DNA replication / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / DNA synthesis involved in DNA repair / leading strand elongation / G1/S-Specific Transcription / DNA replication origin binding / SARS-CoV-1 modulates host translation machinery / DNA replication initiation / Activation of the pre-replicative complex / viral genome replication / methyltransferase activity / Defective pyroptosis / double-strand break repair via nonhomologous end joining / nuclear matrix / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / methylation / cysteine-type deubiquitinase activity / DNA replication / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / host cell perinuclear region of cytoplasm / single-stranded RNA binding / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA repair / virus-mediated perturbation of host defense response / nucleotide binding / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / proteolysis / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA polymerase alpha, subunit B, N-terminal domain superfamily / : / DNA polymerase alpha subunit B, OB domain / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit ...DNA polymerase alpha, subunit B, N-terminal domain superfamily / : / DNA polymerase alpha subunit B, OB domain / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / Eukaryotic and archaeal DNA primase, large subunit / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / : / Coronavirus 3Ecto domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / : / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit / Replicase polyprotein 1a / DNA primase small subunit / DNA primase large subunit / DNA polymerase alpha subunit B
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsKilkenny TJ / Pellegrini L
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: Protein Sci / Year: 2022
Title: Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase α-primase.
Authors: Mairi L Kilkenny / Charlotte E Veale / Amir Guppy / Steven W Hardwick / Dimitri Y Chirgadze / Neil J Rzechorzek / Joseph D Maman / Luca Pellegrini /
Abstract: The molecular mechanisms that drive the infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the causative agent of coronavirus disease 2019 (COVID-19)-are under intense ...The molecular mechanisms that drive the infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the causative agent of coronavirus disease 2019 (COVID-19)-are under intense current scrutiny to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated. Recent proteomic screens of the interactions between viral and host proteins have identified the human proteins targeted by SARS-CoV-2. The DNA polymerase α (Pol α)-primase complex or primosome-responsible for initiating DNA synthesis during genomic duplication-was identified as a target of nonstructural protein 1 (nsp1), a major virulence factor in the SARS-CoV-2 infection. Here, we validate the published reports of the interaction of nsp1 with the primosome by demonstrating direct binding with purified recombinant components and providing a biochemical characterization of their interaction. Furthermore, we provide a structural basis for the interaction by elucidating the cryo-electron microscopy structure of nsp1 bound to the primosome. Our findings provide biochemical evidence for the reported targeting of Pol α by the virulence factor nsp1 and suggest that SARS-CoV-2 interferes with Pol α's putative role in the immune response during the viral infection.
History
DepositionJun 1, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7opl
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13020.png

Downloads & links

-
Map

FileDownload / File: emd_13020.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 160 pix.
= 210.24 Å		1.31 Å/pix.
x 160 pix.
= 210.24 Å		1.31 Å/pix.
x 160 pix.
= 210.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.314 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.008
Minimum - Maximum-0.015819203 - 0.075377904
Average (Standard dev.)0.0004861129 (±0.0034148486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 210.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3141.3141.314
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z210.240210.240210.240
α/β/γ90.00090.00090.000
start NX/NY/NZ7810892
NX/NY/NZ127111124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0160.0750.000

-
Supplemental data

-
Additional map: Sharpened map, calculated from the two half maps...

Fileemd_13020_additional_1.map
AnnotationSharpened map, calculated from the two half maps using local, anisotropic sharpening in Phenix.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map #1

Fileemd_13020_half_map_1.map
AnnotationHalf map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map #2

Fileemd_13020_half_map_2.map
AnnotationHalf map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of DNA polymerase alpha - primase bound to SARS COV-2 nsp1

EntireName: Complex of DNA polymerase alpha - primase bound to SARS COV-2 nsp1
Components
  • Complex: Complex of DNA polymerase alpha - primase bound to SARS COV-2 nsp1
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Protein or peptide: DNA polymerase alpha subunit B
    • Protein or peptide: DNA primase small subunit
    • Protein or peptide: DNA primase large subunit
    • Protein or peptide: Non-structural protein 1
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTER

-
Supramolecule #1: Complex of DNA polymerase alpha - primase bound to SARS COV-2 nsp1

SupramoleculeName: Complex of DNA polymerase alpha - primase bound to SARS COV-2 nsp1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310 KDa

-
Macromolecule #1: DNA polymerase alpha catalytic subunit

MacromoleculeName: DNA polymerase alpha catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 133.702562 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAWSHPQFE KGGGSGGGSG GGSWSHPQFE KLEVLFQGPE FGADEEQVFH FYWLDAYEDQ YNQPGVVFLF GKVWIESAET HVSCCVMVK NIERTLYFLP REMKIDLNTG KETGTPISMK DVYEEFDEKI ATKYKIMKFK SKPVEKNYAF EIPDVPEKSE Y LEVKYSAE ...String:
MSAWSHPQFE KGGGSGGGSG GGSWSHPQFE KLEVLFQGPE FGADEEQVFH FYWLDAYEDQ YNQPGVVFLF GKVWIESAET HVSCCVMVK NIERTLYFLP REMKIDLNTG KETGTPISMK DVYEEFDEKI ATKYKIMKFK SKPVEKNYAF EIPDVPEKSE Y LEVKYSAE MPQLPQDLKG ETFSHVFGTN TSSLELFLMN RKIKGPCWLE VKSPQLLNQP VSWCKVEAMA LKPDLVNVIK DV SPPPLVV MAFSMKTMQN AKNHQNEIIA MAALVHHSFA LDKAAPKPPF QSHFCVVSKP KDCIFPYAFK EVIEKKNVKV EVA ATERTL LGFFLAKVHK IDPDIIVGHN IYGFELEVLL QRINVCKAPH WSKIGRLKRS NMPKLGGRSG FGERNATCGR MICD VEISA KELIRCKSYH LSELVQQILK TERVVIPMEN IQNMYSESSQ LLYLLEHTWK DAKFILQIMC ELNVLPLALQ ITNIA GNIM SRTLMGGRSE RNEFLLLHAF YENNYIVPDK QIFRKPQQKL GDEDEEIDGD TNKYKKGRKK AAYAGGLVLD PKVGFY DKF ILLLDFNSLY PSIIQEFNIC FTTVQRVASE AQKVTEDGEQ EQIPELPDPS LEMGILPREI RKLVERRKQV KQLMKQQ DL NPDLILQYDI RQKALKLTAN SMYGCLGFSY SRFYAKPLAA LVTYKGREIL MHTKEMVQKM NLEVIYGDTD SIMINTNS T NLEEVFKLGN KVKSEVNKLY KLLEIDIDGV FKSLLLLKKK KYAALVVEPT SDGNYVTKQE LKGLDIVRRD WCDLAKDTG NFVIGQILSD QSRDTIVENI QKRLIEIGEN VLNGSVPVSQ FEINKALTKD PQDYPDKKSL PHVHVALWIN SQGGRKVKAG DTVSYVICQ DGSNLTASQR AYAPEQLQKQ DNLTIDTQYY LAQQIHPVVA RICEPIDGID AVLIATWLGL DPTQFRVHHY H KDEENDAL LGGPAQLTDE EKYRDCERFK CPCPTCGTEN IYDNVFDGSG TDMEPSLYRC SNIDCKASPL TFTVQLSNKL IM DIRRFIK KYYDGWLICE EPTCRNRTRH LPLQFSRTGP LCPACMKATL QPEYSDKSLY TQLCFYRYIF DAECALEKLT TDH EKDKLK KQFFTPKVLQ DYRKLKNTAE QFLSRSGYSE VNLSKLFAGC AVKS

UniProtKB: DNA polymerase alpha catalytic subunit

-
Macromolecule #2: DNA polymerase alpha subunit B

MacromoleculeName: DNA polymerase alpha subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.855434 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSFSPSAT PSQKYNSRSN RGEVVTSFGL AQGVSWSGRG GAGNISLKVL GCPEALTGSY KSMFQKLPDI REVLTCKIEE LGSELKEHY KIEAFTPLLA PAQEPVTLLG QIGCDSNGKL NNKSVILEGD REHSSGAQIP VDLSELKEYS LFPGQVVIME G INTTGRKL ...String:
MGSSFSPSAT PSQKYNSRSN RGEVVTSFGL AQGVSWSGRG GAGNISLKVL GCPEALTGSY KSMFQKLPDI REVLTCKIEE LGSELKEHY KIEAFTPLLA PAQEPVTLLG QIGCDSNGKL NNKSVILEGD REHSSGAQIP VDLSELKEYS LFPGQVVIME G INTTGRKL VATKLYEGVP LPFYQPTEED ADFEQSMVLV ACGPYTTSDS ITYDPLLDLI AVINHDRPDV CILFGPFLDA KH EQVENCL LTSPFEDIFK QCLRTIIEGT RSSGSHLVFV PSLRDVHHEP VYPQPPFSYS DLSREDKKQV QFVSEPCSLS ING VIFGLT STDLLFHLGA EEISSSSGTS DRFSRILKHI LTQRSYYPLY PPQEDMAIDY ESFYVYAQLP VTPDVLIIPS ELRY FVKDV LGCVCVNPGR LTKGQVGGTF ARLYLRRPAA DGAERQSPCI AVQVVRI

UniProtKB: DNA polymerase alpha subunit B

-
Macromolecule #3: DNA primase small subunit

MacromoleculeName: DNA primase small subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.590801 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HGENLYFQGT SMETFDPTEL PELLKLYYRR LFPYSQYYRW LNYGGVIKNY FQHREFSFTL KDDIYIRYQS FNNQSDLEK EMQKMNPYKI DIGAVYSHRP NQHNTVKLGA FQAQEKELVF DIDMTDYDDV RRCCSSADIC PKCWTLMTMA I RIIDRALK ...String:
MHHHHHHHHH HGENLYFQGT SMETFDPTEL PELLKLYYRR LFPYSQYYRW LNYGGVIKNY FQHREFSFTL KDDIYIRYQS FNNQSDLEK EMQKMNPYKI DIGAVYSHRP NQHNTVKLGA FQAQEKELVF DIDMTDYDDV RRCCSSADIC PKCWTLMTMA I RIIDRALK EDFGFKHRLW VYSGRRGVHC WVCDESVRKL SSAVRSGIVE YLSLVKGGQD VKKKVHLSEK IHPFIRKSIN II KKYFEEY ALVNQDILEN KESWDKILAL VPETIHDELQ QSFQKSHNSL QRWEHLKKVA SRYQNNIKND KYGPWLEWEI MLQ YCFPRL DINVSKGINH LLKSPFSVHP KTGRISVPID LQKVDQFDPF TVPTISFICR ELDAISTNEE EKEENEAESD VKHR TRDYK KTSLAPYVKV FEHFLENLDK SRKGELLKKS DLQKDF

UniProtKB: DNA primase small subunit

-
Macromolecule #4: DNA primase large subunit

MacromoleculeName: DNA primase large subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.890918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENL EDEYEPRRRD HISHFILRLA YCQSEELRRW FIQQEMDLLR FRFSILPKDK IQDFLKDSQL QFEAISDEEK T LREQEIVA ...String:
MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENL EDEYEPRRRD HISHFILRLA YCQSEELRRW FIQQEMDLLR FRFSILPKDK IQDFLKDSQL QFEAISDEEK T LREQEIVA SSPSLSGLKL GFESIYKIPF ADALDLFRGR KVYLEDGFAY VPLKDIVAII LNEFRAKLSK ALALTARSLP AV QSDERLQ PLLNHLSHSY TGQDYSTQGN VGKISLDQID LLSTKSFPPC MRQLHKALRE NHHLRHGGRM QYGLFLKGIG LTL EQALQF WKQEFIKGKM DPDKFDKGYS YNIRHSFGKE GKRTDYTPFS CLKIILSNPP SQGDYHGCPF RHSDPELLKQ KLQS YKISP GGISQILDLV KGTHYQVACQ KYFEMIHNVD DCGFSLNHPN QFFCESQRIL NGGKDIKKEP IQPETPQPKP SVQKT KDAS SALASLNSSL EMDMEGLEDY FSEDS

UniProtKB: DNA primase large subunit

-
Macromolecule #5: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 12.955852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMGHVQLSL PVLQVRDVLV RGFGDSVEEA LSEAREHLKN GTCGLVELEK GVLPQLEQPY VFIKRSDALS TNHGHKVVEL VAEMDGIQY GRSGITLGVL VPHVGETPIA YRNVLLRKNG

UniProtKB: Replicase polyprotein 1a

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
25.0 mMHepes
150.0 mMKCl
1.0 1mMDTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe nsp1 protein was added in 10-fold stoichiometric excess

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 2919 / Average exposure time: 1.31 sec. / Average electron dose: 46.91 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: -0.0007 µm / Nominal defocus min: -0.0025 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 709068
Startup modelType of model: OTHER
Details: The initial 3D model was generated using a Stochastic Gradient Descent algorithm as implemented in Relion 3.1.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 233476
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1) / Details: As implemented in Relion 3.1.
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1) / Details: As implemented in Relion 3.1.
Final 3D classificationSoftware - Name: RELION (ver. 3.1)

-
Atomic model buiding 1

Initial model
PDB IDChain

5exr

chain_id: A, source_name: PDB, initial_model_type: experimental model

5exr

chain_id: B, source_name: PDB, initial_model_type: experimental model

5exr

chain_id: C, source_name: PDB, initial_model_type: experimental model

5exr

chain_id: D, source_name: PDB, initial_model_type: experimental model

7k3n

chain_id: E, source_name: PDB, initial_model_type: experimental model

2hsx

chain_id: E, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7opl:
CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1

+
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