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- PDB-6yxj: Crystal structure of SARS-CoV macrodomain II in complex with huma... -

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Basic information

Entry
Database: PDB / ID: 6yxj
TitleCrystal structure of SARS-CoV macrodomain II in complex with human Paip1
Components
  • Non-structural protein 3
  • Polyadenylate-binding protein-interacting protein 1
KeywordsVIRAL PROTEIN / coronavirus / virus-host interaction / macrodomain fold / HEAT repeats.
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / positive regulation of cytoplasmic translation ...mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / positive regulation of cytoplasmic translation / positive regulation by host of viral process / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA stabilization / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / regulation of translational initiation / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / translational initiation / SARS-CoV-1 activates/modulates innate immune responses / 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 / viral translation / ubiquitinyl hydrolase 1 / methylation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / virus-mediated perturbation of host defense response / proteolysis / RNA binding / zinc ion binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus ...: / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / 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 / 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 replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto 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 (CoV) Nsp3 Y 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 / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Armadillo-type fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Replicase polyprotein 1a / Polyadenylate-binding protein-interacting protein 1
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsLei, J. / Hilgenfeld, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Embo J. / Year: 2021
Title: The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation.
Authors: Lei, J. / Ma-Lauer, Y. / Han, Y. / Thoms, M. / Buschauer, R. / Jores, J. / Thiel, V. / Beckmann, R. / Deng, W. / Leonhardt, H. / Hilgenfeld, R. / von Brunn, A.
History
DepositionMay 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 3
B: Polyadenylate-binding protein-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)42,2482
Polymers42,2482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.386, 92.386, 166.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Non-structural protein 3 / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO


Mass: 15593.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: 1a / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P0C6U8, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Polyadenylate-binding protein-interacting protein 1 / Poly(A)-binding protein-interacting protein 1


Mass: 26654.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAIP1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9H074

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.86 Å3/Da / Density % sol: 74.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M (NH4)2SO4, 0.1 M HEPES pH 7.3, 18% PEG 3,350, 15% glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9184
SYNCHROTRONBESSY 14.220.97968
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 23, 2011
MAR CCD 165 mm2CCDJan 21, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979681
ReflectionResolution: 3.5→80.02 Å / Num. obs: 10784 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 117.76 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.8
Reflection shellResolution: 3.5→3.69 Å / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1549 / CC1/2: 0.753 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→30.94 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.589
RfactorNum. reflection% reflectionSelection details
Rfree0.3355 735 6.89 %RANDOM
Rwork0.3127 ---
obs0.3142 10666 98.3 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 255.06 Å2 / Biso min: 135.61 Å2
Baniso -1Baniso -2Baniso -3
1--47.4946 Å20 Å20 Å2
2---47.4946 Å20 Å2
3---94.9892 Å2
Refine analyzeLuzzati coordinate error obs: 1.09 Å
Refinement stepCycle: final / Resolution: 3.5→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 0 0 2726
Num. residues----346
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1004SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it2765HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion369SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2193SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2765HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3732HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion19.98
LS refinement shellResolution: 3.5→3.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 37
RfactorNum. reflection% reflection
Rfree0.3485 19 6.4 %
Rwork0.3844 278 -
all0.3825 297 -
obs--100 %

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