[English] 日本語
Yorodumi
- PDB-5c0w: Structure of a 12-subunit nuclear exosome complex bound to single... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c0w
TitleStructure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates
Components
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • Exosome complex protein LRP1
  • RNA synthetic
KeywordsHYDROLASE/RNA / hydrolase / RNA / nuclease / hydrolase-RNA complex
Function / homology
Function and homology information


nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing ...nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / mRNA 3'-UTR AU-rich region binding / rRNA primary transcript binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / regulation of telomere maintenance / nonfunctional rRNA decay / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / maturation of 5.8S rRNA / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / RNA processing / enzyme regulator activity / RNA endonuclease activity / mRNA processing / double-stranded RNA binding / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / regulation of gene expression / double-stranded DNA binding / endonuclease activity / tRNA binding / single-stranded RNA binding / nucleotide binding / protein-containing complex binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Exosome-associated factor Rrp47/DNA strand repair C1D / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / Exosome complex exonuclease RRP44, S1 domain ...Exosome-associated factor Rrp47/DNA strand repair C1D / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / : / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / : / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / HRDC domain superfamily / Large family of predicted nucleotide-binding domains / 3'-5' exonuclease / PIN domain / K Homology domain, type 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / K Homology domain, type 1 superfamily / PIN-like domain superfamily / S1 domain profile. / HRDC-like superfamily / Ribosomal protein S1-like RNA-binding domain / S1 domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex protein LRP1 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 ...RNA / RNA (> 10) / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex protein LRP1 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Exosome complex exonuclease RRP6 / Exosome complex component RRP42
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
AuthorsMakino, D.L. / Conti, E.
Funding support Germany, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European CommissionERC 294371 Germany
European CommissionMarie Curie ITN RNPnet Germany
German Research FoundationSFB646, SFB1035, GRK1721, FOR1680, CIPSM Germany
Louis Jeantet Germany
CitationJournal: Nature / Year: 2015
Title: RNA degradation paths in a 12-subunit nuclear exosome complex.
Authors: Makino, D.L. / Schuch, B. / Stegmann, E. / Baumgartner, M. / Basquin, C. / Conti, E.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_struct_ref_seq_depositor_info ...pdbx_data_processing_status / pdbx_struct_ref_seq_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exosome complex component RRP45
B: Exosome complex component SKI6
C: Exosome complex component RRP43
D: Exosome complex component RRP46
E: Exosome complex component RRP42
F: Exosome complex component MTR3
G: Exosome complex component RRP40
H: Exosome complex component RRP4
I: Exosome complex component CSL4
J: Exosome complex exonuclease DIS3
K: Exosome complex exonuclease RRP6
L: Exosome complex protein LRP1
R: RNA synthetic
N: RNA synthetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,70516
Polymers514,61614
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53810 Å2
ΔGint-283 kcal/mol
Surface area183520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.380, 195.380, 463.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Exosome complex component ... , 9 types, 9 molecules ABCDEFGHI

#1: Protein Exosome complex component RRP45 / Ribosomal RNA-processing protein 45


Mass: 34001.859 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q05636
#2: Protein Exosome complex component SKI6 / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27794.926 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP41
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P46948
#3: Protein Exosome complex component RRP43 / Ribosomal RNA-processing protein 43


Mass: 44109.000 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25359
#4: Protein Exosome complex component RRP46 / Ribosomal RNA-processing protein 46


Mass: 26913.988 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P53256
#5: Protein Exosome complex component RRP42 / Ribosomal RNA-processing protein 42


Mass: 29294.398 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP42 / Mutation: V138I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q12277
#6: Protein Exosome complex component MTR3 / mRNA transport regulator 3


Mass: 27559.869 Da / Num. of mol.: 1 / Fragment: Exosome complex component MTR3 / Mutation: T75S, M161T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P48240
#7: Protein Exosome complex component RRP40 / Ribosomal RNA-processing protein 40


Mass: 26875.668 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Plasmid: pECK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q08285
#8: Protein Exosome complex component RRP4 / Ribosomal RNA-processing protein 4


Mass: 39714.445 Da / Num. of mol.: 1 / Fragment: Exosome complex component RRP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Plasmid: pECK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P38792
#9: Protein Exosome complex component CSL4 / CEP1 synthetic lethal protein 4


Mass: 31911.594 Da / Num. of mol.: 1 / Fragment: Exosome complex component CSL4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Plasmid: pETMCN-CDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P53859

-
Exosome complex exonuclease ... , 2 types, 2 molecules JK

#10: Protein Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 114081.008 Da / Num. of mol.: 1 / Fragment: Exosome complex exonuclease RRP44 / Mutation: D171N, D551N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#11: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 79649.438 Da / Num. of mol.: 1 / Fragment: Exosome complex exonuclease RRP6 / Mutation: D296N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

-
Protein / RNA chain , 2 types, 3 molecules LRN

#12: Protein Exosome complex protein LRP1 / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 21086.297 Da / Num. of mol.: 1 / Fragment: Exosome complex protein LRP1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LRP1, RRP47, YC1D, YHR081W / Plasmid: pCDF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P38801
#13: RNA chain RNA synthetic


Mass: 5811.628 Da / Num. of mol.: 2 / Fragment: RNA synthetic / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 2 molecules

#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#15: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 14

-
Sample preparation

CrystalDensity Matthews: 4.96 Å3/Da / Density % sol: 75.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 4.1-4.4%(w/v) PEG 8000, 0.1M MES pH 5.5, 0.2M KCl, 0.01M MgCl2, 283K and 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2398 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.51
ReflectionResolution: 4.6→59.09 Å / Num. obs: 40273 / % possible obs: 69.5 % / Observed criterion σ(I): -3 / Redundancy: 3.435 % / Rmerge F obs: 0.988 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.126 / Χ2: 0.978 / Net I/σ(I): 6 / Num. measured all: 138355
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
4.6-4.81.040.5110.7080.451735683316621.00224.3
4.8-50.3720.4860.592062582419220.68133
5-5.50.70.3680.8353951104549370.51144.7
5.5-60.6860.4711.338793771958310.62975.5
6-6.20.7880.3692.24408244321380.46187.5
6.2-6.50.7530.3782.628311311729900.45995.9
6.5-6.80.840.3253.368084259125430.38798.1
6.8-70.8440.2974.155620150014900.34499.3
7-7.20.8690.2984.355226133513270.34299.4
7.2-7.50.9130.2635.848624175117420.29399.5
7.5-7.80.9470.2157.78953147714740.23599.8
7.8-80.9520.1948.347918578540.21499.6
8-90.9740.13711.319834332933120.1599.5
9-100.9820.1114.412997213021300.12100
10-200.9850.09116.5329368515951510.199.8
200.9780.08216.9841548367700.09192.1

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFD, 4WFC, 4WFD, 4OO1, 2VNU, 2HBJ, 4WP8

4ifd

4wfc

4wfd

4oo1

2vnu

2hbj

4wp8


Resolution: 4.6→59.09 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 2306 5.74 %Random selection
Rwork0.2713 38175 --
obs0.2773 40199 69.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 484.78 Å2 / Biso mean: 341.334 Å2 / Biso min: 276.25 Å2
Refinement stepCycle: final / Resolution: 4.6→59.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30801 352 10 0 31163
Biso mean--403.25 --
Num. residues----3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01331731
X-RAY DIFFRACTIONf_angle_d0.9943110
X-RAY DIFFRACTIONf_chiral_restr0.0535054
X-RAY DIFFRACTIONf_plane_restr0.0065513
X-RAY DIFFRACTIONf_dihedral_angle_d11.7511848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.6021-4.71720.5182500.517893198123
4.7172-4.84460.4083460.471689393922
4.8446-4.98710.4133720.4171371144333
4.9871-5.1480.4166920.40791741183343
5.148-5.33190.3953920.38381747183943
5.3319-5.54520.33051040.35591971207548
5.5452-5.79740.36921500.35352852300270
5.7974-6.10270.33881680.3323185335377
6.1027-6.48470.37421860.32683623380989
6.4847-6.98460.31972050.333874407993
6.9846-7.68610.32392050.30873890409595
7.6861-8.79520.26522060.26953946415295
8.7952-11.06910.26062110.22563992420395
11.0691-59.09840.26172200.2474159437994
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.221.2945-0.05253.34110.01161.3659-0.5687-0.394-0.5945-0.18990.231-0.3756-0.8246-0.556502.82750.260.11713.81840.14984.0118118.7537-51.05149.891
23.46891.0281-1.67562.6137-0.21761.9348-0.65720.1322-0.3974-0.1663-0.3839-0.38290.7386-0.2113-03.3941-0.1183-0.10732.8934-0.31823.9709102.4405-78.787650.0408
31.071-0.4571-0.0021-0.07240.22341.0751.2772.1301-1.0312-1.2479-2.21380.24150.4321-1.8335-1.78773.81321.3986-0.32638.2185-0.97794.101560.6746-46.918151.634
40.6463-0.64740.15590.96460.65461.15370.3488-1.2262-1.93162.2418-1.7511-0.71780.51931.687-0.42983.714-1.68450.22544.42731.16145.2852105.7613-67.891487.8317
51.6305-0.06730.22430.0482-0.08210.1196-0.50070.40682.10340.90740.7710.83960.58322.59580.74043.27870.0407-0.03436.0719-1.62583.8619112.4201-20.442286.0857
60.12680.35850.39860.32070.53640.69450.8787-0.26841.27920.17982.6396-0.3189-0.1355-1.16191.38064.9107-0.40890.96192.62990.79235.5132105.9967-93.2772.5389
70.3698-0.0895-0.32050.02560.08260.28020.0857-0.2908-0.10980.28420.28910.1414-0.346-0.70820.16075.74430.80870.12453.5008-1.17137.56142.5912-56.227544.5386
80.2537-0.0869-0.12220.09850.05541.5870.86681.1706-0.4607-1.8815-0.92052.56990.0795-1.21831.22194.611-0.558-1.84456.10630.70296.539640.6134-50.092674.0655
90.705-0.91291.276-0.3818-0.93220.4511.21120.4067-0.6578-1.7127-0.16870.56091.7079-0.6451-04.4115-0.19140.00723.517-0.23654.181672.2833-53.6536118.664
10-0.4731-1.19240.3282.08050.32623.1111-0.3388-0.0568-0.3454-0.04540.4279-0.05070.1250.108704.4977-0.2922-0.52414.31290.09843.9494107.5917-36.1458114.0286
112.0174-3.55450.13193.0430.52914.11260.94560.05081.44450.1674-1.14620.4133-1.4304-0.4281-04.2564-0.00950.39683.38440.12963.9992117.6527-1.670929.3872
123.35842.3257-2.05441.6806-2.62672.42740.0402-0.0491-0.82950.45680.0298-0.8503-0.9365-0.0580.00064.0705-0.1337-0.26323.4582-0.013.9778131.9442-62.9144-5.6008
131.2166-0.4569-0.00550.82960.41830.77840.1332-0.0595-1.02920.42-0.23442.1237-0.69720.682-0.00456.9353.15122.54258.512.15924.827484.5625-48.7656144.7401
141.95822.5069-2.66764.4388-4.88085.023-0.42891.2176-0.89550.36962.9993-0.6524-2.05622.61471.75436.4336-1.5999-0.58322.32870.20294.621766.6998-33.4146155.567
150.19620.10530.00880.6966-0.62680.8503-1.4689-1.2632-0.07660.8147-0.75650.9267-0.3061-2.4496-6.13627.0986-4.84180.08096.2792-0.0474.996273.8044-41.0603148.5481
162.5385-4.19580.44946.7597-0.10460.16411.05392.27640.7447-0.1149-0.1456-1.36141.1346-0.24340.11737.374-1.0937-1.18654.40070.09542.612992.0381-36.4892156.0318
171.0072-1.02370.30670.6349-0.14950.1374-1.0122-1.35611.18050.8609-2.03380.50592.0190.6174-0.52974.06321.32140.4965.72810.29664.5849127.7182-70.369577.3318
180.2152-0.0930.13630.0412-0.05490.08650.4770.1944-0.00860.04570.56470.58051.0071-1.2117-0.20785.3490.81310.41935.4838-1.86715.4358113.8331-46.8619-5.2241
190.36210.2575-0.6140.2527-0.46921.0877-0.18370.48440.79990.1023-0.0125-0.1016-0.0158-0.16910.27716.85591.27231.45393.57441.12644.2062105.5525-54.73335.3191
200.00570.068-0.0548-0.009-0.04820.04470.43422.01570.7639-1.1346-0.77841.0852-1.06991.139304.8108-0.52120.0143.9411-0.87415.508397.0735-50.5771102.16
213.10261.85940.13741.0211-0.00740.9265-0.9529-2.52942.1953-0.72022.34323.0816-0.50910.905-0.18977.7648-0.6921-0.92143.40781.06163.924965.9332-33.3942144.9312
220.51370.47990.79570.59570.79331.2329-0.15760.1384-1.87720.7223-0.7138-0.89450.3236-0.4216-0.51125.11852.1990.67645.9502-0.35014.706844.0764-45.2821161.2633
235.3652-2.8027-3.03541.531.71061.8839-3.12740.60491.9417-1.1473-1.60223.11040.8806-0.0384-6.86083.70472.4401-0.12147.54290.84025.1258.5405-41.9191144.3483
242.171-1.96353.3771.3409-1.72582.0471.37541.26130.4818-1.322-1.43750.42490.94551.58920.00334.04510.34670.16294.29930.42823.7195113.0201-31.95737.4749
25-0.2353-0.0568-0.31870.09570.03810.10981.89871.75181.9976-3.84260.7190.46920.54583.61431.66537.13510.9917-0.02993.5808-0.12565.5691136.0993-24.9276-0.6874
266.957-0.95310.11253.78660.82221.08130.452-0.20120.9702-0.7569-0.87570.34791.0792-0.36410.00013.1759-0.2027-0.36513.98470.49134.1033107.0665-25.755559.4867
273.04032.4152-0.8064-0.1502-2.35780.51010.5506-0.45220.0293-0.0715-0.87590.2398-0.7980.3756-0.0324.7134-0.20110.28943.8266-0.20223.918478.2892-69.666738.5163
285.6571.1223-0.70823.01481.51890.51330.31420.8815-0.1094-1.0185-0.52110.3084-0.2515-0.08370.01012.96590.7515-0.19953.853-0.08313.6475.4585-22.181651.8527
290.4185-0.2195-0.60362.13041.49251.20730.6597-0.814-0.9659-0.8614-0.7848-0.10440.0151-0.6736-03.9575-0.44830.34094.6652-0.12873.356881.183-39.666290.919
301.74090.49491.9720.75531.39822.56282.03780.95020.38761.8341-2.324-0.1512-0.25081.872603.61240.09920.23184.7108-0.39064.642773.7755-17.315786.629
31-0.0984-0.05630.0716-0.01530.0132-0.11560.9466-0.5334-2.42642.31250.92960.03760.03910.78570.91512.8049-0.584-0.17165.0785-0.10086.706860.5101-76.437141.6211
320.47450.257-0.30710.20220.02280.3276-0.23750.9857-1.99911.22293.1116-0.21210.88880.6128-04.2563-0.7713-0.41634.109-0.19163.775558.7912-87.510961.1812
332.72811.89270.53641.67420.49910.12981.2188-0.486-1.78471.2426-1.6127-0.0942-1.3110.0791-0.00013.97610.27690.41264.67030.02734.980876.5465-73.943281.3084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and ((resseq 124:291))chain A
2X-RAY DIFFRACTION2chain DD1 - 222
3X-RAY DIFFRACTION3(chain F and not (resid 5:21))F21 - 250
4X-RAY DIFFRACTION4chain 'G' and ((resseq 62:150))G62 - 150
5X-RAY DIFFRACTION5chain 'H' and ((resseq 53:102))H53 - 102
6X-RAY DIFFRACTION6chain G and resid 3:61G3 - 61
7X-RAY DIFFRACTION7chain 'K' and ((resseq 563:566))K0
8X-RAY DIFFRACTION8(chain K and resid 538:562) or (chain I and resid 1:113)K538 - 562
9X-RAY DIFFRACTION8(chain K and resid 538:562) or (chain I and resid 1:113)I1 - 113
10X-RAY DIFFRACTION9chain K and resid 421:537K421 - 537
11X-RAY DIFFRACTION10chain 'K' and ((resseq 125:420))K0
12X-RAY DIFFRACTION11(chain J and resid 491:910) or (chain R and resid -6:-1) or (chain J and resid 1101)J9 - 238
13X-RAY DIFFRACTION11(chain J and resid 9:238) or (chain J and resid 1102)J1102
14X-RAY DIFFRACTION12(chain J and resid 491:910) or (chain R and resid -6:-1) or (chain J and resid 1101)J491 - 910
15X-RAY DIFFRACTION12(chain J and resid 491:910) or (chain R and resid -6:-1) or (chain J and resid 1101)R-6 - -1
16X-RAY DIFFRACTION12(chain J and resid 491:910) or (chain R and resid -6:-1) or (chain J and resid 1101)J1101
17X-RAY DIFFRACTION13chain 'K' and ((resseq 74:106))K74 - 106
18X-RAY DIFFRACTION14chain 'K' and ((resseq 5:26))K5 - 26
19X-RAY DIFFRACTION15chain 'L' and ((resseq 42:69))L42 - 69
20X-RAY DIFFRACTION16chain 'L' and ((resseq 70:117))L70 - 117
21X-RAY DIFFRACTION17chain 'G' and ((resseq 151:238))G0
22X-RAY DIFFRACTION18chain R and resid -9:-7R-9 - -7
23X-RAY DIFFRACTION19chain 'R' and ((resseq -12:-10))R0
24X-RAY DIFFRACTION20chain NN-13 - -8
25X-RAY DIFFRACTION21chain 'L' and resid 2:41L2 - 41
26X-RAY DIFFRACTION22chain 'K' and ((resseq 27:37))K27 - 37
27X-RAY DIFFRACTION23chain 'K' and ((resseq 38:61))K38 - 61
28X-RAY DIFFRACTION24(chain J and resid 249:490)J249 - 490
29X-RAY DIFFRACTION25(chain J and resid 911:1001)J911 - 1001
30X-RAY DIFFRACTION26chain BB1 - 244
31X-RAY DIFFRACTION27chain C or (chain F and resid 5:20)C0
32X-RAY DIFFRACTION28chain E or (chain H and resid 2:17)E0
33X-RAY DIFFRACTION29chain H and resid 103:195H103 - 195
34X-RAY DIFFRACTION30chain 'H' and ((resseq 196:356))H0
35X-RAY DIFFRACTION31chain K and resid 567:596K567 - 596
36X-RAY DIFFRACTION32chain 'K' and ((resseq 597:615))K0
37X-RAY DIFFRACTION33chain 'I' and ((resseq 124:291))I0

+
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