[English] 日本語
Yorodumi
- PDB-2br2: RNase PH core of the archaeal exosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2br2
TitleRNase PH core of the archaeal exosome
Components
  • EXOSOME COMPLEX EXONUCLEASE 1
  • EXOSOME COMPLEX EXONUCLEASE 2
KeywordsHYDROLASE / EXOSOME / RNASE PH / PHOSPHOROLYTIC / EXORIBONUCLEASE / RNA DEGRADATION / ARCHAEAL
Function / homology
Function and homology information


U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / rRNA catabolic process ...U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / rRNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity
Similarity search - Function
Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / 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 / Ribosomal Protein S5; domain 2 ...Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / 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 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorslorentzen, E. / Fribourg, S. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The Archaeal Exosome Core is a Hexameric Ring Structure with Three Catalytic Subunits.
Authors: Lorentzen, E. / Walter, P. / Fribourg, S. / Evguenieva-Hackenberg, E. / Klug, G. / Conti, E.
History
DepositionApr 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
C: EXOSOME COMPLEX EXONUCLEASE 2
D: EXOSOME COMPLEX EXONUCLEASE 1
E: EXOSOME COMPLEX EXONUCLEASE 2
F: EXOSOME COMPLEX EXONUCLEASE 1
G: EXOSOME COMPLEX EXONUCLEASE 2
H: EXOSOME COMPLEX EXONUCLEASE 1
I: EXOSOME COMPLEX EXONUCLEASE 2
J: EXOSOME COMPLEX EXONUCLEASE 1
K: EXOSOME COMPLEX EXONUCLEASE 2
L: EXOSOME COMPLEX EXONUCLEASE 1
M: EXOSOME COMPLEX EXONUCLEASE 2
N: EXOSOME COMPLEX EXONUCLEASE 1
O: EXOSOME COMPLEX EXONUCLEASE 2
P: EXOSOME COMPLEX EXONUCLEASE 1
Q: EXOSOME COMPLEX EXONUCLEASE 2
R: EXOSOME COMPLEX EXONUCLEASE 1
S: EXOSOME COMPLEX EXONUCLEASE 2
T: EXOSOME COMPLEX EXONUCLEASE 1
U: EXOSOME COMPLEX EXONUCLEASE 2
V: EXOSOME COMPLEX EXONUCLEASE 1
W: EXOSOME COMPLEX EXONUCLEASE 2
X: EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)694,54837
Polymers694,08724
Non-polymers46113
Water1,76598
1
A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
C: EXOSOME COMPLEX EXONUCLEASE 2
D: EXOSOME COMPLEX EXONUCLEASE 1
E: EXOSOME COMPLEX EXONUCLEASE 2
F: EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,6289
Polymers173,5226
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: EXOSOME COMPLEX EXONUCLEASE 2
H: EXOSOME COMPLEX EXONUCLEASE 1
I: EXOSOME COMPLEX EXONUCLEASE 2
J: EXOSOME COMPLEX EXONUCLEASE 1
K: EXOSOME COMPLEX EXONUCLEASE 2
L: EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,6289
Polymers173,5226
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
M: EXOSOME COMPLEX EXONUCLEASE 2
N: EXOSOME COMPLEX EXONUCLEASE 1
O: EXOSOME COMPLEX EXONUCLEASE 2
P: EXOSOME COMPLEX EXONUCLEASE 1
Q: EXOSOME COMPLEX EXONUCLEASE 2
R: EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,66310
Polymers173,5226
Non-polymers1424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
S: EXOSOME COMPLEX EXONUCLEASE 2
T: EXOSOME COMPLEX EXONUCLEASE 1
U: EXOSOME COMPLEX EXONUCLEASE 2
V: EXOSOME COMPLEX EXONUCLEASE 1
W: EXOSOME COMPLEX EXONUCLEASE 2
X: EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,6289
Polymers173,5226
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)206.880, 212.720, 434.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
91Q
101S
111U
121W
12B
22D
32F
42H
52J
62L
72N
82P
92R
102T
112V
122X
13D
23L
33P
43R
53T

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPROAA1 - 741 - 74
211METMETPROPROCC1 - 741 - 74
311METMETPROPROEE1 - 741 - 74
411METMETPROPROGG1 - 741 - 74
511METMETPROPROII1 - 741 - 74
611METMETPROPROKK1 - 741 - 74
711METMETPROPROMM1 - 741 - 74
811METMETPROPROOO1 - 741 - 74
911METMETPROPROQQ1 - 741 - 74
1011METMETPROPROSS1 - 741 - 74
1111METMETPROPROUU1 - 741 - 74
1211METMETPROPROWW1 - 741 - 74
121GLYGLYSERSERAA82 - 12182 - 121
221GLYGLYSERSERCC82 - 12182 - 121
321GLYGLYSERSEREE82 - 12182 - 121
421GLYGLYSERSERGG82 - 12182 - 121
521GLYGLYSERSERII82 - 12182 - 121
621GLYGLYSERSERKK82 - 12182 - 121
721GLYGLYSERSERMM82 - 12182 - 121
821GLYGLYSERSEROO82 - 12182 - 121
921GLYGLYSERSERQQ82 - 12182 - 121
1021GLYGLYSERSERSS82 - 12182 - 121
1121GLYGLYSERSERUU82 - 12182 - 121
1221GLYGLYSERSERWW82 - 12182 - 121
131ALAALAILEILEAA123 - 131123 - 131
231ALAALAILEILECC123 - 131123 - 131
331ALAALAILEILEEE123 - 131123 - 131
431ALAALAILEILEGG123 - 131123 - 131
531ALAALAILEILEII123 - 131123 - 131
631ALAALAILEILEKK123 - 131123 - 131
731ALAALAILEILEMM123 - 131123 - 131
831ALAALAILEILEOO123 - 131123 - 131
931ALAALAILEILEQQ123 - 131123 - 131
1031ALAALAILEILESS123 - 131123 - 131
1131ALAALAILEILEUU123 - 131123 - 131
1231ALAALAILEILEWW123 - 131123 - 131
141LYSLYSALAALAAA135 - 203135 - 203
241LYSLYSALAALACC135 - 203135 - 203
341LYSLYSALAALAEE135 - 203135 - 203
441LYSLYSALAALAGG135 - 203135 - 203
541LYSLYSALAALAII135 - 203135 - 203
641LYSLYSALAALAKK135 - 203135 - 203
741LYSLYSALAALAMM135 - 203135 - 203
841LYSLYSALAALAOO135 - 203135 - 203
941LYSLYSALAALAQQ135 - 203135 - 203
1041LYSLYSALAALASS135 - 203135 - 203
1141LYSLYSALAALAUU135 - 203135 - 203
1241LYSLYSALAALAWW135 - 203135 - 203
151VALVALPROPROAA205 - 231205 - 231
251VALVALPROPROCC205 - 231205 - 231
351VALVALPROPROEE205 - 231205 - 231
451VALVALPROPROGG205 - 231205 - 231
551VALVALPROPROII205 - 231205 - 231
651VALVALPROPROKK205 - 231205 - 231
751VALVALPROPROMM205 - 231205 - 231
851VALVALPROPROOO205 - 231205 - 231
951VALVALPROPROQQ205 - 231205 - 231
1051VALVALPROPROSS205 - 231205 - 231
1151VALVALPROPROUU205 - 231205 - 231
1251VALVALPROPROWW205 - 231205 - 231
161LEULEUGLYGLYAA233 - 242233 - 242
261LEULEUGLYGLYCC233 - 242233 - 242
361LEULEUGLYGLYEE233 - 242233 - 242
461LEULEUGLYGLYGG233 - 242233 - 242
561LEULEUGLYGLYII233 - 242233 - 242
661LEULEUGLYGLYKK233 - 242233 - 242
761LEULEUGLYGLYMM233 - 242233 - 242
861LEULEUGLYGLYOO233 - 242233 - 242
961LEULEUGLYGLYQQ233 - 242233 - 242
1061LEULEUGLYGLYSS233 - 242233 - 242
1161LEULEUGLYGLYUU233 - 242233 - 242
1261LEULEUGLYGLYWW233 - 242233 - 242
171GLYGLYLEULEUAA244 - 266244 - 266
271GLYGLYLEULEUCC244 - 266244 - 266
371GLYGLYLEULEUEE244 - 266244 - 266
471GLYGLYLEULEUGG244 - 266244 - 266
571GLYGLYLEULEUII244 - 266244 - 266
671GLYGLYLEULEUKK244 - 266244 - 266
771GLYGLYLEULEUMM244 - 266244 - 266
871GLYGLYLEULEUOO244 - 266244 - 266
971GLYGLYLEULEUQQ244 - 266244 - 266
1071GLYGLYLEULEUSS244 - 266244 - 266
1171GLYGLYLEULEUUU244 - 266244 - 266
1271GLYGLYLEULEUWW244 - 266244 - 266
181GLUGLUILEILEAA268 - 275268 - 275
281GLUGLUILEILECC268 - 275268 - 275
381GLUGLUILEILEEE268 - 275268 - 275
481GLUGLUILEILEGG268 - 275268 - 275
581GLUGLUILEILEII268 - 275268 - 275
681GLUGLUILEILEKK268 - 275268 - 275
781GLUGLUILEILEMM268 - 275268 - 275
881GLUGLUILEILEOO268 - 275268 - 275
981GLUGLUILEILEQQ268 - 275268 - 275
1081GLUGLUILEILESS268 - 275268 - 275
1181GLUGLUILEILEUU268 - 275268 - 275
1281GLUGLUILEILEWW268 - 275268 - 275
112ARGARGASPASPBB19 - 18219 - 182
212ARGARGASPASPDD19 - 18219 - 182
312ARGARGASPASPFF19 - 18219 - 182
412ARGARGASPASPHH19 - 18219 - 182
512ARGARGASPASPJJ19 - 18219 - 182
612ARGARGASPASPLL19 - 18219 - 182
712ARGARGASPASPNN19 - 18219 - 182
812ARGARGASPASPPP19 - 18219 - 182
912ARGARGASPASPRR19 - 18219 - 182
1012ARGARGASPASPTT19 - 18219 - 182
1112ARGARGASPASPVV19 - 18219 - 182
1212ARGARGASPASPXX19 - 18219 - 182
122TRPTRPARGARGBB184 - 233184 - 233
222TRPTRPARGARGDD184 - 233184 - 233
322TRPTRPARGARGFF184 - 233184 - 233
422TRPTRPARGARGHH184 - 233184 - 233
522TRPTRPARGARGJJ184 - 233184 - 233
622TRPTRPARGARGLL184 - 233184 - 233
722TRPTRPARGARGNN184 - 233184 - 233
822TRPTRPARGARGPP184 - 233184 - 233
922TRPTRPARGARGRR184 - 233184 - 233
1022TRPTRPARGARGTT184 - 233184 - 233
1122TRPTRPARGARGVV184 - 233184 - 233
1222TRPTRPARGARGXX184 - 233184 - 233
132ALAALAVALVALBB235 - 248235 - 248
232ALAALAVALVALDD235 - 248235 - 248
332ALAALAVALVALFF235 - 248235 - 248
432ALAALAVALVALHH235 - 248235 - 248
532ALAALAVALVALJJ235 - 248235 - 248
632ALAALAVALVALLL235 - 248235 - 248
732ALAALAVALVALNN235 - 248235 - 248
832ALAALAVALVALPP235 - 248235 - 248
932ALAALAVALVALRR235 - 248235 - 248
1032ALAALAVALVALTT235 - 248235 - 248
1132ALAALAVALVALVV235 - 248235 - 248
1232ALAALAVALVALXX235 - 248235 - 248
113GLUGLULYSLYSDD8 - 188 - 18
213GLUGLULYSLYSLL8 - 188 - 18
313GLUGLULYSLYSPP8 - 188 - 18
413GLUGLULYSLYSRR8 - 188 - 18
513GLUGLULYSLYSTT8 - 188 - 18

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
EXOSOME COMPLEX EXONUCLEASE 2 / EXOSOME COMPLEX EXONUCLEASE RRP41-RRP42


Mass: 30227.625 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC0, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein
EXOSOME COMPLEX EXONUCLEASE 1


Mass: 27612.936 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63 %
Crystal growpH: 6.5 / Details: 50 MM MES, 2.4 M SODIUM MALONATE, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.951
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 2.79→220 Å / Num. obs: 233146 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.7
Reflection shellResolution: 2.79→3.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYR

1oyr


Resolution: 2.8→218.22 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.892 / SU B: 27.552 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 7031 3 %RANDOM
Rwork0.215 ---
obs0.216 226114 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→218.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46176 0 13 98 46287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02246834
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.99763463
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75255998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9724.9211839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.239158525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.115287
X-RAY DIFFRACTIONr_chiral_restr0.0820.27605
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0234199
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.220459
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.231626
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.21789
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.2161
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.461.530811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77248633
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.148317644
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0444.514830
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1837tight positional0.030.05
12C1837tight positional0.040.05
13E1837tight positional0.030.05
14G1837tight positional0.030.05
15I1837tight positional0.030.05
16K1837tight positional0.040.05
17M1837tight positional0.030.05
18O1837tight positional0.040.05
19Q1837tight positional0.030.05
110S1837tight positional0.030.05
111U1837tight positional0.030.05
112W1837tight positional0.030.05
21B1757tight positional0.030.05
22D1757tight positional0.030.05
23F1757tight positional0.030.05
24H1757tight positional0.030.05
25J1757tight positional0.030.05
26L1757tight positional0.040.05
27N1757tight positional0.030.05
28P1757tight positional0.030.05
29R1757tight positional0.030.05
210T1757tight positional0.030.05
211V1757tight positional0.030.05
212X1757tight positional0.030.05
31D69tight positional0.040.05
32L69tight positional0.040.05
33P69tight positional0.040.05
34R69tight positional0.030.05
35T69tight positional0.030.05
11A1837tight thermal0.050.5
12C1837tight thermal0.050.5
13E1837tight thermal0.050.5
14G1837tight thermal0.050.5
15I1837tight thermal0.050.5
16K1837tight thermal0.060.5
17M1837tight thermal0.050.5
18O1837tight thermal0.060.5
19Q1837tight thermal0.050.5
110S1837tight thermal0.050.5
111U1837tight thermal0.050.5
112W1837tight thermal0.050.5
21B1757tight thermal0.050.5
22D1757tight thermal0.050.5
23F1757tight thermal0.050.5
24H1757tight thermal0.050.5
25J1757tight thermal0.050.5
26L1757tight thermal0.060.5
27N1757tight thermal0.050.5
28P1757tight thermal0.050.5
29R1757tight thermal0.060.5
210T1757tight thermal0.050.5
211V1757tight thermal0.050.5
212X1757tight thermal0.050.5
31D69tight thermal0.070.5
32L69tight thermal0.040.5
33P69tight thermal0.050.5
34R69tight thermal0.060.5
35T69tight thermal0.050.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 516
Rwork0.342 16231

+
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://pdbjlvh1.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