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- PDB-6z46: Structure of the S. acidocaldarius 20S proteasome (Saci0613/Saci0662) -

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Basic information

Entry
Database: PDB / ID: 6z46
TitleStructure of the S. acidocaldarius 20S proteasome (Saci0613/Saci0662)
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE / 20S / proteasome / archaea / sulfolobus acidocaldarius
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Peptidase T1A, proteasome beta-subunit / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit ...Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Peptidase T1A, proteasome beta-subunit / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta / Proteasome subunit beta 1 / Proteasome subunit alpha
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.698 Å
AuthorsRobinson, N.P. / Bray, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Isaac Newton Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Science / Year: 2020
Title: The proteasome controls ESCRT-III-mediated cell division in an archaeon.
Authors: Tarrason Risa, G. / Hurtig, F. / Bray, S. / Hafner, A.E. / Harker-Kirschneck, L. / Faull, P. / Davis, C. / Papatziamou, D. / Mutavchiev, D.R. / Fan, C. / Meneguello, L. / Arashiro Pulschen, ...Authors: Tarrason Risa, G. / Hurtig, F. / Bray, S. / Hafner, A.E. / Harker-Kirschneck, L. / Faull, P. / Davis, C. / Papatziamou, D. / Mutavchiev, D.R. / Fan, C. / Meneguello, L. / Arashiro Pulschen, A. / Dey, G. / Culley, S. / Kilkenny, M. / Souza, D.P. / Pellegrini, L. / de Bruin, R.A.M. / Henriques, R. / Snijders, A.P. / Saric, A. / Lindas, A.C. / Robinson, N.P. / Baum, B.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Author supporting evidence / Database references / Category: citation_author / pdbx_audit_support
Item: _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha
H: Proteasome subunit beta
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit alpha
Q: Proteasome subunit alpha
R: Proteasome subunit alpha
S: Proteasome subunit alpha
T: Proteasome subunit alpha
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)677,87628
Polymers677,87628
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100740 Å2
ΔGint-387 kcal/mol
Surface area198270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.287, 193.654, 323.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 42 or resid 48...
21(chain B and (resid 15 through 42 or resid 48...
31(chain C and (resid 15 through 42 or resid 48...
41(chain D and (resid 15 through 42 or resid 48...
51(chain E and (resid 15 through 42 or resid 48...
61(chain F and (resid 15 through 42 or resid 48...
71(chain G and (resid 15 through 42 or resid 48...
81(chain O and (resid 15 through 42 or resid 48...
91(chain P and (resid 15 through 58 or resid 67...
101(chain Q and (resid 15 through 42 or resid 48...
111(chain S and (resid 15 through 42 or resid 48...
121(chain T and (resid 15 through 42 or resid 48...
131(chain U and (resid 15 through 42 or resid 48...
12(chain H and (resid 2 through 8 or resid 12...
22(chain I and (resid 2 through 8 or resid 12...
32(chain J and (resid 2 through 8 or resid 12...
42(chain K and (resid 2 through 8 or resid 12...
52(chain L and (resid 2 through 8 or resid 12...
62(chain M and (resid 2 through 8 or resid 12...
72(chain N and (resid 2 through 8 or resid 12...
82(chain V and (resid 2 through 8 or resid 12...
92(chain W and (resid 2 through 8 or resid 12...
102(chain X and (resid 2 through 8 or resid 12...
112(chain Y and (resid 2 through 8 or resid 12...
122(chain Z and (resid 2 through 8 or resid 12...
132(chain a and (resid 2 through 35 or resid 42...
142(chain b and (resid 2 through 8 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 15 through 42 or resid 48...A15 - 42
121(chain A and (resid 15 through 42 or resid 48...A48 - 58
131(chain A and (resid 15 through 42 or resid 48...A67 - 71
141(chain A and (resid 15 through 42 or resid 48...A190 - 200
151(chain A and (resid 15 through 42 or resid 48...A6 - 230
161(chain A and (resid 15 through 42 or resid 48...A190 - 200
171(chain A and (resid 15 through 42 or resid 48...A217 - 226
211(chain B and (resid 15 through 42 or resid 48...B15 - 42
221(chain B and (resid 15 through 42 or resid 48...B48 - 58
231(chain B and (resid 15 through 42 or resid 48...B67 - 71
241(chain B and (resid 15 through 42 or resid 48...B190 - 200
251(chain B and (resid 15 through 42 or resid 48...B14 - 242
261(chain B and (resid 15 through 42 or resid 48...B190 - 200
271(chain B and (resid 15 through 42 or resid 48...B217 - 226
311(chain C and (resid 15 through 42 or resid 48...C15 - 42
321(chain C and (resid 15 through 42 or resid 48...C48 - 58
331(chain C and (resid 15 through 42 or resid 48...C67 - 71
341(chain C and (resid 15 through 42 or resid 48...C190 - 200
351(chain C and (resid 15 through 42 or resid 48...C15 - 242
361(chain C and (resid 15 through 42 or resid 48...C190 - 200
371(chain C and (resid 15 through 42 or resid 48...C217 - 226
411(chain D and (resid 15 through 42 or resid 48...D15 - 42
421(chain D and (resid 15 through 42 or resid 48...D48 - 58
431(chain D and (resid 15 through 42 or resid 48...D67 - 71
441(chain D and (resid 15 through 42 or resid 48...D78 - 141
451(chain D and (resid 15 through 42 or resid 48...D151 - 182
461(chain D and (resid 15 through 42 or resid 48...D190 - 226
511(chain E and (resid 15 through 42 or resid 48...E15 - 42
521(chain E and (resid 15 through 42 or resid 48...E48 - 58
531(chain E and (resid 15 through 42 or resid 48...E67 - 71
541(chain E and (resid 15 through 42 or resid 48...E190 - 200
551(chain E and (resid 15 through 42 or resid 48...E14 - 241
561(chain E and (resid 15 through 42 or resid 48...E190 - 200
571(chain E and (resid 15 through 42 or resid 48...E217 - 226
611(chain F and (resid 15 through 42 or resid 48...F15 - 42
621(chain F and (resid 15 through 42 or resid 48...F48 - 58
631(chain F and (resid 15 through 42 or resid 48...F67 - 71
641(chain F and (resid 15 through 42 or resid 48...F190 - 200
651(chain F and (resid 15 through 42 or resid 48...F14 - 241
661(chain F and (resid 15 through 42 or resid 48...F190 - 200
671(chain F and (resid 15 through 42 or resid 48...F217 - 226
711(chain G and (resid 15 through 42 or resid 48...G15 - 42
721(chain G and (resid 15 through 42 or resid 48...G48 - 58
731(chain G and (resid 15 through 42 or resid 48...G67 - 71
741(chain G and (resid 15 through 42 or resid 48...G190 - 200
751(chain G and (resid 15 through 42 or resid 48...G15 - 242
761(chain G and (resid 15 through 42 or resid 48...G190 - 200
771(chain G and (resid 15 through 42 or resid 48...G217 - 226
811(chain O and (resid 15 through 42 or resid 48...O15 - 42
821(chain O and (resid 15 through 42 or resid 48...O48 - 58
831(chain O and (resid 15 through 42 or resid 48...O67 - 71
841(chain O and (resid 15 through 42 or resid 48...O78 - 141
851(chain O and (resid 15 through 42 or resid 48...O15 - 237
861(chain O and (resid 15 through 42 or resid 48...O15 - 237
871(chain O and (resid 15 through 42 or resid 48...O192 - 200
881(chain O and (resid 15 through 42 or resid 48...O217 - 226
911(chain P and (resid 15 through 58 or resid 67...P15 - 58
921(chain P and (resid 15 through 58 or resid 67...P67 - 141
931(chain P and (resid 15 through 58 or resid 67...P151 - 182
941(chain P and (resid 15 through 58 or resid 67...P15 - 237
1011(chain Q and (resid 15 through 42 or resid 48...Q15 - 42
1021(chain Q and (resid 15 through 42 or resid 48...Q48 - 58
1031(chain Q and (resid 15 through 42 or resid 48...Q67 - 71
1041(chain Q and (resid 15 through 42 or resid 48...Q78 - 141
1051(chain Q and (resid 15 through 42 or resid 48...Q151 - 200
1061(chain Q and (resid 15 through 42 or resid 48...Q217 - 226
1111(chain S and (resid 15 through 42 or resid 48...S15 - 42
1121(chain S and (resid 15 through 42 or resid 48...S48 - 71
1131(chain S and (resid 15 through 42 or resid 48...S78 - 141
1141(chain S and (resid 15 through 42 or resid 48...S151 - 182
1151(chain S and (resid 15 through 42 or resid 48...S190 - 200
1161(chain S and (resid 15 through 42 or resid 48...S217 - 226
1211(chain T and (resid 15 through 42 or resid 48...T15 - 42
1221(chain T and (resid 15 through 42 or resid 48...T48 - 58
1231(chain T and (resid 15 through 42 or resid 48...T67 - 71
1241(chain T and (resid 15 through 42 or resid 48...T78 - 141
1251(chain T and (resid 15 through 42 or resid 48...T15 - 241
1261(chain T and (resid 15 through 42 or resid 48...T15 - 241
1271(chain T and (resid 15 through 42 or resid 48...T190 - 200
1281(chain T and (resid 15 through 42 or resid 48...T217 - 226
1311(chain U and (resid 15 through 42 or resid 48...U15 - 42
1321(chain U and (resid 15 through 42 or resid 48...U48 - 58
1331(chain U and (resid 15 through 42 or resid 48...U67 - 71
1341(chain U and (resid 15 through 42 or resid 48...U78 - 141
1351(chain U and (resid 15 through 42 or resid 48...U151 - 182
1361(chain U and (resid 15 through 42 or resid 48...U190 - 200
1371(chain U and (resid 15 through 42 or resid 48...U217 - 226
112(chain H and (resid 2 through 8 or resid 12...H2 - 8
122(chain H and (resid 2 through 8 or resid 12...H12 - 35
132(chain H and (resid 2 through 8 or resid 12...H42 - 67
142(chain H and (resid 2 through 8 or resid 12...H75 - 120
152(chain H and (resid 2 through 8 or resid 12...H123 - 139
162(chain H and (resid 2 through 8 or resid 12...H144 - 170
212(chain I and (resid 2 through 8 or resid 12...I2 - 8
222(chain I and (resid 2 through 8 or resid 12...I12 - 35
232(chain I and (resid 2 through 8 or resid 12...I42 - 67
242(chain I and (resid 2 through 8 or resid 12...I75 - 120
252(chain I and (resid 2 through 8 or resid 12...I123 - 139
262(chain I and (resid 2 through 8 or resid 12...I144 - 170
312(chain J and (resid 2 through 8 or resid 12...J2 - 8
322(chain J and (resid 2 through 8 or resid 12...J12 - 35
332(chain J and (resid 2 through 8 or resid 12...J42 - 67
342(chain J and (resid 2 through 8 or resid 12...J123 - 139
352(chain J and (resid 2 through 8 or resid 12...J144 - 170
412(chain K and (resid 2 through 8 or resid 12...K2 - 8
422(chain K and (resid 2 through 8 or resid 12...K12 - 35
432(chain K and (resid 2 through 8 or resid 12...K42 - 67
442(chain K and (resid 2 through 8 or resid 12...K123 - 139
452(chain K and (resid 2 through 8 or resid 12...K144 - 170
512(chain L and (resid 2 through 8 or resid 12...L2 - 8
522(chain L and (resid 2 through 8 or resid 12...L12 - 35
532(chain L and (resid 2 through 8 or resid 12...L42 - 67
542(chain L and (resid 2 through 8 or resid 12...L123 - 139
552(chain L and (resid 2 through 8 or resid 12...L144 - 170
612(chain M and (resid 2 through 8 or resid 12...M2 - 8
622(chain M and (resid 2 through 8 or resid 12...M12 - 35
632(chain M and (resid 2 through 8 or resid 12...M42 - 67
642(chain M and (resid 2 through 8 or resid 12...M123 - 139
652(chain M and (resid 2 through 8 or resid 12...M144 - 170
712(chain N and (resid 2 through 8 or resid 12...N2 - 8
722(chain N and (resid 2 through 8 or resid 12...N12 - 35
732(chain N and (resid 2 through 8 or resid 12...N42 - 67
742(chain N and (resid 2 through 8 or resid 12...N123 - 139
752(chain N and (resid 2 through 8 or resid 12...N144 - 170
812(chain V and (resid 2 through 8 or resid 12...V2 - 8
822(chain V and (resid 2 through 8 or resid 12...V12 - 35
832(chain V and (resid 2 through 8 or resid 12...V42 - 67
842(chain V and (resid 2 through 8 or resid 12...V123 - 139
852(chain V and (resid 2 through 8 or resid 12...V144 - 170
912(chain W and (resid 2 through 8 or resid 12...W2 - 8
922(chain W and (resid 2 through 8 or resid 12...W12 - 67
932(chain W and (resid 2 through 8 or resid 12...W75 - 120
942(chain W and (resid 2 through 8 or resid 12...W123 - 139
952(chain W and (resid 2 through 8 or resid 12...W144 - 170
1012(chain X and (resid 2 through 8 or resid 12...X2 - 8
1022(chain X and (resid 2 through 8 or resid 12...X12 - 35
1032(chain X and (resid 2 through 8 or resid 12...X42 - 67
1042(chain X and (resid 2 through 8 or resid 12...X75 - 120
1052(chain X and (resid 2 through 8 or resid 12...X123 - 139
1062(chain X and (resid 2 through 8 or resid 12...X144 - 170
1112(chain Y and (resid 2 through 8 or resid 12...Y2 - 8
1122(chain Y and (resid 2 through 8 or resid 12...Y12 - 35
1132(chain Y and (resid 2 through 8 or resid 12...Y2 - 185
1142(chain Y and (resid 2 through 8 or resid 12...Y0
1152(chain Y and (resid 2 through 8 or resid 12...Y144 - 170
1212(chain Z and (resid 2 through 8 or resid 12...Z2 - 8
1222(chain Z and (resid 2 through 8 or resid 12...Z12 - 35
1232(chain Z and (resid 2 through 8 or resid 12...Z42 - 67
1242(chain Z and (resid 2 through 8 or resid 12...Z75 - 120
1252(chain Z and (resid 2 through 8 or resid 12...Z123 - 170
1312(chain a and (resid 2 through 35 or resid 42...a2 - 35
1322(chain a and (resid 2 through 35 or resid 42...a42 - 67
1332(chain a and (resid 2 through 35 or resid 42...a75 - 120
1342(chain a and (resid 2 through 35 or resid 42...a123 - 139
1352(chain a and (resid 2 through 35 or resid 42...a144 - 170
1412(chain b and (resid 2 through 8 or resid 12...b2 - 8
1422(chain b and (resid 2 through 8 or resid 12...b12 - 35
1432(chain b and (resid 2 through 8 or resid 12...b42 - 67
1442(chain b and (resid 2 through 8 or resid 12...b123 - 139
1452(chain b and (resid 2 through 8 or resid 12...b144 - 170

NCS ensembles :
ID
1
2

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Components

#1: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 26633.562 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: sulfolobus acidocaldarius proteasome alpha subunit (saci0613)
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: psmA, ATY89_03330, ATZ20_06355 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U3GK31, UniProt: Q4JB24*PLUS, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 21786.170 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: psmB, ATY89_03090, ATZ20_06115 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U3GVH3, UniProt: Q4JAY3*PLUS, proteasome endopeptidase complex

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6, 6% PEG 6000, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 292.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.698→48.19 Å / Num. obs: 73138 / % possible obs: 99.21 % / Redundancy: 1.9779 % / CC1/2: 0.969 / CC star: 0.992 / Net I/σ(I): 5.64
Reflection shellResolution: 3.698→3.83 Å / Num. unique obs: 6972 / CC1/2: 0.555 / CC star: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIX1.14_3260model building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2Q

1j2q


Resolution: 3.698→48.19 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.28
RfactorNum. reflection% reflection
Rfree0.3344 3676 5.03 %
Rwork0.2873 --
obs0.2897 73061 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 289.54 Å2 / Biso mean: 76.9182 Å2 / Biso min: 25.29 Å2
Refinement stepCycle: final / Resolution: 3.698→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41427 0 0 0 41427
Num. residues----5391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9678X-RAY DIFFRACTION3.543TORSIONAL
12B9678X-RAY DIFFRACTION3.543TORSIONAL
13C9678X-RAY DIFFRACTION3.543TORSIONAL
14D9678X-RAY DIFFRACTION3.543TORSIONAL
15E9678X-RAY DIFFRACTION3.543TORSIONAL
16F9678X-RAY DIFFRACTION3.543TORSIONAL
17G9678X-RAY DIFFRACTION3.543TORSIONAL
18O9678X-RAY DIFFRACTION3.543TORSIONAL
19P9678X-RAY DIFFRACTION3.543TORSIONAL
110Q9678X-RAY DIFFRACTION3.543TORSIONAL
111S9678X-RAY DIFFRACTION3.543TORSIONAL
112T9678X-RAY DIFFRACTION3.543TORSIONAL
113U9678X-RAY DIFFRACTION3.543TORSIONAL
21H9559X-RAY DIFFRACTION3.543TORSIONAL
22I9559X-RAY DIFFRACTION3.543TORSIONAL
23J9559X-RAY DIFFRACTION3.543TORSIONAL
24K9559X-RAY DIFFRACTION3.543TORSIONAL
25L9559X-RAY DIFFRACTION3.543TORSIONAL
26M9559X-RAY DIFFRACTION3.543TORSIONAL
27N9559X-RAY DIFFRACTION3.543TORSIONAL
28V9559X-RAY DIFFRACTION3.543TORSIONAL
29W9559X-RAY DIFFRACTION3.543TORSIONAL
210X9559X-RAY DIFFRACTION3.543TORSIONAL
211Y9559X-RAY DIFFRACTION3.543TORSIONAL
212Z9559X-RAY DIFFRACTION3.543TORSIONAL
213a9559X-RAY DIFFRACTION3.543TORSIONAL
214b9559X-RAY DIFFRACTION3.543TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6981-3.74680.42291210.3502240890
3.7468-3.79810.39871380.33852636100
3.7981-3.85230.37381500.33532647100
3.8523-3.90980.44121250.33882625100
3.9098-3.97080.36491320.33542691100
3.9708-4.03590.36831460.32932660100
4.0359-4.10550.38451580.32452625100
4.1055-4.18010.30411530.30262647100
4.1801-4.26040.3281430.29162660100
4.2604-4.34730.32221390.2812668100
4.3473-4.44180.32681460.27922638100
4.4418-4.54510.36671420.28672671100
4.5451-4.65860.37941480.26672646100
4.6586-4.78450.31051620.26732660100
4.7845-4.92510.31991550.27782689100
4.9251-5.08390.32731280.27922650100
5.0839-5.26540.31621180.27952697100
5.2654-5.4760.3631410.29992671100
5.476-5.72480.34741340.30762716100
5.7248-6.02610.3191520.32672100
6.0261-6.40290.3521490.29112687100
6.4029-6.8960.34981480.28672694100
6.896-7.58750.37261170.2632730100
7.5875-8.67990.23861490.2237271799
8.6799-10.91490.22231250.2091278699
10.9149-48.190.35341570.3441279496

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  • 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

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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

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