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- PDB-9c98: Yeast 20S proteasome soaked with isolated TMC-86A -

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Basic information

Entry
Database: PDB / ID: 9c98
TitleYeast 20S proteasome soaked with isolated TMC-86A
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / 3-deoxy-7-phosphoheptulonate synthase ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / chorismate biosynthetic process / proteasome endopeptidase complex / Ub-specific processing proteases / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / aromatic amino acid family biosynthetic process / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / amino acid biosynthetic process / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / endoplasmic reticulum membrane / mitochondrion / metal ion binding / nucleus / cytosol
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...DAHP synthetase, class II / Class-II DAHP synthetase family / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Phospho-2-dehydro-3-deoxyheptonate aldolase / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 ...: / Phospho-2-dehydro-3-deoxyheptonate aldolase / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsMeneghello, R. / Rustiguel, J.K.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Other private1709-19681
Sao Paulo Research Foundation (FAPESP)2014/10753-9 Brazil
Sao Paulo Research Foundation (FAPESP)2019/17721-9 Brazil
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: High-throughput protein crystallography to empower natural product-based drug discovery.
Authors: Meneghello, R. / Rustiguel, J.K. / de Araujo, E.A. / de Felicio, R. / Fernandes, A.Z.N. / Ferreira, E.L.F. / Gubiani, J.R. / Takeda, A.A.S. / Araujo, A. / de Lima Silva, C.C. / Bertonha, A.F. ...Authors: Meneghello, R. / Rustiguel, J.K. / de Araujo, E.A. / de Felicio, R. / Fernandes, A.Z.N. / Ferreira, E.L.F. / Gubiani, J.R. / Takeda, A.A.S. / Araujo, A. / de Lima Silva, C.C. / Bertonha, A.F. / Urano, R.P.M. / Trindade, D.M. / Cunha, T.M. / Cardoso, A.C. / Berlinck, R.G.S. / Nascimento, A.F.Z. / Trivella, D.B.B.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Probable proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Probable proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)737,276115
Polymers728,27828
Non-polymers8,99987
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.315, 298.278, 144.573
Angle α, β, γ (deg.)90.000, 108.795, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "O"
d_1ens_2chain "B"
d_2ens_2(chain "P" and (resid 1 through 217 or resid 221 through 246))
d_1ens_3chain "C"
d_2ens_3chain "Q"
d_1ens_4(chain "D" and resid 0 through 243)
d_2ens_4(chain "R" and (resid 0 through 117 or resid 123...
d_1ens_5(chain "E" and (resid 3 through 201 or (resid 202...
d_2ens_5(chain "S" and resid 3 through 233)
d_1ens_6(chain "F" and (resid 1 through 177 or (resid 178...
d_2ens_6chain "T"
d_1ens_7chain "G"
d_2ens_7(chain "U" and resid 2 through 242)
d_1ens_8chain "H"
d_2ens_8chain "V"
d_1ens_9chain "I"
d_2ens_9chain "W"
d_1ens_10chain "J"
d_2ens_10chain "X"
d_1ens_11chain "K"
d_2ens_11chain "Y"
d_1ens_12chain "L"
d_2ens_12chain "Z"
d_1ens_13chain "M"
d_2ens_13chain "a"
d_1ens_14chain "N"
d_2ens_14chain "b"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1THRTHRLEULEUAA2 - 2502 - 250
d_21ens_1THRTHRLEULEUOH2 - 2502 - 250
d_11ens_2GLYGLYLYSLYSBB1 - 2462 - 247
d_21ens_2GLYGLYLYSLYSPI1 - 2172 - 218
d_22ens_2ASPASPLYSLYSPI221 - 246222 - 247
d_11ens_3GLYGLYGLNGLNCC1 - 2413 - 243
d_21ens_3GLYGLYGLNGLNQJ1 - 2413 - 243
d_11ens_4TYRTYRSERSERDD0 - 2438 - 251
d_21ens_4TYRTYRGLUGLURK0 - 1178 - 125
d_22ens_4GLUGLUSERSERRK123 - 243131 - 251
d_11ens_5ASNASNILEILEEE3 - 2334 - 234
d_21ens_5ASNASNILEILESL3 - 2334 - 234
d_11ens_6GLYGLYASNASNFF1 - 2444 - 247
d_21ens_6GLYGLYASNASNTM1 - 2444 - 247
d_11ens_7GLYGLYGLNGLNGG2 - 24211 - 251
d_21ens_7GLYGLYGLNGLNUN2 - 24211 - 251
d_11ens_8THRTHRCYSCYSHO1 - 2211 - 221
d_12ens_8LIGLIGLIGLIGHCA301
d_21ens_8THRTHRCYSCYSVV1 - 2211 - 221
d_22ens_8LIGLIGLIGLIGVFA301
d_11ens_9SERSERASPASPIP1 - 2042 - 205
d_21ens_9SERSERASPASPWW1 - 2042 - 205
d_11ens_10METMETPHEPHEJQ1 - 1951 - 195
d_21ens_10METMETPHEPHEXX1 - 1951 - 195
d_11ens_11THRTHRGLYGLYKR1 - 2121 - 212
d_12ens_11LIGLIGLIGLIGKDA301
d_21ens_11THRTHRGLYGLYYY1 - 2121 - 212
d_22ens_11LIGLIGLIGLIGYGA301
d_11ens_12GLNGLNASPASPLS1 - 2221 - 222
d_21ens_12GLNGLNASPASPZZ1 - 2221 - 222
d_11ens_13THRTHRILEILEMT1 - 2331 - 233
d_21ens_13THRTHRILEILEaAA1 - 2331 - 233
d_11ens_14THRTHRLEULEUNU1 - 1961 - 196
d_12ens_14LIGLIGLIGLIGNEA201
d_21ens_14THRTHRLEULEUbBA1 - 1961 - 196
d_22ens_14LIGLIGLIGLIGbHA201

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10
ens_11
ens_12
ens_13
ens_14

NCS oper:
IDCodeMatrixVector
1given(-0.996619302846, -0.01171560528, -0.0813185697552), (-0.00305199745579, -0.983818193993, 0.179143647615), (-0.0821014646985, 0.178786201263, 0.980456446627)-67.0891679194, 9.07309496217, -3.34774275793
2given(-0.996228857611, -0.0192999740187, -0.0845906275337), (0.00404623703122, -0.984219757218, 0.176904204213), (-0.0866700134392, 0.17589479954, 0.98058621664)-66.8576549522, 9.36811298091, -3.43157532632
3given(-0.996816828438, -0.000271475533928, -0.0797253839364), (-0.0130688034428, -0.985911223524, 0.166758105371), (-0.0786474215683, 0.167269201084, 0.982769351094)-67.8263218392, 8.64816137786, -2.67083845195
4given(-0.996516409968, -0.0134643548944, -0.0823028299165), (-0.00186014266526, -0.983046998036, 0.183344319577), (-0.0833761628659, 0.182858718138, 0.979597419692)-67.114366132, 9.03040273983, -3.7539334315
5given(-0.996315907801, -0.0110398944148, -0.0850454736853), (-0.00482989734366, -0.982882111719, 0.184172274118), (-0.0856229172283, 0.183904527387, 0.979207761842)-67.3055806558, 9.13866179639, -3.88331573277
6given(-0.996525747747, -0.00703322101498, -0.0829877574023), (-0.00835559805547, -0.98295792453, 0.183640688805), (-0.0828650593293, 0.183696087073, 0.979484113979)-67.2924050905, 9.17442871252, -3.75359667749
7given(-0.996442115886, -0.0121280779118, -0.0834027542416), (-0.00389445860366, -0.981908964816, 0.189313544168), (-0.0841899214936, 0.18896479709, 0.978368214212)-67.075873772, 9.57307803973, -4.05929151539
8given(-0.996351834005, -0.00729348127169, -0.085028395297), (-0.00809500847485, -0.983771841402, 0.179241275669), (-0.0849558339, 0.179275679322, 0.98012383763)-67.3750691809, 8.84812091713, -3.6294643916
9given(-0.9963301553, -0.00947482614126, -0.0850673222141), (-0.00607666326586, -0.983516580505, 0.180715826743), (-0.0853773728961, 0.180569553196, 0.979849652067)-67.3207862844, 9.00099535695, -3.67569556008
10given(-0.996537309547, -0.00871493372044, -0.0826888179331), (-0.00667596385864, -0.982894592403, 0.18404796041), (-0.082878357775, 0.183962686854, 0.979432952099)-67.3364986161, 8.9147745138, -3.679090904
11given(-0.996384699575, -0.00711377097411, -0.0846576914129), (-0.00838317246904, -0.98339199459, 0.181300599546), (-0.0845414269585, 0.181354843439, 0.979777101125)-67.3525092591, 8.8575184324, -3.73841777903
12given(-0.996406411153, -0.00785861630997, -0.0843356743239), (-0.00757922452271, -0.983419936511, 0.18118439179), (-0.0843612421057, 0.181172488592, 0.979826367377)-67.3502489361, 8.91966650327, -3.72508660978
13given(-0.99638233034, -0.00890104494793, -0.0845164077918), (-0.00654878066426, -0.983500889252, 0.180784718138), (-0.0847311351216, 0.180684178166, 0.979884616933)-67.3319206692, 8.98533696392, -3.72367662094
14given(-0.996438055936, -0.00842231683588, -0.0839062885696), (-0.00701321133944, -0.983276276152, 0.181985108246), (-0.0840357992116, 0.181925340005, 0.979714833569)-67.2958152673, 9.08101051033, -3.67690644367

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Components

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Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639
#2: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303
#4: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379
#5: Protein Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302
#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243

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Protein , 1 types, 2 molecules FT

#6: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31443.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21242

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25451
#10: Protein Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22141
#11: Protein Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23724
#13: Protein Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30657
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 4 types, 424 molecules

#15: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: SO4
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-A1AU6 / N-[(2S)-3-hydroxy-1-{[(4S)-1-hydroxy-2-(hydroxymethyl)-6-methyl-3-oxoheptan-4-yl]amino}-1-oxopropan-2-yl]butanamide


Mass: 346.419 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H30N2O6 / Feature type: SUBJECT OF INVESTIGATION
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: MES 100 mM pH 6.9, MPD 25% and magnesium acetate 20 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 3.04→48.54 Å / Num. obs: 240562 / % possible obs: 99.91 % / Redundancy: 6.8 % / Biso Wilson estimate: 58.03 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.327 / Rpim(I) all: 0.1349 / Rrim(I) all: 0.3542 / Net I/σ(I): 5.48
Reflection shellResolution: 3.04→3.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 3.273 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 7289 / CC1/2: 0.262 / Rpim(I) all: 1.35 / Rrim(I) all: 3.545 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→48.54 Å / SU ML: 0.3974 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 8947 4.98 %
Rwork0.1744 170763 -
obs0.1767 179710 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.44 Å2
Refinement stepCycle: LAST / Resolution: 3.04→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49387 0 501 337 50225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002750698
X-RAY DIFFRACTIONf_angle_d0.591868596
X-RAY DIFFRACTIONf_chiral_restr0.04477660
X-RAY DIFFRACTIONf_plane_restr0.00438791
X-RAY DIFFRACTIONf_dihedral_angle_d13.116718688
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.72057426559
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.776461379973
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS1.08302857884
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS0.713729261746
ens_5d_2EEX-RAY DIFFRACTIONTorsion NCS0.68348905703
ens_6d_2FFX-RAY DIFFRACTIONTorsion NCS0.660506988661
ens_7d_2GGX-RAY DIFFRACTIONTorsion NCS0.694960703021
ens_8d_2OHX-RAY DIFFRACTIONTorsion NCS0.546255634241
ens_9d_2PIX-RAY DIFFRACTIONTorsion NCS0.515527895203
ens_10d_2QJX-RAY DIFFRACTIONTorsion NCS0.713792164666
ens_11d_2RKX-RAY DIFFRACTIONTorsion NCS0.617925263198
ens_12d_2SLX-RAY DIFFRACTIONTorsion NCS0.588264076539
ens_13d_2TMX-RAY DIFFRACTIONTorsion NCS0.520386406819
ens_14d_2UNX-RAY DIFFRACTIONTorsion NCS0.47628409838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.070.38963120.32775724X-RAY DIFFRACTION99.88
3.07-3.110.33562850.29685661X-RAY DIFFRACTION99.93
3.11-3.150.33832810.27895701X-RAY DIFFRACTION99.85
3.15-3.190.30722940.25385678X-RAY DIFFRACTION99.9
3.19-3.230.32033160.24065653X-RAY DIFFRACTION99.92
3.23-3.270.28592910.23475726X-RAY DIFFRACTION99.9
3.27-3.320.27522930.22425617X-RAY DIFFRACTION99.9
3.32-3.370.26072990.21935719X-RAY DIFFRACTION99.9
3.37-3.420.2723030.21765672X-RAY DIFFRACTION99.88
3.42-3.480.27263120.21835638X-RAY DIFFRACTION99.97
3.48-3.540.26942930.20445697X-RAY DIFFRACTION99.98
3.54-3.60.25272800.18695723X-RAY DIFFRACTION99.98
3.6-3.670.23222930.18445692X-RAY DIFFRACTION99.98
3.67-3.750.23493180.17735625X-RAY DIFFRACTION99.98
3.75-3.830.22613060.1695691X-RAY DIFFRACTION99.93
3.83-3.920.2142820.15885725X-RAY DIFFRACTION99.98
3.92-4.020.23332730.16365708X-RAY DIFFRACTION99.98
4.02-4.130.20222940.15695687X-RAY DIFFRACTION99.98
4.13-4.250.21123110.15545697X-RAY DIFFRACTION99.97
4.25-4.380.19263010.14645685X-RAY DIFFRACTION100
4.38-4.540.1713070.14235699X-RAY DIFFRACTION99.98
4.54-4.720.17882980.13775663X-RAY DIFFRACTION99.95
4.72-4.940.17873040.14145688X-RAY DIFFRACTION99.9
4.94-5.20.20123220.15375681X-RAY DIFFRACTION99.98
5.2-5.520.21152990.16045706X-RAY DIFFRACTION99.98
5.52-5.950.21292820.17615707X-RAY DIFFRACTION99.87
5.95-6.540.22462750.17515731X-RAY DIFFRACTION99.54
6.55-7.490.17893070.15495683X-RAY DIFFRACTION99.97
7.49-9.420.15753070.12185736X-RAY DIFFRACTION99.98
9.42-48.540.17163090.15015750X-RAY DIFFRACTION99.49

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