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- PDB-5l4k: The human 26S proteasome lid -

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Basic information

Entry
Database: PDB / ID: 5l4k
TitleThe human 26S proteasome lid
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • 26S proteasome complex subunit DSS1
KeywordsSTRUCTURAL PROTEIN / proteostasis / AAA-ATPase
Function / homology
Function and homology information


Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / integrator complex / proteasome accessory complex / meiosis I / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex ...Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / integrator complex / proteasome accessory complex / meiosis I / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Somitogenesis / K63-linked deubiquitinase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / Impaired BRCA2 binding to RAD51 / proteasome binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / polyubiquitin modification-dependent protein binding / protein deubiquitination / endopeptidase activator activity / proteasome assembly / mRNA export from nucleus / enzyme regulator activity / regulation of proteasomal protein catabolic process / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / stem cell differentiation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Regulation of RUNX3 expression and activity / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / double-strand break repair via homologous recombination / Vif-mediated degradation of APOBEC3G / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / double-strand break repair via nonhomologous end joining / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / HDR through Homologous Recombination (HRR) / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Metalloprotease DUBs / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / metallopeptidase activity / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / azurophil granule lumen / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / response to ethanol / ubiquitin-dependent protein catabolic process
Similarity search - Function
: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain ...: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 7/8 / DSS1/SEM1 / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN11 C-terminal domain / DSS1_SEM1 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / Proteasome/cyclosome repeat / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / von Willebrand factor type A domain / PCI/PINT associated module / HEAT repeats / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / von Willebrand factor A-like domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 ...26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSchweitzer, A. / Aufderheide, A. / Rudack, T. / Beck, F.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of the human 26S proteasome at a resolution of 3.9 Å.
Authors: Andreas Schweitzer / Antje Aufderheide / Till Rudack / Florian Beck / Günter Pfeifer / Jürgen M Plitzko / Eri Sakata / Klaus Schulten / Friedrich Förster / Wolfgang Baumeister /
Abstract: Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades ...Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Assembly

Deposited unit
W: 26S proteasome non-ATPase regulatory subunit 4
V: 26S proteasome non-ATPase regulatory subunit 14
T: 26S proteasome non-ATPase regulatory subunit 8
Y: 26S proteasome complex subunit DSS1
Z: 26S proteasome non-ATPase regulatory subunit 2
N: 26S proteasome non-ATPase regulatory subunit 1
S: 26S proteasome non-ATPase regulatory subunit 3
P: 26S proteasome non-ATPase regulatory subunit 12
Q: 26S proteasome non-ATPase regulatory subunit 11
R: 26S proteasome non-ATPase regulatory subunit 6
U: 26S proteasome non-ATPase regulatory subunit 7
O: 26S proteasome non-ATPase regulatory subunit 13


Theoretical massNumber of molelcules
Total (without water)616,87312
Polymers616,87312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area49450 Å2
ΔGint-290 kcal/mol
Surface area220080 Å2
MethodPISA

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Components

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26S proteasome non-ATPase regulatory subunit ... , 11 types, 11 molecules WVTZNSPQRUO

#1: Protein 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 40781.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55036
#2: Protein 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 34620.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O00487, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#3: Protein 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 39667.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48556
#5: Protein 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome ...26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 100313.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13200
#6: Protein 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105958.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99460
#7: Protein 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 61066.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43242
#8: Protein 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


Mass: 52979.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00232
#9: Protein 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome ...26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


Mass: 47526.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00231
#10: Protein 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer- ...26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


Mass: 45592.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15008
#11: Protein 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein ...26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


Mass: 37086.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51665
#12: Protein 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome ...26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


Mass: 42995.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNM6

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Protein , 1 types, 1 molecules Y

#4: Protein 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot ...Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60896

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human 26S proteasome lid / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 45 e/Å2 / Film or detector model: OTHER / Num. of grids imaged: 19 / Num. of real images: 40211
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement
EM software
IDNameVersionCategory
1TOM Toolboxparticle selection
4CTFFINDCTF correction
7MDFFmodel fitting
12RELION1.43D reconstruction
13PHENIXmodel refinement
Image processingDetails: Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 688742
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 461402 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementResolution: 3.9→3.9 Å / SU ML: 1.03 / σ(F): 1.57 / Phase error: 46.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.4039 72545 2.49 %
Rwork0.4025 --
obs0.4025 2910189 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0340310
ELECTRON MICROSCOPYf_angle_d2.54254461
ELECTRON MICROSCOPYf_dihedral_angle_d17.76624722
ELECTRON MICROSCOPYf_chiral_restr0.096190
ELECTRON MICROSCOPYf_plane_restr0.0167022
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

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)
11.252-0.36710.1540.8806-0.00611.47610.0675-1.1644-0.4740.8709-0.08790.62830.4958-0.41480.55121.93330.13580.43881.8545-0.22140.3197104.8521340.5149335.533
20.64460.02270.0040.57150.28990.16790.0891-0.53740.09830.02940.0973-1.2166-0.34110.1036-0.01790.5615-0.3945-0.2022-0.16-0.39090.9486181.3667339.0347284.1382
3-0.1402-0.0961-0.26670.7307-0.10380.16070.73430.19111.0317-1.1195-0.5605-0.2179-0.51750.2310.57840.0886-0.9580.7052-3.23872.9049-1.402148.0504346.8379243.7802
40.92480.2131-0.29210.4787-0.3460.4428-0.08831.2585-0.2601-0.98390.58430.38390.3751-0.69870.20890.74011.0668-1.70410.9180.36690.6416102.2255349.8882230.1998
50.1061-0.1258-0.05610.20850.09620.0782-0.23690.17750.5226-0.15990.08310.6786-0.1123-0.3019-0.00142.69560.9289-0.43671.4610.33362.112891.6655384.4199245.1031
60.0506-0.01720.02240.5950.05170.0425-0.3278-0.26730.00130.8182-0.38820.26670.0558-0.3137-1.2922-0.00360.65530.8967-0.06580.09810.567597.1549314.2907304.3314
70.4753-0.0705-0.32160.05050.03270.3477-0.2430.3227-0.50610.0430.00420.46670.6662-0.47650.4201-1.9924-0.73380.95820.31290.4510.477294.4667291.4467286.2832
80.72970.37140.27630.4775-0.41930.25370.53570.1164-0.4831-0.97870.04711.1394-0.1232-1.07280.3168-0.9436-1.0805-1.35522.92760.16262.478367.1482304.2696250.1638
90.1004-0.0099-0.00850.12130.03770.07270.0371-0.437-0.10910.27510.0049-0.01240.03020.01510.01561.6305-0.10141.15732.24580.26091.768780.5023302.1103331.8394
100.0848-0.0872-0.05330.07920.05250.063700.2168-0.0933-0.0809-0.04190.1603-0.0259-0.3175-0.00050.95130.1101-0.0321.1937-0.25351.5935131.8604361.639242.3978
110.2939-0.1599-0.03220.24710.30170.3028-0.09870.8324-0.475-0.3621-0.18410.159-0.1218-0.03430.00012.433-0.7598-0.12593.2502-0.68593.5329128.8382230.9531221.0618
120.7216-0.09920.17941.6316-0.35850.808-0.35980.4774-0.22910.67690.21961.4146-0.0975-0.32561.26070.0955-0.125-0.3783-0.1591-1.1648-1.6931108.9813332.4448270.9597
130.49980.05-0.16420.27510.25870.6934-0.583-1.0583-0.75870.616-0.0177-0.82070.15670.2855-0.28920.8247-0.0999-0.69650.4333-0.6485-0.2247159.3045325.9652321.9276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1(chain O and resseq 1:340 )
2ELECTRON MICROSCOPY2(chain Q and resseq 1:392 )
3ELECTRON MICROSCOPY3(chain R and resseq 1:358 )
4ELECTRON MICROSCOPY4(chain S and resseq 1:466 )
5ELECTRON MICROSCOPY5(chain T and resseq 1:322 )
6ELECTRON MICROSCOPY6(chain U and resseq 1:183 )
7ELECTRON MICROSCOPY7(chain V and resseq 1:229 )
8ELECTRON MICROSCOPY8chain N
9ELECTRON MICROSCOPY9chain W
10ELECTRON MICROSCOPY10chain Y
11ELECTRON MICROSCOPY11chain Z
12ELECTRON MICROSCOPY12(chain O and resseq 341:376 ) or (chain P and resseq 420:456 ) or (chain Q and resseq 393:422 ) or (chain R and resseq 359:389 ) or (chain S and resseq 467:534 ) or (chain T and resseq 323:350 ) or (chain U and resseq 184:324 ) or (chain V and resseq 230:309 )
13ELECTRON MICROSCOPY13(chain P and resseq 1:419 )

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  • 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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