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- PDB-9d1i: Structure of Ubiquitin bound to KLHDC3-EloB/C -

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Basic information

Entry
Database: PDB / ID: 9d1i
TitleStructure of Ubiquitin bound to KLHDC3-EloB/C
Components
  • Elongin-B
  • Elongin-C
  • Kelch domain-containing protein 3
  • Ubiquitin
KeywordsLIGASE / KLHDC3 / Ubiquitin / C-degron / Cullin-RING / E3
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / VCB complex / elongin complex / reciprocal meiotic recombination / symbiont entry into host cell via disruption of host cell glycocalyx / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / symbiont entry into host cell via disruption of host cell envelope ...XBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / VCB complex / elongin complex / reciprocal meiotic recombination / symbiont entry into host cell via disruption of host cell glycocalyx / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / symbiont entry into host cell via disruption of host cell envelope / virus tail / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / Vif-mediated degradation of APOBEC3G / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Inactivation of CSF3 (G-CSF) signaling / transcription elongation by RNA polymerase II / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
: / Kelch motif / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Elongin-C / Elongin B / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain ...: / Kelch motif / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Elongin-C / Elongin B / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Pectin lyase fold / Pectin lyase fold/virulence factor / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tail fiber / Elongin-C / Elongin-B / Kelch domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchulman, B.A. / Scott, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG011085 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases.
Authors: Daniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade ...Authors: Daniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade Harper / Gary Kleiger / Brenda A Schulman /
Abstract: Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the ...Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate's C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10's recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch domain-containing protein 3
B: Elongin-B
C: Elongin-C
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5185
Polymers77,4264
Non-polymers921
Water11,043613
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.709, 121.440, 153.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-854-

HOH

31A-919-

HOH

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Kelch domain-containing protein 3 / Testis intracellular mediator protein


Mass: 43245.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC3, PEAS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BQ90
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15370
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 13855.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15369
#4: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 2 types, 614 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10%PEG5KMME, 0.1M HEPES pH=7.0, 5% Tascsimate pH=7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 72013 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.035 / Rrim(I) all: 0.107 / Χ2: 1.786 / Net I/σ(I): 4.5 / Num. measured all: 632350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.077.50.55370410.9030.9740.2020.590.27598.3
2.07-2.158.40.44471250.940.9840.1580.4720.29799.7
2.15-2.258.80.35671720.9590.990.1250.3780.312100
2.25-2.378.20.28771170.970.9920.1060.3060.3699.9
2.37-2.529.40.22671740.9830.9960.0770.2390.38100
2.52-2.719.40.1771930.990.9980.0580.180.454100
2.71-2.999.20.12171980.9940.9980.0420.1280.62100
2.99-3.428.50.08672060.9950.9990.0310.0920.99699.8
3.42-4.319.50.06472790.9960.9990.0220.0682.061100
4.31-508.90.07175080.9870.9970.0250.07511.26499.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.29 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 3519 5.02 %
Rwork0.1666 --
obs0.1677 70047 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4905 0 6 613 5524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075039
X-RAY DIFFRACTIONf_angle_d0.8996845
X-RAY DIFFRACTIONf_dihedral_angle_d15.8411811
X-RAY DIFFRACTIONf_chiral_restr0.058752
X-RAY DIFFRACTIONf_plane_restr0.008888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.23981320.24492412X-RAY DIFFRACTION88
2.03-2.060.19451310.22212495X-RAY DIFFRACTION92
2.06-2.090.22581200.19752573X-RAY DIFFRACTION94
2.09-2.120.25251270.19152572X-RAY DIFFRACTION95
2.12-2.150.21781440.17792598X-RAY DIFFRACTION95
2.15-2.190.24421340.1732617X-RAY DIFFRACTION96
2.19-2.230.16581320.17842605X-RAY DIFFRACTION97
2.23-2.270.18951430.17172641X-RAY DIFFRACTION97
2.27-2.320.20381340.16752655X-RAY DIFFRACTION97
2.32-2.370.18941410.1692626X-RAY DIFFRACTION97
2.37-2.430.22771370.18292683X-RAY DIFFRACTION97
2.43-2.490.23461540.18542655X-RAY DIFFRACTION98
2.49-2.550.23561310.19022678X-RAY DIFFRACTION98
2.55-2.630.23781300.18172690X-RAY DIFFRACTION98
2.63-2.710.21051450.17462712X-RAY DIFFRACTION99
2.72-2.810.20621540.1712704X-RAY DIFFRACTION99
2.81-2.920.20061370.17852688X-RAY DIFFRACTION99
2.92-3.060.17481600.17542736X-RAY DIFFRACTION99
3.06-3.220.1941500.1692711X-RAY DIFFRACTION99
3.22-3.420.16961750.16652673X-RAY DIFFRACTION99
3.42-3.680.16891330.16152766X-RAY DIFFRACTION100
3.68-4.050.16961390.14522764X-RAY DIFFRACTION99
4.05-4.640.15011580.1242743X-RAY DIFFRACTION99
4.64-5.840.18641500.15192765X-RAY DIFFRACTION99
5.85-38.290.1851280.1822766X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0385-1.52750.38271.8071-0.55441.47610.0631-0.0357-0.1304-0.17090.060.07770.0385-0.1828-0.12710.2174-0.0328-0.00930.21120.02060.1974-19.7984-9.8494-13.935
22.6123-0.129-1.83534.37681.17761.9841-0.03560.4997-0.037-0.5708-0.03820.7575-0.0893-0.73980.03140.2468-0.0264-0.07860.39840.0240.3175-32.6546-6.0288-19.4342
35.0028-3.08180.9265.902-0.01482.9574-0.0452-0.3193-0.56080.0510.2291.003-0.1222-0.7281-0.15330.17730.00770.0460.32970.06770.3023-32.1353-4.987-7.309
42.43131.14950.11393.84280.65143.95470.0150.10310.1003-0.02170.07640.3176-0.1823-0.3217-0.09620.24650.0666-0.00950.25080.0420.2476-27.72545.3578-16.515
52.1396-1.1773-1.22545.0544-0.754.2608-0.02210.218-0.0224-0.31170.02840.2598-0.3419-0.72720.00960.19860.0464-0.03860.32320.02260.2607-29.98538.7956-17.2575
61.6219-0.58160.12291.787-0.31321.6520.02540.20620.1429-0.31630.009-0.0843-0.1248-0.0745-0.03540.3247-0.01620.01990.23070.03670.2046-12.54027.9218-28.6342
75.18791.2412.07583.48930.19453.52950.08320.1963-0.1594-0.1964-0.0443-0.26820.29680.114-0.06280.2620.00810.06590.1925-0.00680.1975-4.8551-6.7726-26.7228
85.3010.22263.37271.5774-0.225.0720.07780.1003-0.2502-0.1288-0.0415-0.06470.1242-0.0113-0.03650.1757-0.01270.01270.15210.02940.1816-12.8654-11.5546-18.384
94.7892-2.03453.57682.7011-3.07935.26440.08190.1274-0.2817-0.2861-0.02140.05290.3614-0.0193-0.08850.20720.00040.03490.1498-0.03070.2092-13.796-18.5176-15.2755
103.9961-2.31271.53564.224-1.87242.91510.0479-0.2489-0.4283-0.09380.11550.09580.3252-0.2078-0.23060.2433-0.06160.01960.25490.06330.3574-18.9148-24.8731-3.5868
118.4651-1.99893.94725.30684.32797.61350.16931.01930.54-0.3216-0.1521-0.1667-0.49970.66860.01290.15750.01270.0330.29570.05460.442719.0474-23.3676-2.5954
126.0022-1.73470.10912.7287-1.59025.0999-0.11730.41320.6457-0.0955-0.1024-0.5559-0.12280.37730.20180.19990.0162-0.01520.22460.06790.448727.3789-23.68860.3884
137.2083-3.68464.39564.2221-2.36475.25840.35981.0694-0.0097-0.4777-0.4221-0.06790.29880.61340.06660.29090.05520.02530.32060.01450.350118.7808-25.9513-5.6838
149.3609-4.74951.66449.5401-4.25129.4735-0.0868-0.9899-0.0880.41870.0788-0.1559-0.55170.54340.03890.32130.0236-0.0050.33940.0120.313532.3065-33.53110.6063
152.47593.536-0.67625.3720.45486.58430.1307-0.4677-1.99370.2064-0.01811.05180.7363-1.0101-0.07960.29140.0026-0.00920.39160.07470.78119.449-36.37225.3116
167.29191.24481.6713.28730.79874.0837-0.3527-0.61220.29560.31430.1636-0.554-0.3161-0.05570.16040.2120.1121-0.00070.2726-0.00220.295711.4025-19.55288.043
171.5162-0.7684-2.73394.37584.7378.0141-0.4035-0.88490.60920.41250.0684-0.3447-0.2289-0.0580.36890.39180.1435-0.0470.4611-0.08730.46335.1538-14.149614.1638
185.6084-1.06450.61554.9075-0.96711.8574-0.121-0.3359-0.06170.12410.12820.22550.0366-0.06420.02310.20980.03410.01090.2110.0420.32015.5497-22.60021.2759
196.634-0.59910.51273.49750.12917.55760.11890.118-0.1445-0.1419-0.1355-0.1823-0.1652-0.17660.13310.16840.07370.01140.15860.07780.2908-0.1798-22.9677-3.5823
207.01821.3953-1.58932.11110.52830.7513-0.23731.6071-1.1667-0.3641-0.07250.1377-0.1573-0.02710.32531.1988-0.1101-0.15040.9268-0.10940.6873-27.2003-10.8442-50.8382
215.69890.2844-0.81122.68012.44552.4231-0.06040.55820.0989-0.8145-0.4291.59830.2496-0.80510.46950.9892-0.1498-0.33041.0724-0.09560.744-35.3389-4.256-47.136
227.77744.11083.42094.26170.54425.3766-0.27131.66881.2722-1.9554-0.22450.9677-1.0061-1.61750.50931.39560.1181-0.36221.2598-0.02790.7576-29.12084.0839-51.8572
231.8232-0.01152.2570.00190.00922.8121-0.21331.01010.3147-1.36250.02790.2251-0.295-0.48290.16141.2502-0.0696-0.19220.94440.04990.3745-27.4864-2.7395-48.3512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 281 )
8X-RAY DIFFRACTION8chain 'A' and (resid 282 through 306 )
9X-RAY DIFFRACTION9chain 'A' and (resid 307 through 348 )
10X-RAY DIFFRACTION10chain 'A' and (resid 349 through 377 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 9 )
12X-RAY DIFFRACTION12chain 'B' and (resid 10 through 60 )
13X-RAY DIFFRACTION13chain 'B' and (resid 61 through 79 )
14X-RAY DIFFRACTION14chain 'B' and (resid 80 through 89 )
15X-RAY DIFFRACTION15chain 'B' and (resid 90 through 97 )
16X-RAY DIFFRACTION16chain 'C' and (resid 17 through 38 )
17X-RAY DIFFRACTION17chain 'C' and (resid 39 through 61 )
18X-RAY DIFFRACTION18chain 'C' and (resid 62 through 83 )
19X-RAY DIFFRACTION19chain 'C' and (resid 84 through 112 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 16 )
21X-RAY DIFFRACTION21chain 'D' and (resid 17 through 44 )
22X-RAY DIFFRACTION22chain 'D' and (resid 45 through 56 )
23X-RAY DIFFRACTION23chain 'D' and (resid 57 through 76 )

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  • 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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