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- PDB-4lcd: Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin liga... -

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Basic information

Entry
Database: PDB / ID: 4lcd
TitleStructure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3
Components
  • E3 ubiquitin-protein ligase RSP5
  • Protein SNA3
  • Ubiquitin
KeywordsLigase/protein binding / Ligase / E3 / Rsp5 / NEDD4 / Ubiquitin / HECT / Sna3 / thioester / maleimide / crosslink / Ligase-protein binding complex
Function / homology
Function and homology information


regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / protein catabolic process => GO:0030163 / fungal-type vacuole lumen ...regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / protein catabolic process => GO:0030163 / fungal-type vacuole lumen / RHOQ GTPase cycle / RHOU GTPase cycle / positive regulation of ubiquitin-dependent endocytosis / regulation of multivesicular body size / ribophagy / ubiquitin-dependent endocytosis / regulation of mRNA export from nucleus / mitochondria-associated ubiquitin-dependent protein catabolic process / regulation of rRNA processing / actin cortical patch / endosome transport via multivesicular body sorting pathway / cellular bud tip / late endosome to vacuole transport via multivesicular body sorting pathway / nonfunctional rRNA decay / positive regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / fungal-type vacuole / HECT-type E3 ubiquitin transferase / fungal-type vacuole membrane / poly(A)+ mRNA export from nucleus / Regulation of PTEN stability and activity / positive regulation of endocytosis / protein K63-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / cytosolic ribosome / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondrion organization / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / phosphatidylinositol binding / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1
Similarity search - Function
Uncharacterized protein family UPF0057 signature. / Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type ...Uncharacterized protein family UPF0057 signature. / Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Protein SNA3 / E3 ubiquitin-protein ligase RSP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKamadurai, H.B. / Miller, D. / Schulman, B.A.
CitationJournal: Elife / Year: 2013
Title: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3.
Authors: Kamadurai, H.B. / Qiu, Y. / Deng, A. / Harrison, J.S. / Macdonald, C. / Actis, M. / Rodrigues, P. / Miller, D.J. / Souphron, J. / Lewis, S.M. / Kurinov, I. / Fujii, N. / Hammel, M. / Piper, ...Authors: Kamadurai, H.B. / Qiu, Y. / Deng, A. / Harrison, J.S. / Macdonald, C. / Actis, M. / Rodrigues, P. / Miller, D.J. / Souphron, J. / Lewis, S.M. / Kurinov, I. / Fujii, N. / Hammel, M. / Piper, R. / Kuhlman, B. / Schulman, B.A.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RSP5
B: E3 ubiquitin-protein ligase RSP5
C: Protein SNA3
D: Protein SNA3
E: Ubiquitin
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)125,2296
Polymers125,2296
Non-polymers00
Water00
1
A: E3 ubiquitin-protein ligase RSP5
C: Protein SNA3
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)62,6143
Polymers62,6143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RSP5
D: Protein SNA3
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)62,6143
Polymers62,6143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.046, 78.923, 96.722
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 ubiquitin-protein ligase RSP5 / Reverses SPT-phenotype protein 5


Mass: 50470.703 Da / Num. of mol.: 2 / Fragment: WW3 + HECT (UNP residues 383-809) / Mutation: C455L, C517G, C721A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MDP1, NPI1, RSP5, SYGP-ORF41, YER125W / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli)
References: UniProt: P39940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Protein SNA3


Mass: 2560.615 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC FRAGMENT (UNP residues 104-127) / Mutation: K125A / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14359
#3: Protein Ubiquitin


Mass: 9582.997 Da / Num. of mol.: 2 / Fragment: UNP residues 1-75 / Mutation: G75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC, UBIQUITIN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / pH: 7.2
Details: 0.1M Bis Tris Propane, 21% w/v PEG3350, 1% w/v polypropylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2012
RadiationMonochromator: CRYO-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 21931 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.072 / Net I/σ(I): 15.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.361 / % possible all: 92.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.4 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.299 1088 5.1 %
Rwork0.251 --
obs0.253 21323 95 %
all-21931 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.4 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-26.4355 Å20 Å27.4434 Å2
2---25.3352 Å2-0 Å2
3----1.1004 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 0 0 7944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098125
X-RAY DIFFRACTIONf_angle_d1.04311020
X-RAY DIFFRACTIONf_dihedral_angle_d22.7684929
X-RAY DIFFRACTIONf_chiral_restr0.0641200
X-RAY DIFFRACTIONf_plane_restr0.0051445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.2410.36551600.3122515X-RAY DIFFRACTION96
3.241-3.41160.34681380.29982589X-RAY DIFFRACTION98
3.4116-3.6250.29651270.28322589X-RAY DIFFRACTION98
3.625-3.90430.36481190.26192559X-RAY DIFFRACTION96
3.9043-4.29620.30171210.24692451X-RAY DIFFRACTION92
4.2962-4.91530.25971510.22832560X-RAY DIFFRACTION96
4.9153-6.18330.30681390.2562463X-RAY DIFFRACTION92
6.1833-29.39680.2691330.22132509X-RAY DIFFRACTION92
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)
15.2715-1.12450.11342.05572.10931.8637-0.18560.3399-0.3479-0.03750.6471-0.5874-0.34340.4572-0.28850.7605-0.07970.18850.8663-0.08820.938232.099814.8546-45.311
21.7256-0.23270.32055.3025-0.57950.8217-0.01070.35470.1576-0.1661-0.2145-0.91380.21660.19150.13450.5242-0.00970.12120.6669-0.03150.56517.468533.8688-48.8044
33.3193-0.7446-1.84875.1436-1.20782.55910.0253-0.09740.24270.74310.1674-0.0866-0.34950.0214-0.17760.3716-0.03840.01860.4556-0.01450.45374.722737.399-41.0586
42.8458-1.5051-1.0622.80810.43710.60120.313-0.2773-0.1330.68940.27171.5527-0.7881-0.0681-0.39170.99070.04960.33320.90860.23151.2298-14.567430.9851-31.101
54.49660.6092-1.32354.2974-2.25520.9395-0.21990.1041-0.0763-0.1660.42080.8660.4709-0.3928-0.09930.50310.01820.05850.6107-0.03660.5803-4.585927.6311-40.6678
64.77220.4651.42474.2257-1.30982.8726-0.0233-0.60630.1870.16030.0515-0.6293-0.14090.3762-0.06530.56540.0329-0.09670.71-0.05160.750532.657535.5578-28.6129
73.0776-0.35390.33382.5447-0.0780.10330.0715-0.38950.33270.3121-0.0899-0.74410.08150.1173-0.04620.790.0584-0.17730.5907-0.06980.582612.96878.15626.1542
84.4623-0.0987-0.57424.98520.47822.8979-0.1125-0.0271-0.2908-0.02280.04-0.3403-0.0730.24530.06020.5860.0306-0.06140.4305-0.0020.48380.9948-8.371-2.2336
92.4509-0.29181.72143.1008-1.61513.0377-0.17430.5741-0.0974-0.78220.43310.66830.28360.0406-0.2461.09750.0106-0.09930.76220.02680.6597-10.62750.9605-19.7457
101.9352-0.2378-0.40633.5022-1.69321.9465-0.0634-0.11750.1524-0.31040.37670.8504-0.6923-0.5615-0.07610.94180.0351-0.04520.5825-0.01080.6807-12.82913.4437-12.0324
114.7511-1.3725-0.08482.0305-0.5581.2625-0.32220.0802-0.131-0.40180.1621-0.58410.17960.43170.03020.932-0.03240.16010.7633-0.14720.82826.2209-2.9365-6.1502
129.8127-0.3222-5.64415.98450.23671.9665-2.54180.4766-1.21770.1303-0.8973-0.37360.52432.33092.55410.76120.2270.12041.32030.08981.429644.088913.3397-42.5946
13-0.0494-0.1296-0.13690.01220.0038-0.0424-0.1524-0.2929-0.28071.1551-0.6516-0.48430.36041.8136-01.5318-0.1402-0.3591.55920.15261.879532.397216.86513.0303
144.20142.48050.12425.67861.85742.4191-0.05270.15441.3742-0.0642-1.48310.7306-0.7952-0.20591.26921.1382-0.1513-0.2571.2915-0.00480.964829.390768.1771-29.9695
150.0588-0.1358-0.01390.63660.58370.4730.0899-0.5471.20630.6633-0.4734-0.4906-0.64040.837-0.25441.3818-0.3133-0.19791.20350.14771.330532.995265.9863-29.831
161.2578-1.61320.03792.1224-0.24625.21010.7243-0.83441.5187-0.48-0.88230.2352-0.08921.311-0.60840.8984-0.1863-0.56181.2471-0.23941.585539.655661.2162-29.7234
172.6024-2.23740.99762.3686-1.06692.79081.0190.2004-0.39410.3704-0.8056-2.5715-1.08750.92970.57830.7277-0.3032-0.28360.96-0.20831.672334.733158.0498-37.2538
180.6745-0.96340.27894.51980.38090.26490.19960.38050.2817-1.0772-0.4496-0.79530.3409-0.5930.56691.62380.2022-0.17611.0285-0.04321.443134.595270.7204-39.5919
191.81751.6325-1.0233.5276-0.16455.04760.58031.3779-0.11520.3659-0.6875-1.4244-0.7210.62740.21190.8255-0.1447-0.17521.05260.05390.841730.998554.5827-36.4393
202.0791-0.1316-1.01860.4945-2.63032.0187-1.74590.3007-1.8808-0.88090.6404-0.12160.4733-0.6341.66781.25210.2240.17611.54880.03711.139625.3532-35.5433-6.7395
212.20331.82810.33951.21041.36234.13490.41980.33940.1159-0.2468-0.4309-0.8666-1.34640.213-0.37471.03570.0870.44740.95540.0111.158228.47-34.2462-4.9283
223.2929-0.3282-1.7112.14911.82812.1380.1415-0.2253-0.38370.71320.6033-1.0724-1.12940.3752-0.54650.4180.30130.08471.44080.02481.117133.9679-29.6301-1.595
233.076-0.51970.48271.3375-0.95223.47750.5872-0.53560.65470.2968-0.7078-1.7797-0.4673-0.04680.47311.04920.2009-0.24011.0030.15961.803433.1856-21.5266-0.1723
241.35241.1221.97337.24470.73292.9821-0.239-0.1801-0.4428-0.1978-0.5874-1.61960.0908-0.44610.57381.05680.2717-0.16131.1857-0.19461.410222.2005-29.26633.8672
253.94171.00640.04075.84521.56951.2476-0.3521-0.4922-0.36890.7135-0.6249-0.891-0.0712-0.65590.60161.02550.0138-0.18971.2830.02791.270825.8255-37.45515.5813
264.836-1.5416-0.43835.9678-0.41944.23181.0791-0.8887-0.6514-0.1418-0.1750.3681-0.20121.6498-0.50330.65790.0611-0.02740.9478-0.16811.174723.5418-23.0862-0.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 383:429)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 430:511)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 512:575)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 576:625)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 626:695)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 696:806)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 384:473)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 474:557)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 558:632)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 633:680)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 681:806)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 105:112)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 104:117)
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 1:6)
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 7:22)
16X-RAY DIFFRACTION16CHAIN E AND (RESSEQ 23:34)
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 35:49)
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 50:64)
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 65:75)
20X-RAY DIFFRACTION20CHAIN F AND (RESSEQ 1:7)
21X-RAY DIFFRACTION21CHAIN F AND (RESSEQ 8:22)
22X-RAY DIFFRACTION22CHAIN F AND (RESSEQ 23:34)
23X-RAY DIFFRACTION23CHAIN F AND (RESSEQ 35:40)
24X-RAY DIFFRACTION24CHAIN F AND (RESSEQ 41:49)
25X-RAY DIFFRACTION25CHAIN F AND (RESSEQ 50:64)
26X-RAY DIFFRACTION26CHAIN F AND (RESSEQ 65:75)

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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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