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- PDB-4jio: Bro1 V domain and ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4jio
TitleBro1 V domain and ubiquitin
Components
  • BRO1
  • Ubiquitin
KeywordsPROTEIN BINDING / Membrane Trafficking / ESCRT-I / ESCRT-III / Ubiquitin / Endosome
Function / homology
Function and homology information


intralumenal vesicle formation / ATP export / mitochondria-associated ubiquitin-dependent protein catabolic process / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein localization to endosome / deubiquitinase activator activity / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...intralumenal vesicle formation / ATP export / mitochondria-associated ubiquitin-dependent protein catabolic process / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein localization to endosome / deubiquitinase activator activity / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytosolic ribosome / 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 / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / response to nutrient / 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 / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD
Similarity search - Function
alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 ...alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BRO1 domain-containing protein / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesNaumovozyma castellii (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsPashkova, N. / Gakhar, L. / Piper, R.C.
CitationJournal: Dev.Cell / Year: 2013
Title: The yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes.
Authors: Pashkova, N. / Gakhar, L. / Winistorfer, S.C. / Sunshine, A.B. / Rich, M. / Dunham, M.J. / Yu, L. / Piper, R.C.
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRO1
B: BRO1
U: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)87,8633
Polymers87,8633
Non-polymers00
Water0
1
A: BRO1


Theoretical massNumber of molelcules
Total (without water)39,6131
Polymers39,6131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BRO1


Theoretical massNumber of molelcules
Total (without water)39,6131
Polymers39,6131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
U: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6371
Polymers8,6371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.430, 92.320, 229.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BRO1


Mass: 39612.785 Da / Num. of mol.: 2 / Mutation: K417A, K418A, K419A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naumovozyma castellii (fungus) / Strain: ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630 / Gene: BRO1(AMINO ACIDS 370-708), NCAS0B02080, NCAS_0B02080 / Production host: Escherichia coli (E. coli) / References: UniProt: G0VBG6
#2: Protein Ubiquitin /


Mass: 8636.949 Da / Num. of mol.: 1 / Mutation: A28M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62987

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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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M bis-Tris propane pH 7, 0.2-0.4 M sodium malonate, 15-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9788915 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 4, 2012
RadiationMonochromator: Rosenbaum-Rock monochromator double crystal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788915 Å / Relative weight: 1
ReflectionResolution: 3.5→34.49 Å / Num. all: 17672 / Num. obs: 17664 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 7.14 % / Biso Wilson estimate: 131.32 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.6
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 7.29 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.6→34.488 Å / SU ML: 0.87 / σ(F): 0 / Phase error: 53.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.4211 1612 10.04 %
Rwork0.366 --
obs0.3716 16053 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→34.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 0 0 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023528
X-RAY DIFFRACTIONf_angle_d0.6654903
X-RAY DIFFRACTIONf_dihedral_angle_d4.329727
X-RAY DIFFRACTIONf_chiral_restr0.036686
X-RAY DIFFRACTIONf_plane_restr0.001697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70580.47071330.44441188X-RAY DIFFRACTION99
3.7058-3.82530.49221310.44081158X-RAY DIFFRACTION98
3.8253-3.96180.52341310.41871183X-RAY DIFFRACTION98
3.9618-4.12020.49051310.41461151X-RAY DIFFRACTION97
4.1202-4.30740.44231310.41651178X-RAY DIFFRACTION98
4.3074-4.5340.48511330.41193X-RAY DIFFRACTION99
4.534-4.81740.46261310.38181185X-RAY DIFFRACTION98
4.8174-5.18820.3971340.39931189X-RAY DIFFRACTION98
5.1882-5.70820.50831340.46771221X-RAY DIFFRACTION99
5.7082-6.52930.52571360.50251230X-RAY DIFFRACTION100
6.5293-8.20790.42431400.37861256X-RAY DIFFRACTION100
8.2079-34.48970.32431470.25821309X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6342-1.3056-1.67830.8751.2971.4254-0.6576-0.3788-0.131-0.07541.31420.03080.50741.3392-0.40721.9481-0.3646-0.21851.7397-0.48810.614418.570645.8177162.0302
20.3743-0.33540.0712.7456-3.36134.4635-0.7190.31060.4056-0.38310.1584-0.0163-0.40580.4717-0.5421.47920.2795-0.35771.9877-0.06110.367522.664921.5312168.2526
30.2799-0.35990.05582.60850.97240.53340.1085-0.3409-0.03690.2587-0.39210.90381.6512-0.6828-0.02764.478-1.1220.39031.2971-0.21441.184813.318815.0621188.0237
40.7845-0.66050.63131.71370.52711.59050.9712-1.8825-0.02041.3406-0.78851.3761.2134-2.0742-1.11752.6089-1.1732-0.09382.357-0.05110.29419.975419.9032172.1839
51.22180.4735-1.38941.0650.10762.0435-0.67871.61040.6274-0.0844-0.20070.0566-0.5748-0.66840.86410.79890.2284-1.0271.7409-0.25742.034226.353927.4955142.7517
60.0685-0.0426-0.21690.39040.7461.39570.1994-0.9420.50250.0648-0.2073-0.4324-0.54050.01670.11781.79480.26410.09871.0662-0.4939-0.285815.66956.2909153.7591
70.33910.25-0.53270.5472-0.4391.6024-0.32480.8260.0581-0.71640.0853-0.12380.06340.9986-0.71761.71490.4493-0.72721.683-0.40330.57966.461865.3239185.0396
82.2797-0.76870.22083.73334.72016.6297-0.0478-1.3349-0.27971.69230.16480.9020.7277-1.03210.89971.3129-0.29520.71421.4911-0.11630.5394-5.132356.582193.0845
94.7902-2.5262-4.01361.59291.94313.4703-0.66710.2613-0.5915-0.2438-0.43940.9882-0.1555-2.48140.53850.65430.0764-0.64951.6302-0.41262.4302-1.368457.8914179.2468
100.2587-0.02470.34280.6423-0.53690.8838-0.97850.0030.0936-0.09620.5771-0.1324-0.4153-0.6646-0.65671.2991-0.76820.77842.8877-0.5434-0.559212.22246.7578146.9872
112.5222-0.0656-0.31660.53710.36380.31310.4126-0.5403-0.27631.1686-0.20880.1670.9024-0.91060.44632.1691-0.0311-0.09761.5295-0.25520.420115.327126.4422167.1373
121.453-1.28110.08361.231-0.14540.9103-0.7585-0.30040.0926-1.38851.99740.15060.86720.2318-0.47442.9962-0.9884-0.07522.401-0.03031.063313.442549.136999.9027
138.99730.03230.60625.73681.76865.4132-1.02960.12050.3837-0.09540.40320.08850.9653-0.66270.87760.98110.00590.0761.5378-0.00450.9896-5.237136.4754125.8729
142.4369-0.8469-1.03173.59950.64532.0348-0.59350.4453-0.47180.12110.2875-0.84560.39270.63111.0220.8475-0.37490.27221.29870.09050.327812.71514.085389.0338
151.75320.4796-1.13071.71621.02131.7584-0.1922-1.6380.20420.3694-0.3777-0.24530.13210.24590.1340.53560.47310.27311.88460.36340.342618.072222.312596.6546
169.2485-1.5497-3.56575.09320.57341.842-0.3346-1.5342-0.24610.2472-1.37940.77710.98290.33830.24041.053-0.0555-0.20120.7178-0.17770.5732.967919.7318116.39
170.49180.3859-0.62542.06612.07994.0994-0.8091-0.4506-0.02581.53690.5543-0.0020.45370.2703-0.2951.3717-0.30730.16861.5275-0.79370.555-2.700728.3631135.9828
182.43710.42610.80640.3766-0.03330.3135-0.92841.21660.4325-0.99210.40040.4792-0.74750.3794-0.81182.7981-0.24670.15330.5280.20750.69115.431254.9528118.9452
191.2242-1.97471.62075.5323-2.89822.16550.2641.87020.5429-2.3191-0.98080.1211-1.67881.2163-0.772.9117-1.2075-0.2682.48080.2811.051328.167160.48686.5596
206.46850.8968-6.02672.0343-1.17245.67020.17470.50850.6897-1.1016-0.0274-0.3751-1.50020.945-0.34472.3591-1.2538-0.61712.04131.06761.735928.686357.039694.8132
213.36933.07420.98554.303-0.88582.419-0.54650.69460.2554-1.58-0.3417-0.1409-2.47611.13230.40072.5659-0.20480.02591.5651.05922.569217.497255.3934109.9007
221.34980.1080.52522.78031.77051.2637-0.41170.4368-0.3254-0.2372-0.1455-0.04230.24040.919-1.39580.32430.39370.44681.02690.2447-0.46696.205340.8776135.3093
233.09490.05152.22241.7411-1.951.98520.89941.6707-0.2648-1.6618-0.6941-0.1492-0.09561.1522-0.9737-0.4156-0.6382-0.32720.3874-0.16240.37978.152525.1161104.2801
241.78710.44622.22472.30661.12772.9187-0.19420.6772-0.9648-0.84450.0596-0.23310.6350.54780.12822.13480.18330.18831.9403-0.61380.810619.844454.6346185.2457
250.75510.0016-0.38842.30021.02480.65760.0969-0.10220.15110.3618-0.51750.4197-0.055-0.51930.32311.71840.5966-0.6221.0052-0.87410.859615.731765.3386190.9065
260.8772-0.11840.50996.09252.77521.64321.13380.468-0.3368-0.86290.27510.2036-0.97390.052-0.29141.01790.52770.14281.1505-0.79521.582923.962550.7479186.6389
270.3623-0.01011.50030.59420.76248.4984-0.28630.07830.1070.02260.2917-0.3976-0.63490.2973-0.6750.56390.0373-0.2661.6098-1.1370.755626.721352.8809194.2355
281.42910.95140.21051.0289-0.84552.4652-0.0548-0.128-0.10450.06290.0333-0.48750.0120.47840.25680.2707-0.1201-0.38461.90250.08531.743527.576161.7945194.8343
291.3091.13661.29861.74890.92731.7587-0.2631-0.0271-0.20110.5177-0.0342-0.4274-0.08910.792-0.23051.19890.54-0.80671.85080.15221.797919.558955.8613199.4046
300.9608-0.07921.22691.27140.47181.8236-0.23450.26680.1516-0.21240.01450.1571-0.56560.07980.16041.70370.0532-0.46682.0313-0.52420.383810.290350.2556194.1423
314.0425-2.2467-2.40735.09890.75351.5215-1.8219-0.637-1.89081.48470.643-1.22721.02090.18830.56342.96481.1226-0.20591.4071-0.62942.078818.856743.886194.414
329.3248-0.42240.52635.79260.54930.08560.03011.64740.468-2.5383-0.30621.10880.8168-0.5108-0.13641.96180.0487-1.11542.81750.13691.332316.112348.028183.4232
330.09150.11310.08770.2820.3160.73250.07230.11620.02840.26020.1728-0.24940.08960.13480.06960.70990.40430.2720.9585-0.35471.027116.470458.3089198.9443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 367:449 )A367 - 449
2X-RAY DIFFRACTION2( CHAIN A AND RESID 450:457 )A450 - 457
3X-RAY DIFFRACTION3( CHAIN A AND RESID 458:480 )A458 - 480
4X-RAY DIFFRACTION4( CHAIN A AND RESID 481:514 )A481 - 514
5X-RAY DIFFRACTION5( CHAIN A AND RESID 515:545 )A515 - 545
6X-RAY DIFFRACTION6( CHAIN A AND RESID 546:581 )A546 - 581
7X-RAY DIFFRACTION7( CHAIN A AND RESID 582:591 )A582 - 591
8X-RAY DIFFRACTION8( CHAIN A AND RESID 592:603 )A592 - 603
9X-RAY DIFFRACTION9( CHAIN A AND RESID 604:613 )A604 - 613
10X-RAY DIFFRACTION10( CHAIN A AND RESID 614:652 )A614 - 652
11X-RAY DIFFRACTION11( CHAIN A AND RESID 653:702 )A653 - 702
12X-RAY DIFFRACTION12( CHAIN B AND RESID 368:407 )B368 - 407
13X-RAY DIFFRACTION13( CHAIN B AND RESID 408:454 )B408 - 454
14X-RAY DIFFRACTION14( CHAIN B AND RESID 455:480 )B455 - 480
15X-RAY DIFFRACTION15( CHAIN B AND RESID 481:504 )B481 - 504
16X-RAY DIFFRACTION16( CHAIN B AND RESID 505:515 )B505 - 515
17X-RAY DIFFRACTION17( CHAIN B AND RESID 516:545 )B516 - 545
18X-RAY DIFFRACTION18( CHAIN B AND RESID 546:581 )B546 - 581
19X-RAY DIFFRACTION19( CHAIN B AND RESID 582:603 )B582 - 603
20X-RAY DIFFRACTION20( CHAIN B AND RESID 604:613 )B604 - 613
21X-RAY DIFFRACTION21( CHAIN B AND RESID 614:628 )B614 - 628
22X-RAY DIFFRACTION22( CHAIN B AND RESID 629:652 )B629 - 652
23X-RAY DIFFRACTION23( CHAIN B AND RESID 653:704 )B653 - 704
24X-RAY DIFFRACTION24( CHAIN U AND RESID 1:6 )U1 - 6
25X-RAY DIFFRACTION25( CHAIN U AND RESID 7:11 )U7 - 11
26X-RAY DIFFRACTION26( CHAIN U AND RESID 12:22 )U12 - 22
27X-RAY DIFFRACTION27( CHAIN U AND RESID 23:31 )U23 - 31
28X-RAY DIFFRACTION28( CHAIN U AND RESID 32:37 )U32 - 37
29X-RAY DIFFRACTION29( CHAIN U AND RESID 38:44 )U38 - 44
30X-RAY DIFFRACTION30( CHAIN U AND RESID 45:49 )U45 - 49
31X-RAY DIFFRACTION31( CHAIN U AND RESID 50:59 )U50 - 59
32X-RAY DIFFRACTION32( CHAIN U AND RESID 60:65 )U60 - 65
33X-RAY DIFFRACTION33( CHAIN U AND RESID 66:75 )U66 - 75

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