[English] 日本語
Yorodumi
- PDB-9d1y: Structure of G75R Ubiquitin bound to KLHDC3-EloB/C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d1y
TitleStructure of G75R 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 / elongin complex / reciprocal meiotic recombination / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery ...XBP1(S) activates chaperone genes / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / reciprocal meiotic recombination / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / 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 / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation 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 / RNA Polymerase II Pre-transcription Events / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / transcription corepressor binding / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / 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 / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / TP53 Regulates Transcription of DNA Repair Genes / Degradation of DVL / Fanconi Anemia Pathway
Similarity search - Function
: / Calicin, beta-propeller domain / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Elongin-C / Elongin B / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family ...: / Calicin, beta-propeller domain / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Elongin-C / Elongin B / Kelch-type beta propeller / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Elongin-C / Elongin-B / Kelch domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)77,7106
Polymers77,5264
Non-polymers1842
Water6,521362
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)114.560, 121.543, 152.949
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-637-

HOH

21A-721-

HOH

31A-747-

HOH

41A-765-

HOH

-
Components

-
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: 8676.973 Da / Num. of mol.: 1 / Mutation: G75R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

-
Non-polymers , 2 types, 364 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10%PEG5KMME, 5% Tacsimate pH=7.0, 0.1M HEPES pH=7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33218 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.053 / Rrim(I) all: 0.156 / Χ2: 0.485 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.6-2.698.70.78232750.8490.9580.2760.830.433
2.69-2.88.70.58732570.9040.9740.2080.6240.432
2.8-2.938.60.44932760.9390.9840.160.4770.442
2.93-3.088.50.33433100.9590.990.1210.3560.46
3.08-3.2880.24832730.9710.9930.0930.2650.484
3.28-3.537.90.1733110.9870.9970.0640.1820.501
3.53-3.888.40.1233230.9930.9980.0440.1270.503
3.88-4.458.70.07833420.9970.9990.0280.0830.509
4.45-5.68.30.06533530.9980.9990.0240.0690.49
5.6-5080.06234980.9970.9990.0230.0660.603

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.85 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 1589 4.83 %
Rwork0.1677 --
obs0.1701 32925 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 12 362 5336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085102
X-RAY DIFFRACTIONf_angle_d0.9216925
X-RAY DIFFRACTIONf_dihedral_angle_d15.7491849
X-RAY DIFFRACTIONf_chiral_restr0.053762
X-RAY DIFFRACTIONf_plane_restr0.008894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.23821310.19962757X-RAY DIFFRACTION97
2.68-2.780.31681210.19942811X-RAY DIFFRACTION98
2.78-2.890.24331490.21662791X-RAY DIFFRACTION98
2.89-3.020.25491430.19832820X-RAY DIFFRACTION99
3.02-3.180.26451300.19442840X-RAY DIFFRACTION99
3.18-3.380.25571330.18182862X-RAY DIFFRACTION100
3.38-3.640.24981360.18662874X-RAY DIFFRACTION100
3.64-4.010.20871370.15052860X-RAY DIFFRACTION100
4.01-4.590.14211470.12462880X-RAY DIFFRACTION100
4.59-5.770.18812050.13472833X-RAY DIFFRACTION100
5.78-45.850.21591570.17183008X-RAY DIFFRACTION99
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)
12.8756-0.9279-0.53921.93620.01912.39730.10520.0895-0.0821-0.17670.01490.2913-0.1235-0.4861-0.09060.2248-0.0306-0.03180.30250.02530.281-27.1684-7.1999-13.9286
21.75430.2279-0.95862.5084-0.23192.1371-0.0460.19490.0872-0.17970.0650.4236-0.286-0.56910.00820.28440.0676-0.02930.36620.02740.3423-28.90937.2614-16.89
31.1970.1213-0.66022.50650.39952.44310.04460.19070.0568-0.41610.03930.0187-0.3968-0.3486-0.00380.35850.0637-0.01360.33390.05050.3-19.439812.568-24.8479
41.1329-0.56470.16581.899-0.96071.55260.0640.16460.0768-0.3031-0.0955-0.13420.03240.02240.01990.3103-0.01460.04860.2818-0.01030.2262-7.9447-0.3503-28.7548
53.3222-0.70880.60922.6947-2.33662.75140.15390.1357-0.3276-0.34240.02070.08590.2574-0.251-0.03090.28980.02220.02880.2526-0.01340.2711-17.1168-11.6331-20.22
61.3559-0.54920.67032.5194-1.85552.9679-0.002-0.0887-0.3822-0.11010.03680.07790.3982-0.1665-0.09340.2932-0.02390.03130.2283-0.01080.3784-15.6104-22.0085-7.2381
78.6696-0.18231.60023.92173.35393.416-0.20130.84250.8493-0.18510.2734-0.5651-0.16940.11240.09310.20180.02060.01660.2741-0.01730.482818.8694-23.3827-2.5318
86.0394-2.30540.69272.0023-0.16493.906-0.12990.41210.9595-0.23680.0973-0.5522-0.67750.08650.08220.3328-0.0107-0.03280.23310.06790.561724.0764-20.71351.5243
95.7131-2.49360.8413.37680.40885.1324-0.308-0.22250.7162-0.0052-0.0623-0.6205-0.06850.46670.06120.30560.0467-0.03580.3255-0.00870.451531.0367-25.50696.7946
103.909-1.65745.38394.79380.28569.0070.6470.1742-0.2314-0.6554-0.0494-0.21720.3714-0.0719-0.5440.2670.01680.07610.51540.01210.476927.3691-34.1077-4.6864
114.7244-2.10132.58944.5449-0.37662.20450.23241.34560.6323-0.5534-0.3701-0.39020.41220.65650.19840.3990.0740.04420.53690.09570.448527.3315-24.668-9.383
124.9029-1.1261.631.6039-0.124.6679-0.256-0.3323-0.53340.25560.3040.2695-0.1554-0.2457-0.03430.27870.03430.0120.19830.0250.43920.6928-31.54373.9335
134.8081-0.08450.89893.01561.37592.71-0.2782-0.56540.41040.21220.1459-0.5328-0.304-0.1090.1450.32820.096-0.00520.34260.01610.421311.3053-19.72748.1165
142.2116-2.8767-1.13684.67833.74685.0332-0.5416-0.81250.0650.45540.0770.368-0.0747-0.34720.51750.35980.13480.00120.50320.00390.46824.2746-17.667613.7078
154.56260.12450.45153.3169-0.33874.6149-0.190.13420.07970.21980.1493-0.0897-0.20660.31880.01210.28070.04280.00490.27210.05350.37616.4067-21.4004-1.5175
162.63631.8006-2.03399.11-6.45187.8035-0.24590.57920.1513-0.0132-0.2061-0.985-0.3017-0.1310.29820.3640.11080.01250.39120.06350.56833.7286-19.1795-11.8723
174.41090.76821.43993.24571.34235.9413-0.0256-0.7221-0.5370.12320.2824-0.4466-0.0706-0.5585-0.20980.22690.01860.03720.29550.12950.3685-3.4052-25.95063.1805
187.84681.84295.21529.34741.98596.84240.79091.6176-1.6497-1.0635-0.29730.37821.0512-0.5531-0.68521.1378-0.0771-0.09891.1103-0.23440.6608-26.5442-10.6235-50.893
191.3452-0.4932-0.91517.0432.13851.09790.04351.6095-0.1128-1.4386-0.25731.46340.1088-1.77940.33721.2116-0.2883-0.53681.7504-0.01981.1682-36.1062-6.4665-55.9978
205.15970.21520.3014.00363.82778.83840.17991.0984-0.3627-0.7851-0.73632.07121.0555-1.550.55621.0012-0.2422-0.32631.1426-0.25541.0363-36.9597-6.4814-47.2389
213.42643.9559-0.43945.6146-3.36378.02070.184-0.01700.02880.26691.40020.1465-1.2225-0.15050.6917-0.04080.01180.9668-0.00240.6159-31.9662-2.6949-41.7515
229.34580.1561-0.41874.9802-3.93746.6454-0.16081.36140.756-1.1621-0.15631.2059-0.9011-1.24180.29261.0340.1673-0.3961.1074-0.11440.7385-29.39563.9054-52.065
231.576-0.16630.17970.2948-1.03194.21860.01091.0552-0.1774-1.20130.22530.4758-0.6773-0.4693-0.13421.1784-0.1086-0.14280.832-0.0140.341-27.4213-3.2821-48.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 169 )
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 294 )
5X-RAY DIFFRACTION5chain 'A' and (resid 295 through 322 )
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 377 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 9 )
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 35 )
9X-RAY DIFFRACTION9chain 'B' and (resid 36 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 50 )
11X-RAY DIFFRACTION11chain 'B' and (resid 51 through 66 )
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 97 )
13X-RAY DIFFRACTION13chain 'C' and (resid 17 through 38 )
14X-RAY DIFFRACTION14chain 'C' and (resid 39 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 83 )
16X-RAY DIFFRACTION16chain 'C' and (resid 84 through 96 )
17X-RAY DIFFRACTION17chain 'C' and (resid 97 through 112 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 12 )
19X-RAY DIFFRACTION19chain 'D' and (resid 13 through 22 )
20X-RAY DIFFRACTION20chain 'D' and (resid 23 through 34 )
21X-RAY DIFFRACTION21chain 'D' and (resid 35 through 44 )
22X-RAY DIFFRACTION22chain 'D' and (resid 45 through 56 )
23X-RAY DIFFRACTION23chain 'D' and (resid 57 through 76 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more