[English] 日本語
Yorodumi
- PDB-8ebn: Structure of KLHDC2-EloB/C tetrameric assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ebn
TitleStructure of KLHDC2-EloB/C tetrameric assembly
Components
  • Elongin-B
  • Elongin-C
  • Kelch domain-containing protein 2
KeywordsLIGASE / E3 ligase
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / 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 ...ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / 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 / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / 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 / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Galactose oxidase, central domain / Elongin B / Elongin-C / 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 family ...Galactose oxidase, central domain / Elongin B / Elongin-C / 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 family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Elongin-C / Elongin-B / Kelch domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsScott, D.C. / Schulman, B.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01GM125885 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)P30CA021765 United States
CitationJournal: Mol Cell / Year: 2023
Title: E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity.
Authors: Daniel C Scott / Moeko T King / Kheewoong Baek / Clifford T Gee / Ravi Kalathur / Jerry Li / Nicholas Purser / Amanda Nourse / Sergio C Chai / Sivaraja Vaithiyalingam / Taosheng Chen / ...Authors: Daniel C Scott / Moeko T King / Kheewoong Baek / Clifford T Gee / Ravi Kalathur / Jerry Li / Nicholas Purser / Amanda Nourse / Sergio C Chai / Sivaraja Vaithiyalingam / Taosheng Chen / Richard E Lee / Stephen J Elledge / Gary Kleiger / Brenda A Schulman /
Abstract: E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins ...E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2. Without substrate, neddylated CRL2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
C: Elongin-B
D: Elongin-C
E: Elongin-B
F: Elongin-C


Theoretical massNumber of molelcules
Total (without water)143,6986
Polymers143,6986
Non-polymers00
Water1,20767
1
A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
C: Elongin-B
D: Elongin-C
E: Elongin-B
F: Elongin-C

A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
C: Elongin-B
D: Elongin-C
E: Elongin-B
F: Elongin-C


Theoretical massNumber of molelcules
Total (without water)287,39512
Polymers287,39512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area29390 Å2
ΔGint-192 kcal/mol
Surface area85260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.431, 142.431, 140.479
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein Kelch domain-containing protein 2 / Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor- ...Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor-like protein 1 / HCLP-1


Mass: 46154.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y2U9
#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.: 2
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: 13945.732 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: % PEG3350, 0.2 M KSCN, 0.1 M Tris, 0.1M Na/K Tartrate, 2.5% MPD, pH =6.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 49565 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 59.05 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.037 / Rrim(I) all: 0.077 / Χ2: 1.319 / Net I/σ(I): 11.5 / Num. measured all: 197411
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6940.61349480.8290.3450.7050.50999.6
2.69-2.840.44649490.9040.2510.5130.55899.5
2.8-2.933.90.29949460.9450.170.3450.67598.9
2.93-3.083.70.19548120.9640.1150.2270.79596.2
3.08-3.284.20.14849930.9830.0820.1690.98999.6
3.28-3.534.10.10649870.990.0590.1221.40499.4
3.53-3.8840.07949940.9920.0440.0911.86499.5
3.88-4.453.80.05848820.9940.0340.0682.39696.6
4.45-5.64.10.04650110.9960.0260.0532.24899.1
5.6-5040.0350430.9990.0160.0341.73797.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCB
Resolution: 2.6→46.62 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 2542 5.14 %
Rwork0.2111 46922 -
obs0.2131 49464 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.44 Å2 / Biso mean: 74.7516 Å2 / Biso min: 28.57 Å2
Refinement stepCycle: final / Resolution: 2.6→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 0 67 8463
Biso mean---55.66 -
Num. residues----1080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.650.44441550.37262575273099
2.65-2.70.35761270.33572611273899
2.7-2.760.31821320.3092617274999
2.76-2.820.29221480.28122570271899
2.82-2.90.31631340.26932650278499
2.9-2.970.35261460.26532583272997
2.97-3.060.3131250.2592463258894
3.06-3.160.29261240.26012644276899
3.16-3.270.28861290.272426482777100
3.27-3.40.30481420.2612624276699
3.4-3.560.29681310.22322654278599
3.56-3.750.23731440.203926242768100
3.75-3.980.1891610.18692632279399
3.98-4.290.20261760.16892523269998
4.29-4.720.21151420.15172528267095
4.72-5.40.19231300.165426812811100
5.4-6.80.24851370.20762659279699
6.8-46.620.24461590.19142636279596
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)
11.49060.23110.83180.7183-0.27740.9324-0.03220.16640.08330.08540.07660.0478-0.17540.113400.4014-0.0750.09290.22560.01680.423314.9297-32.0701-51.2781
21.6201-0.04770.16260.5723-0.09450.70820.1698-0.0243-0.0471-0.0093-0.0206-0.05580.06990.16110.00010.3605-0.03660.04350.2234-0.01810.379317.175-49.2757-42.9308
30.97830.2557-0.21031.1219-0.04990.9060.1638-0.00830.1085-0.0564-0.0725-0.0808-0.20170.3780.02730.3234-0.11530.07190.3828-0.03760.420634.1361-38.2892-44.939
40.3959-0.34610.32430.2035-0.08780.1286-0.1762-0.4247-0.1988-0.17040.17240.3194-0.3165-0.12600.7077-0.15420.04990.62670.00490.646529.7386-18.9723-69.6946
50.9270.2023-0.40790.7428-0.88840.8497-0.7124-0.03140.1838-0.02270.2608-0.1931-0.4583-0.1336-0.00750.7436-0.1113-0.110.6478-0.16580.649222.2859-23.4449-2.7455
60.13010.1125-0.09430.23780.04240.0824-0.8004-0.25780.94350.27470.4091-0.0852-1.11320.2548-0.00081.18080.0989-0.23991.0179-0.1131.103116.0384-10.6181-0.9817
70.98691.374-0.56742.2059-1.41362.1296-0.136-0.15711.73040.21890.69980.24320.2095-0.08151.49870.67210.4104-0.16111.1363-0.78940.95346.9201-12.65668.6104
80.03120.045-0.05970.0188-0.06770.0770.6897-0.28751.7957-0.3325-0.0849-0.1030.00120.1385-0.00091.10320.21060.05331.0608-0.11291.55215.3376-9.87163.1659
9-0.01760.03-0.03790.5-0.3410.3009-0.5582-0.53880.7913-0.21351.0742-0.2804-0.02490.31170.11740.77720.0509-0.061.2642-0.3590.88020.1229-20.61769.1224
103.37410.94721.39690.36690.32771.3576-0.671-1.21111.32960.68260.15120.3546-0.09390.0622-0.07870.8720.0670.1541.5937-0.38430.68140.0668-25.084112.955
110.1298-0.15550.22411.2944-0.35030.9074-0.0714-1.3490.10220.32040.22060.19160.182-0.33520.55180.5797-0.0597-0.06121.8033-0.3110.04198.3982-33.70210.397
120.1709-0.31650.04092.3009-0.10690.0378-0.1584-0.4842-0.11840.26770.0327-0.62810.2718-0.9143-0.12540.6816-0.2038-0.04331.1764-0.03920.283410.0166-36.54716.7944
130.22280.116-0.19520.5221-0.49380.4405-0.2343-0.0705-0.0535-0.08470.1411-0.2750.52920.2697-0.00380.5856-0.0022-0.03510.778-0.08150.578219.5505-34.47576.562
140.48020.2644-0.19660.1559-0.23660.19440.2646-0.3984-0.41280.1559-0.35310.16090.6472-0.22290.00220.5123-0.125-0.00410.49230.08490.420413.785-53.1783-20.5435
150.1213-0.305-0.04940.5331-0.01920.0296-0.0029-0.14480.48580.02790.30120.3795-0.35290.19930.0050.566-0.11850.06490.47010.01290.4088.3568-40.1447-30.3158
160.2522-0.2209-0.00890.75920.11970.47180.3002-0.8634-0.80810.4897-0.36850.09730.2021-0.1975-0.02570.5539-0.18190.0960.65430.1610.5273-11.2281-61.779-7.0989
170.2347-0.5364-0.21351.43230.87660.83110.1802-0.3476-0.26340.1286-0.19940.977-0.1486-0.6536-0.4930.448-0.19590.13990.61510.24080.754-23.3596-63.6337-8.224
181.5919-0.2326-0.13590.01810.00560.0188-0.11950.2535-0.56330.3723-0.28720.97390.3738-0.532-0.15950.7257-0.22230.30330.59310.29120.9194-16.0609-72.9482-5.3755
190.00740.00610.03080.25360.12960.08730.1209-0.4359-0.82851.28960.2088-0.5354-0.10160.45160.05380.8829-0.1774-0.0170.94060.34030.722-5.0661-64.4659-0.9296
200.9225-0.2056-0.35620.19080.0560.4261-0.2950.2538-0.6351-0.1995-0.2338-0.35310.36110.343-0.72370.5906-0.19510.13440.37340.07010.8607-16.1031-71.2063-14.8734
210.425-0.0640.44430.0190.1173.2271-0.0106-0.1407-0.2708-0.1548-0.17010.44910.1332-0.812-0.25730.765-0.18550.22080.24530.06870.6627-1.1072-65.1062-23.8027
220.3424-0.36890.21310.6498-0.87382.32450.4837-0.4022-0.32790.0743-0.24790.34721.3461-0.46250.25670.4282-0.20270.19660.44620.02490.5579-11.7566-54.8071-20.1325
230.06020.0736-0.05170.12660.03030.03740.3521-0.4919-0.0266-0.0391-0.1580.4008-0.41490.30780.00060.5815-0.10510.13940.5326-0.00580.4642-10.076-47.1777-15.3198
240.23730.13590.06220.1009-0.01480.08930.1119-0.03870.4654-0.1950.1033-0.4330.3587-0.05720.00230.4942-0.05030.07620.32540.03830.4506-9.427-49.5202-25.1592
250.4156-0.50430.15220.4591-0.12390.05260.0507-0.8636-0.42440.37940.05280.39840.29690.37060.02340.5656-0.15530.06850.61580.03070.4055-1.5586-53.1038-11.3505
260.21-0.02120.140.12230.12150.32850.3454-0.52640.0213-0.1645-0.27390.02580.2077-0.6668-0.01840.7598-0.15790.08750.65760.08440.52514.4904-51.0369-3.0474
270.4318-0.1892-0.27320.43510.71761.24920.27070.22210.0642-0.0414-0.7384-0.2426-0.1062-0.0946-0.28810.4498-0.19290.13840.39970.05630.42844.9226-50.1293-20.7071
280.0285-0.01280.05780.09020.19070.6035-0.11550.16880.46260.50410.7362-0.00120.2108-0.30980.01630.6092-0.14340.03080.7659-0.00550.473658.7164-30.4204-70.8783
290.1047-0.07350.10170.0921-0.02290.04390.2358-0.05990.92330.16250.1101-0.23240.347-0.21220.01530.581-0.1585-0.04521.05910.06510.555660.9692-32.5474-74.8717
300.18180.04730.05490.51390.13820.2909-0.27820.2346-0.4705-0.46490.2633-0.2580.0552-0.62010.00390.3976-0.26570.15041.42750.14940.473467.4601-38.4517-76.8755
311.04350.19221.73030.70260.02393.04350.691.59570.2289-0.611-0.1566-1.11090.08532.01920.15010.4663-0.33050.07841.29510.17760.830670.8729-30.7442-78.3122
320.0893-0.1291-0.0820.50070.33540.2585-0.40951.0579-0.0456-0.4465-0.1636-0.2817-0.54840.2905-0.54310.8306-0.57410.19440.87540.0470.656861.3904-27.1141-70.5332
330.5017-0.3399-0.01540.08490.03880.1150.08160.52010.1221-0.0232-0.2085-0.0041-1.04720.2926-0.06340.8151-0.08370.14350.87490.27930.583454.569-21.0841-85.6727
340.3903-0.2169-0.11150.24640.04920.0567-0.24230.8517-0.3676-0.3538-0.0445-0.09270.0690.4748-0.00020.6766-0.16610.09830.8792-0.08480.528248.0348-39.0106-81.203
350.6087-0.2431-0.10080.3096-0.1580.1547-0.14620.14160.17020.0977-0.35910.0078-0.21220.4903-0.03910.6645-0.24620.13360.78940.00470.48945.9146-32.8577-78.0864
360.33640.061-0.1701-0.001-0.02030.0986-0.3292-0.3453-0.0559-0.27630.3864-0.3963-0.21520.27340.01150.7926-0.2110.12280.7460.00480.472444.3084-29.2748-62.5924
370.25-0.09310.00610.06330.04870.05090.2730.2557-0.2945-0.00580.0449-0.21430.0456-0.32440.00030.6646-0.15380.03970.77990.10720.52837.1553-27.4324-79.0231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 94 )A27 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 221 )A95 - 221
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 363 )A222 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 406 )A364 - 406
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 106 )B27 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 148 )B107 - 148
7X-RAY DIFFRACTION7chain 'B' and (resid 149 through 188 )B149 - 188
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 207 )B189 - 207
9X-RAY DIFFRACTION9chain 'B' and (resid 208 through 233 )B208 - 233
10X-RAY DIFFRACTION10chain 'B' and (resid 234 through 271 )B234 - 271
11X-RAY DIFFRACTION11chain 'B' and (resid 272 through 296 )B272 - 296
12X-RAY DIFFRACTION12chain 'B' and (resid 297 through 340 )B297 - 340
13X-RAY DIFFRACTION13chain 'B' and (resid 341 through 363 )B341 - 363
14X-RAY DIFFRACTION14chain 'B' and (resid 364 through 387 )B364 - 387
15X-RAY DIFFRACTION15chain 'B' and (resid 388 through 406 )B388 - 406
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 23 )C1 - 23
17X-RAY DIFFRACTION17chain 'C' and (resid 24 through 41 )C24 - 41
18X-RAY DIFFRACTION18chain 'C' and (resid 42 through 56 )C42 - 56
19X-RAY DIFFRACTION19chain 'C' and (resid 57 through 72 )C57 - 72
20X-RAY DIFFRACTION20chain 'C' and (resid 73 through 90 )C73 - 90
21X-RAY DIFFRACTION21chain 'C' and (resid 91 through 97 )C91 - 97
22X-RAY DIFFRACTION22chain 'D' and (resid 17 through 27 )D17 - 27
23X-RAY DIFFRACTION23chain 'D' and (resid 28 through 46 )D28 - 46
24X-RAY DIFFRACTION24chain 'D' and (resid 47 through 66 )D47 - 66
25X-RAY DIFFRACTION25chain 'D' and (resid 67 through 83 )D67 - 83
26X-RAY DIFFRACTION26chain 'D' and (resid 84 through 96 )D84 - 96
27X-RAY DIFFRACTION27chain 'D' and (resid 97 through 112 )D97 - 112
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 8 )E1 - 8
29X-RAY DIFFRACTION29chain 'E' and (resid 9 through 23 )E9 - 23
30X-RAY DIFFRACTION30chain 'E' and (resid 24 through 35 )E24 - 35
31X-RAY DIFFRACTION31chain 'E' and (resid 36 through 56 )E36 - 56
32X-RAY DIFFRACTION32chain 'E' and (resid 57 through 79 )E57 - 79
33X-RAY DIFFRACTION33chain 'E' and (resid 80 through 99 )E80 - 99
34X-RAY DIFFRACTION34chain 'F' and (resid 17 through 47 )F17 - 47
35X-RAY DIFFRACTION35chain 'F' and (resid 48 through 83 )F48 - 83
36X-RAY DIFFRACTION36chain 'F' and (resid 84 through 96 )F84 - 96
37X-RAY DIFFRACTION37chain 'F' and (resid 97 through 112 )F97 - 112

+
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://pdbjlvh1.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