[English] 日本語
Yorodumi
- PDB-9bol: Crystal structure of the complex between VHL, ElonginB, ElonginC,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bol
TitleCrystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsTRANSCRIPTION / VHL / degradation / degrader
Function / homology
Function and homology information


regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / 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 / negative regulation of signal transduction / 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 / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / protein serine/threonine kinase binding / negative regulation of autophagy / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / cilium / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / 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
: / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMurray, J.M. / Wu, H. / Fuhrmann, J. / Fairbrother, W.J. / DiPasquale, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Potency-Enhanced Peptidomimetic VHL Ligands with Improved Oral Bioavailability.
Authors: Wu, H. / Murray, J. / Ishisoko, N. / Frommlet, A. / Deshmukh, G. / DiPasquale, A. / Mulvihill, M.M. / Zhang, D. / Quinn, J.G. / Blake, R.A. / Fairbrother, W.J. / Fuhrmann, J.
History
DepositionMay 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,79517
Polymers86,2126
Non-polymers1,58311
Water6,287349
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9299
Polymers43,1063
Non-polymers8226
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-42 kcal/mol
Surface area17170 Å2
MethodPISA
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8668
Polymers43,1063
Non-polymers7605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-40 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.460, 47.740, 100.350
Angle α, β, γ (deg.)103.62, 94.66, 98.33
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: 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: Escherichia coli (E. coli) / References: UniProt: Q15370
#2: 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: 10843.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 20514.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337

-
Non-polymers , 5 types, 360 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-A1ARP / (4R)-1-[(2S)-2-(4-cyclopropyl-1H-1,2,3-triazol-1-yl)-3,3-dimethylbutanoyl]-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide


Mass: 522.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H34N6O3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→46.66 Å / Num. obs: 52695 / % possible obs: 91.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.6
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Num. unique obs: 3923 / CC1/2: 0.771

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→46.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.95 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24791 2487 4.9 %RANDOM
Rwork0.20171 ---
obs0.20394 48292 88.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.831 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.13 Å2-1.33 Å2
2--2.57 Å2-0.1 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.99→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 104 349 5920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175402
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.687809
X-RAY DIFFRACTIONr_angle_other_deg1.0871.5912534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48621.195318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08915979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7521551
X-RAY DIFFRACTIONr_chiral_restr0.0440.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.472.5582738
X-RAY DIFFRACTIONr_mcbond_other0.472.5582737
X-RAY DIFFRACTIONr_mcangle_it0.8053.8323419
X-RAY DIFFRACTIONr_mcangle_other0.8053.8323420
X-RAY DIFFRACTIONr_scbond_it0.4672.6653011
X-RAY DIFFRACTIONr_scbond_other0.4672.6653012
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7913.9554385
X-RAY DIFFRACTIONr_long_range_B_refined4.530.3656091
X-RAY DIFFRACTIONr_long_range_B_other4.530.3676092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 179 -
Rwork0.303 3597 -
obs--88.95 %
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)
13.4360.3615-0.17377.5312-2.7936.83330.19890.2595-0.4756-0.763-0.2810.48790.0302-0.29270.08210.23690.1179-0.19860.216-0.13850.2002-22.3958-7.5343-36.3661
23.72185.131-0.68497.31670.07595.21370.0502-0.01150.3896-0.0192-0.14120.6699-0.1163-0.2270.0910.17460.1381-0.20970.268-0.12320.3268-24.8964-5.9107-36.5843
32.7548-1.7507-1.63058.40855.99514.9407-0.1335-0.06730.0213-0.30120.03110.4116-0.0191-0.18750.10230.27290.021-0.22780.3666-0.05040.3612-32.4463-5.1912-40.803
45.21680.39491.97936.1019-1.67914.32130.29150.43730.0844-0.8791-0.20251.22380.026-0.1167-0.0890.48550.1226-0.33610.4172-0.05520.3561-31.1836-0.7308-46.3628
52.5634-0.51830.64043.5623-4.82716.5804-0.11510.31430.2126-0.53270.0849-0.07210.6163-0.1520.03030.62360.0824-0.14250.4105-0.16160.3965-23.519-12.5421-47.5651
60.96171.05291.52676.74153.163212.138-0.01420.2332-0.3228-0.5336-0.50320.39130.32220.1160.51750.18350.0637-0.0670.2321-0.150.3151-16.9814-14.3072-34.2827
74.29061.4371-0.64781.45390.7341.0284-0.22950.99340.4344-0.47570.19030.2394-0.332-0.30810.03920.56690.1298-0.23220.5646-0.13090.4081-27.00671.0841-48.0492
89.3826-0.67023.45180.0568-0.34182.7023-0.09480.3529-0.02650.0067-0.0084-0.0004-0.11270.24150.10320.30310.0055-0.02420.270.00620.2346-22.88292.3186-50.9729
910.44060.60478.00363.1249-0.5666.5086-0.10270.60180.2476-0.4311-0.1119-0.27240.04180.48430.21460.26490.09790.06560.26610.03540.2115-6.78793.9301-35.6914
101.16821.71790.5642.8215-0.915310.6005-0.0952-0.02430.0148-0.1136-0.0271-0.0045-0.1957-0.00830.12230.20860.00760.00310.23480.00350.30477.14352.5422-24.5997
119.93841.317-3.5937.6081-2.81664.0637-0.0770.08130.4915-0.8522-0.12380.92590.3063-0.29890.20080.13250.0472-0.09560.1374-0.10010.3324-23.09346.0294-29.8639
124.43230.3070.14395.9333-2.865311.730.15320.2399-0.4394-0.1092-0.02950.8270.225-0.3306-0.12370.07340.0322-0.0790.1142-0.07830.2303-25.52520.3241-25.4151
136.3981-2.93543.25957.49632.87866.5305-0.1129-0.10970.2986-0.0918-0.0130.3639-0.1988-0.26430.12590.1384-0.00270.01540.1622-0.00750.2064-23.62126.2325-17.3662
1411.8028-0.904-3.61114.791-0.90412.10190.19790.060.788-0.1015-0.01930.5602-0.3129-0.3388-0.17860.31480.0721-0.03850.2163-0.07790.2481-21.256911.5444-25.1307
150.51571.1929-0.615910.0252-1.73342.7940.09190.1633-0.1061-0.3401-0.14990.3740.0222-0.08230.05790.070.0587-0.07630.1391-0.0490.1-16.7312-4.4598-25.0308
167.01861.4198-4.56139.0727-2.36168.7481-0.0086-0.0803-0.3478-0.2148-0.24920.72410.6125-0.2990.25780.11320.0022-0.02480.0736-0.04110.1057-13.9854-13.8322-21.6599
177.211-3.6052-4.79774.32783.09445.09540.06720.0132-0.0234-0.0479-0.0787-0.1137-0.12210.08710.01150.1314-0.0017-0.04440.11450.0380.1172-8.08552.5501-21.2214
182.3381-0.01450.5315.2419-3.12894.69370.0015-0.20840.01360.1699-0.07220.1761-0.1075-0.12350.07070.074-0.0105-0.01760.0259-0.00850.0247-6.411-26.7049-5.5246
191.55050.0336-0.15445.90660.13491.34080.1177-0.0480.24310.3583-0.1089-0.2729-0.08840.188-0.00880.107-0.018-0.03880.07980.01880.0813-3.7629-7.5992-13.6573
2011.13560.8233-7.38742.6842-2.59048.9730.1468-0.49710.37350.11970.16440.4609-0.1285-0.6746-0.31110.465-0.00890.03260.3657-0.06080.3262-11.4037-13.99493.0607
212.49691.7119-1.76743.9607-1.25584.0548-0.1014-0.2542-0.24140.0296-0.0154-0.09970.26490.53520.11680.2010.09290.00480.27290.03580.0357-3.0867-25.4814-44.1078
227.86141.1560.977212.24274.2393.6544-0.0236-0.1980.3490.4-0.06450.1315-0.08580.09820.08810.22610.07550.04230.2756-0.00380.0858-10.156-20.0537-36.2142
233.9918-0.05012.07941.0199-0.98127.2904-0.03570.0860.00730.13890.0930.1264-0.3031-0.0364-0.05730.20370.03410.00930.16920.0070.1755-16.1368-22.322-44.0976
243.03434.9678-0.65668.8088-3.985912.6945-0.0320.03910.19060.10190.24060.3475-0.5698-0.833-0.20860.19830.0445-0.03210.22710.00770.0874-12.801-17.1496-54.2488
2512.4166-0.51294.50750.1118-0.20591.67320.17480.089-0.03680.0626-0.16610.02980.13810.1181-0.00870.31070.0190.0210.3626-0.03520.1215-1.7649-19.8008-42.0232
268.0133-3.85340.18358.6606-0.0750.0104-0.15110.083-0.12410.29480.1935-0.1848-0.0208-0.0092-0.04240.29480.00650.00650.30580.00560.31857.9353-23.7479-29.5567
271.048-3.08271.09079.4237-4.69297.5008-0.1042-0.04-0.01450.28940.05150.0158-0.17760.12820.05280.2224-0.011-0.00030.2773-0.03270.16732.6771-16.7102-34.9742
284.84941.35030.71337.8011-6.785212.5769-0.5192-0.560.23380.18780.001-1.0653-0.0607-0.14690.51820.28450.013-0.08640.3524-0.10170.2472.4841-9.9984-48.0501
295.0748-6.15268.53818.1427-10.762814.631-0.2748-0.26250.29250.47190.06010.1278-0.6397-0.27910.21460.4793-0.0410.0450.3836-0.07820.4152-1.10283.7198-63.6383
301.00550.9501-0.83469.6231-1.3372.3642-0.0399-0.1291-0.02190.0667-0.0093-0.09850.15150.14630.04920.11020.0147-0.00960.2441-0.00490.13786.5914-21.1902-55.4484
316.79042.66693.70655.6014-0.105710.89180.1315-0.3624-0.54830.05930.0448-0.11260.8285-0.059-0.17630.13710.02980.0210.23930.04910.07041.3444-25.6645-58.8463
329.2656-1.1597-0.98893.4654-5.01688.3432-0.0896-0.4006-0.2836-0.1717-0.1395-0.25790.33760.22150.22910.2067-0.0098-0.00460.21810.05030.31876.3276-24.4516-68.2079
335.51560.34240.14328.53542.53783.6889-0.1263-0.2721-0.4796-0.1130.2811-1.10280.4320.4972-0.15480.2348-0.00690.02950.4055-0.02090.197310.7689-19.8165-61.4489
3411.13816.9242.42455.97850.93654.0024-0.023-0.1247-0.07450.0789-0.03510.08070.12220.13430.05810.09980.004-0.00670.15060.00750.0189-4.961-18.0813-61.136
352.7751-2.8565-1.52817.03690.72984.2219-0.13650.1484-0.4513-0.13310.00330.66970.4502-0.30020.13320.1512-0.0067-0.00090.27750.00180.1025-14.6845-17.7571-64.6313
369.5738-6.0651-4.49959.56033.86346.2216-0.0003-0.08890.13310.1473-0.00970.097-0.17010.18950.010.1134-0.0534-0.03440.17760.02270.02220.524-9.6077-67.087
375.22441.59672.07032.36650.84164.6593-0.09210.0943-0.1728-0.29670.0471-0.03540.04770.07390.04490.0945-0.0005-0.00950.03780.03390.0502-28.7885-15.9192-84.7017
386.44881.52942.69072.36170.52254.2229-0.0204-0.41190.1935-0.0903-0.02940.15740.0485-0.09660.04980.0947-0.0106-0.00840.07970.01890.0285-31.0489-14.3708-79.649
394.67064.25591.16248.39721.27181.45060.0345-0.0166-0.1416-0.2087-0.0268-0.24490.03250.2067-0.00770.09780.01170.01630.17690.0350.1208-20.1533-16.4276-77.3764
405.28125.9438-1.489610.8712-0.630.7143-0.28810.0994-1.61080.3936-0.4899-0.27430.3184-0.2870.7780.4448-0.26780.19230.4967-0.10181.1421-36.6765-26.1682-79.9879
414.0927-0.40191.18040.8439-0.20211.72930.1111-0.1632-0.14560.033-0.0321-0.0346-0.097-0.03-0.0790.1025-0.0478-0.00860.18320.01280.0098-13.8659-13.1077-71.8545
425.3797-1.1383-0.71853.6680.13054.9273-0.0173-0.07260.6715-0.02180.1056-0.3093-0.49060.1699-0.08820.2065-0.09030.00710.18010.00920.1736-1.6226-1.5674-77.974
432.5221-1.91520.33835.14710.06364.85190.0530.0086-0.1826-0.0075-0.0546-0.28570.23980.02870.00160.1865-0.02020.03980.2234-0.00360.2277-14.6838-19.0079-88.9205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 23
3X-RAY DIFFRACTION3A24 - 35
4X-RAY DIFFRACTION4A36 - 45
5X-RAY DIFFRACTION5A46 - 60
6X-RAY DIFFRACTION6A61 - 72
7X-RAY DIFFRACTION7A73 - 84
8X-RAY DIFFRACTION8A85 - 89
9X-RAY DIFFRACTION9A90 - 99
10X-RAY DIFFRACTION10A100 - 104
11X-RAY DIFFRACTION11B17 - 27
12X-RAY DIFFRACTION12B28 - 38
13X-RAY DIFFRACTION13B39 - 46
14X-RAY DIFFRACTION14B47 - 66
15X-RAY DIFFRACTION15B67 - 83
16X-RAY DIFFRACTION16B84 - 96
17X-RAY DIFFRACTION17B97 - 112
18X-RAY DIFFRACTION18C61 - 141
19X-RAY DIFFRACTION19C142 - 193
20X-RAY DIFFRACTION20C194 - 209
21X-RAY DIFFRACTION21D1 - 45
22X-RAY DIFFRACTION22D46 - 55
23X-RAY DIFFRACTION23D56 - 65
24X-RAY DIFFRACTION24D66 - 72
25X-RAY DIFFRACTION25D73 - 79
26X-RAY DIFFRACTION26D80 - 84
27X-RAY DIFFRACTION27D85 - 89
28X-RAY DIFFRACTION28D90 - 94
29X-RAY DIFFRACTION29D95 - 104
30X-RAY DIFFRACTION30E17 - 27
31X-RAY DIFFRACTION31E28 - 38
32X-RAY DIFFRACTION32E39 - 45
33X-RAY DIFFRACTION33E46 - 66
34X-RAY DIFFRACTION34E67 - 83
35X-RAY DIFFRACTION35E84 - 96
36X-RAY DIFFRACTION36E97 - 112
37X-RAY DIFFRACTION37F61 - 97
38X-RAY DIFFRACTION38F98 - 121
39X-RAY DIFFRACTION39F122 - 135
40X-RAY DIFFRACTION40F136 - 146
41X-RAY DIFFRACTION41F147 - 169
42X-RAY DIFFRACTION42F170 - 193
43X-RAY DIFFRACTION43F194 - 206

+
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