[English] 日本語
Yorodumi
- PDB-7bbf: Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bbf
TitleCrystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2
Components
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 2
KeywordsLIGASE / E2 conjugating enzyme / ubiquitin chain elongation
Function / homology
Function and homology information


error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity ...error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / regulation of DNA repair / ubiquitin ligase complex / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / antiviral innate immune response / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / : / positive regulation of DNA repair / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / ubiquitin binding / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Nonhomologous End-Joining (NHEJ) / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Stabilization of p53 / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling
Similarity search - Function
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : ...Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsKiss, L. / Neuhaus, D. / James, L.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105181010 United Kingdom
Medical Research Council (MRC, United Kingdom)U105178934 United Kingdom
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination.
Authors: Kiss, L. / Clift, D. / Renner, N. / Neuhaus, D. / James, L.C.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: 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
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin-conjugating enzyme E2 variant 2
E: Ubiquitin-conjugating enzyme E2 variant 2
G: Ubiquitin-conjugating enzyme E2 N
D: Ubiquitin-conjugating enzyme E2 N
A: Ubiquitin-conjugating enzyme E2 N
I: Polyubiquitin-C
C: Polyubiquitin-C
F: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)128,0679
Polymers128,0679
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.840, 145.840, 49.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 4 through 9 or (resid 10...
21(chain D and (resid 4 through 23 or (resid 24...
31(chain G and (resid 4 through 9 or (resid 10...
12(chain B and ((resid 5 and (name N or name...
22(chain E and ((resid 5 and (name N or name...
32(chain H and (resid 5 through 71 or (resid 72...
13(chain C and (resid 1 through 59 or resid 61...
23(chain F and (resid 1 through 5 or (resid 6...
33(chain I and (resid 1 through 5 or (resid 6...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUILEILE(chain A and (resid 4 through 9 or (resid 10...AF4 - 95 - 10
121LYSLYSLYSLYS(chain A and (resid 4 through 9 or (resid 10...AF1011
131GLYGLYILEILE(chain A and (resid 4 through 9 or (resid 10...AF3 - 1524 - 153
141GLYGLYILEILE(chain A and (resid 4 through 9 or (resid 10...AF3 - 1524 - 153
151GLYGLYILEILE(chain A and (resid 4 through 9 or (resid 10...AF3 - 1524 - 153
211LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 235 - 24
221LYSLYSALAALA(chain D and (resid 4 through 23 or (resid 24...DE24 - 2525 - 26
231LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
241LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
251LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
261LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
311LEULEUILEILE(chain G and (resid 4 through 9 or (resid 10...GD4 - 95 - 10
321LYSLYSLYSLYS(chain G and (resid 4 through 9 or (resid 10...GD1011
331METMETILEILE(chain G and (resid 4 through 9 or (resid 10...GD1 - 1522 - 153
112THRTHRTHRTHR(chain B and ((resid 5 and (name N or name...BB510
122THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
132THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
142THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
152THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
212THRTHRTHRTHR(chain E and ((resid 5 and (name N or name...EC510
222THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
232THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
242THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
252THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
312THRTHRPROPRO(chain H and (resid 5 through 71 or (resid 72...HA5 - 7110 - 76
322LYSLYSLYSLYS(chain H and (resid 5 through 71 or (resid 72...HA7277
332SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
342SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
352SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
362SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
113METMETTYRTYR(chain C and (resid 1 through 59 or resid 61...CH1 - 591 - 59
123ILEILEARGARG(chain C and (resid 1 through 59 or resid 61...CH61 - 7261 - 72
133METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
143METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
153METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
163METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
173METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
183METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
213METMETVALVAL(chain F and (resid 1 through 5 or (resid 6...FI1 - 51 - 5
223LYSLYSLYSLYS(chain F and (resid 1 through 5 or (resid 6...FI66
233METMETLEULEU(chain F and (resid 1 through 5 or (resid 6...FI1 - 731 - 73
313METMETVALVAL(chain I and (resid 1 through 5 or (resid 6...IG1 - 51 - 5
323LYSLYSLYSLYS(chain I and (resid 1 through 5 or (resid 6...IG66
333METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74
343METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74
353METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74
363METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.467058080234, -0.883812248909, -0.0270676627517), (0.884188268324, -0.467104115031, -0.00498516586395), (-0.00823746600219, -0.0262612718541, 0.999621173122)70.2326561443, -42.0864235517, 3.04762290417
2given(-0.487293813855, 0.873237847136, 0.000633489190373), (-0.873237820982, -0.487294098228, 0.000412114445697), (0.000668569475094, -0.000352365900229, 0.999999714427)72.2002302673, 43.2891426453, 2.85990601349
3given(-0.434167973493, -0.900821357553, 0.00436492483613), (0.900821991596, -0.434135322012, 0.00680159082084), (-0.00423205022746, 0.00688505318727, 0.999967342363)67.9294463233, -42.1297834466, 3.89645183587
4given(-0.491834013038, 0.870685003853, 0.00263204946845), (-0.870654719988, -0.491839229354, 0.00738451287308), (0.00772412980154, 0.00134034830775, 0.99996927017)72.4517995597, 43.0178986667, 2.45730362017
5given(-0.522082918086, -0.852890303814, -0.00274887315107), (0.852858052369, -0.522087644106, 0.0075917310792), (-0.007910066534, 0.00161911451332, 0.999967404127)73.3613436463, -45.0544462733, -0.341718131093
6given(-0.472445986283, 0.881218286557, -0.0157835827244), (-0.881228272218, -0.47260899149, -0.00880189792165), (-0.0152158565184, 0.00975051798886, 0.999836689219)74.2060232575, 44.5388727484, -2.26592333698

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 16929.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15819
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17182.756 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bicine Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2 % of each Anesthetic alkaloids (lidocaine HCl H2O, procaine HCl, proparacaine HCl, tetracaine HCl)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.54→47.74 Å / Num. obs: 38540 / % possible obs: 99.89 % / Redundancy: 5.3 % / Biso Wilson estimate: 79.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05449 / Net I/σ(I): 15.81
Reflection shellResolution: 2.54→2.63 Å / Rmerge(I) obs: 1.347 / Num. unique obs: 3845 / CC1/2: 0.497

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5S

Resolution: 2.54→47.74 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 35.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 2017 5.24 %
Rwork0.2056 36489 -
obs0.2081 38506 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.52 Å2 / Biso mean: 109.3076 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.54→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8586 0 0 40 8626
Biso mean---85.41 -
Num. residues----1098
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1961X-RAY DIFFRACTION13.874TORSIONAL
12D1961X-RAY DIFFRACTION13.874TORSIONAL
13G1961X-RAY DIFFRACTION13.874TORSIONAL
21B2033X-RAY DIFFRACTION13.874TORSIONAL
22E2033X-RAY DIFFRACTION13.874TORSIONAL
23H2033X-RAY DIFFRACTION13.874TORSIONAL
31C1002X-RAY DIFFRACTION13.874TORSIONAL
32F1002X-RAY DIFFRACTION13.874TORSIONAL
33I1002X-RAY DIFFRACTION13.874TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.610.40061470.353626212768100
2.61-2.680.35941440.321725752719100
2.68-2.750.34771460.315426532799100
2.75-2.840.35571400.316126062746100
2.84-2.950.34641400.332625902730100
2.95-3.060.34241500.302826142764100
3.06-3.20.31871400.274226072747100
3.2-3.370.36641480.278425822730100
3.37-3.580.27611460.257626232769100
3.58-3.860.24211380.213326182756100
3.86-4.240.26961330.187326012734100
4.25-4.860.20491640.170626202784100
4.86-6.120.21581400.174426012741100
6.12-47.740.20161410.13892578271999
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)
17.6926-0.4696-1.59316.69090.89986.01131.126-0.14940.410.6719-0.35460.2321-0.43570.0318-0.56120.6790.0036-0.00230.7366-0.2610.775424.6420.885618.8425
21.8621.42712.49743.41172.81813.15530.0810.2054-0.3388-0.02971.0386-0.7463-0.18651.3529-0.54320.7392-0.10210.05041.2018-0.26160.954435.205717.217615.8274
34.01091.92293.32791.2012.23365.4160.04840.10830.03250.56760.0656-0.9001-0.9821.5397-0.00950.9685-0.3490.06611.3048-0.22310.873241.613732.746224.1491
44.42740.8711.81035.51932.98782.54210.9066-0.5519-0.89460.8723-0.7858-0.63290.13480.5964-0.13310.8041-0.1651-0.10721.2247-0.22210.77835.937918.690527.1786
57.1916-0.89410.67375.1341-1.7412.96711.6664-1.1727-1.20720.91790.031-0.7374-0.23441.0917-0.61071.1421-0.2484-0.09351.7079-0.451.222846.039424.075932.5694
64.35073.3796-2.30039.54990.52732.1071.3875-1.36830.24922.1866-0.5268-1.0830.51821.4742-0.91780.8207-0.1258-0.07451.0218-0.25320.879835.216922.736836.3882
70.04030.00080.19896.89424.68328.16470.604-1.2270.53060.4663-0.659-0.067-0.53460.3307-0.16670.8897-0.22720.06431.1314-0.29330.86933.883630.132231.0577
85.35040.2243-0.01074.7173-1.76498.61030.9329-0.0159-0.4092-0.75130.0797-0.57511.23820.3433-0.17741.246-0.26090.01451.9998-0.49661.224951.823526.618123.1724
96.6095-2.63981.75912.101-0.18383.28130.0881-1.6127-0.276-0.27970.45630.15030.8384-0.3064-0.24440.82940.18020.11971.090.03590.683448.4799-31.400417.4347
105.0993-3.2629-3.21492.11141.93392.1314-0.8355-0.5484-0.44590.52680.810.38130.5614-0.53340.05030.96650.09310.10341.26880.14160.649832.7527-32.562612.2709
114.5790.4241-2.67453.42971.34643.8075-0.1162-0.48040.4251-0.076-0.00090.0293-0.4945-0.65330.07540.64260.30040.00491.08120.03580.529935.449-21.971718.5703
122.20072.7609-0.76632.4659-1.49995.40060.0384-0.64390.3630.4544-0.6043-0.1313-0.44770.17130.31870.71780.241-0.00731.10910.00260.582434.5651-20.303829.2098
133.78080.7844-1.51462.8644-0.09687.0745-0.6981-1.1792-1.32610.65990.21290.92130.7937-0.50530.37910.64970.23680.12911.07630.03110.714326.6704-26.826828.3708
144.032-0.53010.38794.9594-1.47969.159-0.5428-0.1621.4108-0.6943-1.0913-2-0.8756-1.30770.79621.34330.6662-0.05111.2957-0.04681.401223.283-10.917821.953
152.0499-1.5658-1.01587.91515.16267.5059-0.7928-0.38980.22440.09991.34420.2421-1.63191.2103-0.12381.14720.03520.06560.73170.081.336975.039715.42520.9164
160.3139-1.30410.88345.5335-3.68672.44110.40930.6340.9367-0.4335-0.1009-1.8349-0.04611.4114-0.85471.22260.0450.28131.0394-0.3431.621983.18431.613515.765
172.8103-0.0770.95864.8236-0.56124.8662-0.0624-0.0743-0.1082-0.43241.11970.35490.5366-0.9261-1.17871.1164-0.0218-0.04610.81310.07631.2868.365.243515.2379
182.07150.8251-1.79247.0818-2.08676.68811.27080.2096-1.27610.2613-0.18230.65531.68580.7818-0.61741.3510.1871-0.50540.4694-0.10751.497575.9853-8.099623.6507
193.06960.6764-1.14811.341-0.16152.68910.48830.18960.04011.82421.05560.55730.8435-0.2216-1.081.5502-0.0899-0.2210.70590.19731.346368.9631.52128.0372
204.38892.63112.64911.91430.58446.05050.7525-0.4809-1.26220.77791.0113-0.10410.7524-1.0341-0.99581.6180.0003-0.06060.93090.29621.536567.4313-9.24233.7982
211.2989-0.4895-0.93950.6936-0.50725.19840.8447-1.9685-0.21750.4141-0.33011.8634-0.0575-1.0542-0.74481.1118-0.05360.03730.82740.22861.218572.6870.499937.2934
221.7954-1.1671-0.42272.165-2.97088.55170.3894-0.36730.63391.53540.45590.339-1.03412.8321-0.58131.62790.13380.30220.61680.02231.118977.575410.098932.6208
234.2413-1.58120.18284.0813-1.42074.58981.4305-0.5237-0.77260.49030.0735-1.3940.2741.6552-1.10041.24840.0971-0.37930.5643-0.11871.372580.5366-2.321528.9866
248.42472.08981.99152.44310.22822.3037-1.3080.017-0.8226-0.91030.4819-2.1339-0.05320.1230.76341.8469-0.1251-0.13571.13070.14921.461478.8665-15.324635.5328
251.62281.5672-1.00552.37210.88494.5660.46890.3926-0.5783-0.732-0.09651.1029-0.4898-1.37980.11982.1948-0.1742-0.36731.3436-0.05141.593665.2905-15.357923.7632
266.46521.3541-1.90294.6332-0.29327.00750.13750.3359-0.350.26250.3006-0.01460.9055-0.6655-0.43690.7982-0.1091-0.13680.62850.02770.651813.3174.438111.2925
275.4869-5.68824.79887.8393-5.99244.974-1.13922.10192.062-1.04780.2448-2.5479-2.03751.1574-0.36862.2254-0.2163-0.0071.80850.28581.578619.831810.5223-5.3768
286.07690.49121.47743.63912.34833.77830.0521.2574-0.9272-1.03110.5657-1.1698-0.72031.8013-0.75241.4046-0.01620.23071.6306-0.2781.173429.79441.6672-2.6829
295.58670.46061.60051.36850.66225.1168-0.4674-0.87670.55060.13350.14260.5808-0.9093-0.45210.48391.07070.14230.17840.7967-0.0081.610568.599236.044519.2877
302.92991.2403-0.43435.19822.78245.41570.1715-0.34310.29410.0731-0.18980.31910.2426-1.5760.03630.81820.10090.14980.65180.1341.575462.457126.529110.7349
312.42211.5328-0.3886.88391.26826.12960.0653-0.24040.02130.64540.2939-0.50240.8753-0.0343-0.27840.75550.04430.12760.57370.11391.435171.229221.394710.3236
321.11360.62010.29463.9671.01415.7689-0.36940.71880.9669-0.99510.8594-0.1727-1.06940.8231-0.36520.7528-0.02030.23190.49770.02111.508174.012930.10255.8327
335.4795-2.64560.05065.9543-0.50457.46440.7790.53340.77590.649-0.5548-2.00121.762-0.00570.11911.74670.02280.17051.5936-0.05211.651568.792115.8513-6.8833
342.98021.04940.1873.0993-1.18713.10380.5918-0.38370.5571-0.3243-0.5311.7648-0.5782-0.16910.94121.3569-0.3427-0.02581.22290.23662.19354.037917.96120.6064
352.22564.1469-1.18119.1748-0.38894.9899-0.049-0.9335-1.54090.39-0.4719-1.70181.04821.170.36640.58560.1248-0.0530.76290.0210.613469.5474-40.731917.5713
365.66021.29-1.84424.3864-3.83059.7217-0.4002-0.3950.8588-0.46010.295-1.23620.00770.01590.21510.5909-0.04950.06780.67980.05470.619372.1184-29.707510.5053
373.4189-0.98951.55087.3227-2.49055.17140.0707-0.1750.01880.0745-0.01010.0284-0.4579-0.4057-0.04290.48230.06680.06450.5525-0.02910.442261.2894-28.46769.214
382.8495-3.21640.62068.9111-2.91514.02350.17320.3118-0.2635-1.04450.20640.27970.3118-0.4183-0.33160.5744-0.0382-0.02520.5369-0.01740.38659.4212-34.042.0631
395.33534.7431-0.46875.8754-0.88152.12950.01782.0167-1.1166-0.66250.35921.774-0.4771-2.2801-0.07381.36260.1369-0.15751.5320.11650.821752.3903-24.8412-10.0808
404.99210.78460.87774.26161.5277.841-0.27820.33960.6828-0.3556-0.54570.153-1.6323-0.08250.22571.32260.03030.09880.86540.19450.874960.5771-14.0003-2.5495
414.2458-0.95712.02983.3439-0.50524.1708-0.26260.84160.8361-0.1379-0.2633-0.7354-0.69611.56460.16580.8635-0.0547-0.08881.01470.08680.711714.305239.4502-16.0983
425.5422-2.3724-3.36246.8707-1.50956.0174-0.78611.2464-1.2139-1.40590.3087-1.43821.07631.20220.29811.25750.11980.14360.9046-0.07170.690713.585531.1109-18.8313
432.9688-0.57270.28324.0285-1.93455.64480.1336-0.0133-1.07150.06370.1886-0.02631.1914-0.00780.13261.13880.0691-0.02340.785-0.09410.7715.806133.0254-12.4985
443.2391-2.49911.40842.4962-0.87746.9284-0.03820.5942-0.61110.9735-0.52520.60260.07320.97690.33530.99790.10760.01260.7383-0.0030.68779.737738.41-11.0267
450.9271-0.3507-1.22143.36320.55924.52820.2962-0.0907-1.25040.0053-0.39071.28580.1169-1.17430.0831.08570.09620.19711.3664-0.45791.787531.5698-48.0573-10.4849
462.748-0.5389-0.25612.1209-0.56864.34090.46371.57130.78660.3512-1.11260.7946-0.02440.25730.16960.8248-0.03840.05360.935-0.19241.325439.5409-50.5212-17.0743
471.3561-0.41010.08163.8985-1.47034.9420.4454-0.4747-0.1405-0.2941-0.6716-0.0901-0.46422.82290.20211.0287-0.50880.43721.5117-0.54731.436944.2133-47.1882-7.9166
481.44580.5456-0.27842.2487-0.26048.69850.1797-0.8770.13061.414-0.3326-0.4211.37060.15030.30270.5724-0.20910.15621.0229-0.43661.393241.9509-59.4266-9.0367
496.12621.39050.65082.4030.38125.82980.60540.6651-0.0549-0.84120.08420.37280.8172-0.09310.20390.9178-0.19580.13761.2634-0.30211.479633.1593-61.3345-12.6882
500.6201-0.1458-0.57626.95310.16338.00820.6988-0.90260.26510.4398-0.98551.0212-1.4557-1.24440.11720.9732-0.21530.12661.0081-0.16491.55337.0227-50.0949-4.4749
518.08350.06181.80520.0934-0.40122.09720.4305-0.1990.53210.8771-2.28780.88381.2251-0.64251.38111.8856-0.2553-0.21422.4582-0.46611.736547.9532-39.6843-0.5141
523.7726-0.5369-1.8593.05721.56239.6614-1.0710.2776-1.17830.8159-0.8004-0.97361.43011.08831.58551.72050.17940.2491.27830.28961.03697.99446.8303-10.8762
530.0734-0.0244-0.110.1231-0.04550.15350.25970.09-0.3701-1.41280.03070.83770.5167-0.7622-0.12881.08320.13920.29851.02470.23721.2568102.837116.4303-20.9094
544.1556-0.1802-0.38453.72070.79845.0053-0.19591.0723-0.3944-0.93810.41640.81950.89790.5801-0.04871.32870.11140.01881.29640.08750.97792.562714.2613-16.357
552.00630.00713.32514.6051-0.67146.8801-1.3198-0.52891.4709-0.17810.38461.15440.0426-1.48790.93551.11750.30470.24131.46440.23991.16189.976117.0336-8.7849
561.47221.25421.3213.8282-3.11127.480.11880.86921.23950.3095-0.34880.1332-0.36351.76-0.02651.0940.23670.08041.13190.20.9146101.836122.0474-8.4079
576.41161.2696-0.49829.21981.98420.4869-0.7324-0.15070.25680.67990.9513-2.15360.1961.94410.08940.97250.2310.21831.2830.09460.9501107.758615.8769-13.9106
584.28572.39372.49875.6481-0.19657.4244-0.2781-1.91391.25450.5095-1.02291.85870.5979-0.87-0.28071.56480.48530.67651.17580.38320.926594.829513.6515-4.6254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 4 through 35 )H4 - 35
2X-RAY DIFFRACTION2chain 'H' and (resid 36 through 51 )H36 - 51
3X-RAY DIFFRACTION3chain 'H' and (resid 52 through 68 )H52 - 68
4X-RAY DIFFRACTION4chain 'H' and (resid 69 through 87 )H69 - 87
5X-RAY DIFFRACTION5chain 'H' and (resid 88 through 97 )H88 - 97
6X-RAY DIFFRACTION6chain 'H' and (resid 98 through 107 )H98 - 107
7X-RAY DIFFRACTION7chain 'H' and (resid 108 through 136 )H108 - 136
8X-RAY DIFFRACTION8chain 'H' and (resid 137 through 145 )H137 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 21 )B5 - 21
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 30 )B22 - 30
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 78 )B31 - 78
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 114 )B79 - 114
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 134 )B115 - 134
14X-RAY DIFFRACTION14chain 'B' and (resid 135 through 145 )B135 - 145
15X-RAY DIFFRACTION15chain 'E' and (resid 5 through 21 )E5 - 21
16X-RAY DIFFRACTION16chain 'E' and (resid 22 through 30 )E22 - 30
17X-RAY DIFFRACTION17chain 'E' and (resid 31 through 44 )E31 - 44
18X-RAY DIFFRACTION18chain 'E' and (resid 45 through 68 )E45 - 68
19X-RAY DIFFRACTION19chain 'E' and (resid 69 through 87 )E69 - 87
20X-RAY DIFFRACTION20chain 'E' and (resid 88 through 97 )E88 - 97
21X-RAY DIFFRACTION21chain 'E' and (resid 98 through 107 )E98 - 107
22X-RAY DIFFRACTION22chain 'E' and (resid 108 through 114 )E108 - 114
23X-RAY DIFFRACTION23chain 'E' and (resid 115 through 127 )E115 - 127
24X-RAY DIFFRACTION24chain 'E' and (resid 128 through 137 )E128 - 137
25X-RAY DIFFRACTION25chain 'E' and (resid 138 through 145 )E138 - 145
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 113 )G1 - 113
27X-RAY DIFFRACTION27chain 'G' and (resid 114 through 122 )G114 - 122
28X-RAY DIFFRACTION28chain 'G' and (resid 123 through 152 )G123 - 152
29X-RAY DIFFRACTION29chain 'D' and (resid 4 through 30 )D4 - 30
30X-RAY DIFFRACTION30chain 'D' and (resid 31 through 57 )D31 - 57
31X-RAY DIFFRACTION31chain 'D' and (resid 58 through 86 )D58 - 86
32X-RAY DIFFRACTION32chain 'D' and (resid 87 through 113 )D87 - 113
33X-RAY DIFFRACTION33chain 'D' and (resid 114 through 132 )D114 - 132
34X-RAY DIFFRACTION34chain 'D' and (resid 133 through 152 )D133 - 152
35X-RAY DIFFRACTION35chain 'A' and (resid 3 through 17 )A3 - 17
36X-RAY DIFFRACTION36chain 'A' and (resid 18 through 27 )A18 - 27
37X-RAY DIFFRACTION37chain 'A' and (resid 28 through 76 )A28 - 76
38X-RAY DIFFRACTION38chain 'A' and (resid 77 through 113 )A77 - 113
39X-RAY DIFFRACTION39chain 'A' and (resid 114 through 132 )A114 - 132
40X-RAY DIFFRACTION40chain 'A' and (resid 133 through 152 )A133 - 152
41X-RAY DIFFRACTION41chain 'I' and (resid 1 through 22 )I1 - 22
42X-RAY DIFFRACTION42chain 'I' and (resid 23 through 34 )I23 - 34
43X-RAY DIFFRACTION43chain 'I' and (resid 35 through 59 )I35 - 59
44X-RAY DIFFRACTION44chain 'I' and (resid 60 through 74 )I60 - 74
45X-RAY DIFFRACTION45chain 'C' and (resid 1 through 16 )C1 - 16
46X-RAY DIFFRACTION46chain 'C' and (resid 17 through 34 )C17 - 34
47X-RAY DIFFRACTION47chain 'C' and (resid 35 through 44 )C35 - 44
48X-RAY DIFFRACTION48chain 'C' and (resid 45 through 56 )C45 - 56
49X-RAY DIFFRACTION49chain 'C' and (resid 57 through 65 )C57 - 65
50X-RAY DIFFRACTION50chain 'C' and (resid 66 through 71 )C66 - 71
51X-RAY DIFFRACTION51chain 'C' and (resid 72 through 76 )C72 - 76
52X-RAY DIFFRACTION52chain 'F' and (resid 1 through 16 )F1 - 16
53X-RAY DIFFRACTION53chain 'F' and (resid 17 through 22 )F17 - 22
54X-RAY DIFFRACTION54chain 'F' and (resid 23 through 34 )F23 - 34
55X-RAY DIFFRACTION55chain 'F' and (resid 35 through 44 )F35 - 44
56X-RAY DIFFRACTION56chain 'F' and (resid 45 through 54 )F45 - 54
57X-RAY DIFFRACTION57chain 'F' and (resid 55 through 65 )F55 - 65
58X-RAY DIFFRACTION58chain 'F' and (resid 66 through 73 )F66 - 73

+
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