[English] 日本語
Yorodumi
- PDB-4ddg: Crystal structure of human OTUB1/UbcH5b~Ub/Ub -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ddg
TitleCrystal structure of human OTUB1/UbcH5b~Ub/Ub
Components
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
KeywordsHYDROLASE/LIGASE / inhibition / HYDROLASE-LIGASE complex
Function / homology
Function and homology information


negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein deubiquitination / protein K48-linked ubiquitination / protein autoubiquitination ...negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein deubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / 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 / positive regulation of TORC1 signaling / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling
Similarity search - Function
Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin thioesterase OTUB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2987 Å
AuthorsJuang, Y.C. / Sanches, M. / Sicheri, F.
CitationJournal: Mol.Cell / Year: 2012
Title: OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function.
Authors: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / ...Authors: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / Klevit, R.E. / Sicheri, F. / Durocher, D.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C
J: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
K: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
L: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
M: Polyubiquitin-C
N: Polyubiquitin-C
O: Polyubiquitin-C
P: Polyubiquitin-C
Q: Polyubiquitin-C
R: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)377,61718
Polymers377,61718
Non-polymers00
Water00
1
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)188,8099
Polymers188,8099
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-69 kcal/mol
Surface area63270 Å2
MethodPISA
2
J: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
K: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
L: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
M: Polyubiquitin-C
N: Polyubiquitin-C
O: Polyubiquitin-C
P: Polyubiquitin-C
Q: Polyubiquitin-C
R: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)188,8099
Polymers188,8099
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-66 kcal/mol
Surface area63600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.566, 104.928, 148.479
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21H
31I
41Q
51P
61R
12A
22B
32C
42J
52K
62L
13A
23B
33C
43J
53K
63L
14D
24E
34F
44N
54M
64O

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYchain 'G'GG1 - 761 - 76
21METMETGLYGLYchain 'H'HH1 - 761 - 76
31METMETGLYGLYchain 'I'II1 - 761 - 76
41METMETGLYGLYchain 'Q'QQ1 - 761 - 76
51METMETGLYGLYchain 'P'PP1 - 761 - 76
61METMETGLYGLYchain 'R'RR1 - 761 - 76
12ALAALAALAALAchain 'A' and (resseq 1:150 ) and (not element H) and (not element D)AA02
22ALAALAALAALAchain 'B' and (resseq 1:150 ) and (not element H) and (not element D)BB02
32ALAALAALAALAchain 'C' and (resseq 1:150 ) and (not element H) and (not element D)CC02
42ALAALAALAALAchain 'J' and (resseq 1:150 ) and (not element H) and (not element D)JJ02
52ALAALAALAALAchain 'K' and (resseq 1:150 ) and (not element H) and (not element D)KK02
62ALAALAALAALAchain 'L' and (resseq 1:150 ) and (not element H) and (not element D)LL02
13ALAALAALAALAchain 'A' and (resseq 1025:1271 ) and (not element H) and (not element D)AA02
23ALAALAALAALAchain 'B' and (resseq 1025:1271 ) and (not element H) and (not element D)BB02
33ALAALAALAALAchain 'C' and (resseq 1025:1271 ) and (not element H) and (not element D)CC02
43ALAALAALAALAchain 'J' and (resseq 1025:1271 ) and (not element H) and (not element D)JJ02
53ALAALAALAALAchain 'K' and (resseq 1025:1271 ) and (not element H) and (not element D)KK02
63ALAALAALAALAchain 'L' and (resseq 1025:1271 ) and (not element H) and (not element D)LL02
14METMETGLYGLYchain 'D'DD1 - 761 - 76
24METMETGLYGLYchain 'E'EE1 - 761 - 76
34METMETGLYGLYchain 'F'FF1 - 761 - 76
44METMETGLYGLYchain 'N'NN1 - 761 - 76
54METMETGLYGLYchain 'M'MM1 - 761 - 76
64METMETGLYGLYchain 'O'OO1 - 761 - 76

NCS ensembles :
ID
1
2
3
4
DetailsThe biological complex defined by the author consists of: Complex 1: chain H, chain E, residues 1 to 147 of chain C, and residues 1025-1271 of Chain B; Complex 2: chain G, chain D, residues 1 to 147 of chain B, and residues 1025-1271 of Chain A; Complex 3: chain I, chain F, residues 1 to 147 of chain A, and residues 1025-1271 of Chain C; Complex 4: chain Q, chain N, residues 1 to 147 of chain L, and residues 1025-1271 of Chain K; Complex 5: chain P, chain M, residues 1 to 147 of chain K, and residues 1025-1271 of Chain J; Complex 6: chain R, chain O, residues 1 to 147 of chain J, and residues 1025-1271 of Chain L

-
Components

#1: Protein
Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / Otubain-1 / hOTU1 / Ubiquitin-specific-processing protease OTUB1


Mass: 45782.543 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: E2, HSPC263, OTB1, OTU1, OTUB1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P62837, UniProt: Q96FW1, ubiquitin-protein ligase, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-C / Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 12
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 198.25 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.2987→49.29 Å / Num. all: 60666 / Num. obs: 60387 / % possible obs: 99.54 %
Reflection shellResolution: 3.2987→3.5 Å / % possible all: 97.6

-
Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESK AND 2ZFY

2esk

2zfy


Resolution: 3.2987→49.121 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 33.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2802 3053 5.06 %
Rwork0.2332 --
obs0.2356 60385 99.54 %
all-60402 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 110.304 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7794 Å20 Å2-2.5662 Å2
2--3.1302 Å2-0 Å2
3---1.6492 Å2
Refinement stepCycle: LAST / Resolution: 3.2987→49.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26568 0 0 0 26568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427126
X-RAY DIFFRACTIONf_angle_d0.93836660
X-RAY DIFFRACTIONf_dihedral_angle_d16.51110326
X-RAY DIFFRACTIONf_chiral_restr0.074032
X-RAY DIFFRACTIONf_plane_restr0.0054782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G601X-RAY DIFFRACTIONPOSITIONAL0.001
12H601X-RAY DIFFRACTIONPOSITIONAL0.001
13I601X-RAY DIFFRACTIONPOSITIONAL0.001
14Q601X-RAY DIFFRACTIONPOSITIONAL0.001
15P601X-RAY DIFFRACTIONPOSITIONAL0.001
16R601X-RAY DIFFRACTIONPOSITIONAL0.001
21A1191X-RAY DIFFRACTIONPOSITIONAL0.003
22B1191X-RAY DIFFRACTIONPOSITIONAL0.003
23C1191X-RAY DIFFRACTIONPOSITIONAL0.003
24J1191X-RAY DIFFRACTIONPOSITIONAL0.002
25K1191X-RAY DIFFRACTIONPOSITIONAL0.002
26L1191X-RAY DIFFRACTIONPOSITIONAL0.003
31A2026X-RAY DIFFRACTIONPOSITIONAL0.002
32B2026X-RAY DIFFRACTIONPOSITIONAL0.002
33C2026X-RAY DIFFRACTIONPOSITIONAL0.002
34J2026X-RAY DIFFRACTIONPOSITIONAL0.001
35K2026X-RAY DIFFRACTIONPOSITIONAL0.002
36L2026X-RAY DIFFRACTIONPOSITIONAL0.002
41D601X-RAY DIFFRACTIONPOSITIONAL0.001
42E601X-RAY DIFFRACTIONPOSITIONAL0.001
43F601X-RAY DIFFRACTIONPOSITIONAL0.001
44N601X-RAY DIFFRACTIONPOSITIONAL0.001
45M601X-RAY DIFFRACTIONPOSITIONAL0.001
46O601X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2987-3.35020.39611360.37652567X-RAY DIFFRACTION99
3.3502-3.40520.42591450.37182578X-RAY DIFFRACTION100
3.4052-3.46390.41291280.36972597X-RAY DIFFRACTION99
3.4639-3.52680.41141240.32822601X-RAY DIFFRACTION100
3.5268-3.59460.3751390.32472582X-RAY DIFFRACTION100
3.5946-3.6680.40921260.32162610X-RAY DIFFRACTION100
3.668-3.74770.34551450.2932621X-RAY DIFFRACTION100
3.7477-3.83490.35671430.27482588X-RAY DIFFRACTION100
3.8349-3.93070.33761410.28182564X-RAY DIFFRACTION99
3.9307-4.0370.30171540.24652607X-RAY DIFFRACTION100
4.037-4.15570.27741350.2452619X-RAY DIFFRACTION100
4.1557-4.28980.3141380.22612564X-RAY DIFFRACTION100
4.2898-4.4430.26981300.21222635X-RAY DIFFRACTION100
4.443-4.62070.25261250.20752641X-RAY DIFFRACTION100
4.6207-4.83090.27471410.19862591X-RAY DIFFRACTION100
4.8309-5.08530.25761450.21162598X-RAY DIFFRACTION100
5.0853-5.40360.27331380.21832610X-RAY DIFFRACTION100
5.4036-5.82020.27141400.24162654X-RAY DIFFRACTION100
5.8202-6.40470.32061470.25072627X-RAY DIFFRACTION100
6.4047-7.32890.26881710.20212607X-RAY DIFFRACTION100
7.3289-9.22360.19911330.17382659X-RAY DIFFRACTION100
9.2236-49.12680.16841290.17722612X-RAY DIFFRACTION95
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)
14.0807-0.54620.32554.9080.94393.3389-0.419-0.8663-0.26640.54220.5825-0.4760.47961.8712-0.20260.94190.14920.16581.63360.00610.4728-58.9105-14.46029.1567
20.4574-0.38890.25190.6582-0.41360.2849-1.0755-0.82521.45521.0662-0.0036-0.6423-1.5783-0.1924-0.48981.93240.3414-1.60011.0264-0.23341.8534-22.93399.875417.1484
33.078-0.57960.47055.10690.15214.0853-0.2898-0.10990.28450.5541-0.2047-0.23870.18620.1770.5010.1894-0.0208-0.05780.30640.02510.2552-36.0794-9.0058-9.4012
42.3740.0549-0.31741.5529-0.53223.31430.05980.2840.8090.37170.4770.5065-0.964-0.5032-0.28430.42010.12920.13670.41430.30350.7802-54.331913.8772-42.3539
53.3648-0.077-0.98243.19540.32383.83010.2069-0.2358-0.2104-0.27640.08820.02130.37180.2477-0.03520.4495-0.03270.40840.32320.34310.1768-70.490441.049720.0663
63.4590.66620.28952.146-0.39613.1508-0.43520.3382-0.5676-0.03130.1473-0.1456-0.12640.00080.29780.37690.01080.10250.32280.02320.0702-45.202355.8861-10.6272
72.9494-1.18230.69372.0690.7833.731-1.1612-0.06340.97710.2854-0.8336-1.6717-1.25011.02781.11791.12410.0984-0.47241.5070.82552.3957-1.9547-6.997321.3419
84.13830.65121.72962.7618-0.10123.957-0.12680.4125-0.9753-0.3865-0.1439-0.61250.52771.46680.3010.24640.00240.12070.77110.16950.5682-56.1234-3.5318-63.2212
91.16080.1223-0.55182.11241.93583.71890.09780.9546-1.1516-0.242-0.0184-0.97431.18291.03090.28481.08330.2070.42931.5423-0.4931.3303-31.184635.142-21.2524
103.45971.2149-0.65222.2868-0.05460.1409-0.7744-1.9095-0.59161.03450.246-0.2977-0.7385-1.50420.07581.19770.7024-0.09692.435-0.16441.0369-31.3618-12.909626.6998
111.69240.4790.43953.6849-0.14954.8960.1682-0.40190.3535-0.0156-0.26450.04040.7237-0.3778-0.01910.12590.0235-0.15480.7978-0.09380.3539-98.122247.760941.5723
125.20070.402-2.00172.57060.9272.9649-0.5086-0.1912-1.7469-0.0422-0.26820.59530.8081-0.29660.43230.3589-0.21970.2470.5334-0.16810.924-92.0553-15.475-6.5831
133.590.93150.74163.8721-0.35532.15680.00850.0968-0.1019-0.0482-0.23110.05520.01-0.57210.19690.44710.11710.07011.39320.26911.10179.8367-13.3747-80.2532
142.55070.24750.98594.7121-0.28893.7965-0.3027-0.10470.4058-0.1071-0.0958-0.4224-0.77950.05520.36950.41780.0522-0.1560.66580.07190.5706-13.0959-8.5163-61.5791
152.2311-0.6458-0.60114.19690.02213.0654-0.14860.17420.4181-0.3245-0.0793-0.2555-0.710.4860.22040.7401-0.1225-0.33610.45660.11840.5977-26.940410.6581-87.4801
161.18210.60020.36481.1696-0.37972.0293-0.4755-0.53481.26910.2594-0.0378-0.7963-0.56070.8415-2.2680.20540.0083-0.8521.3101-0.74131.99974.872813.396-27.3988
172.96240.3984-1.2623.4864-1.5033.667-0.09640.20170.4343-0.4078-0.09790.16910.1852-0.54540.09820.4329-0.10120.08711.3269-0.40341.266421.52541.502-93.1211
182.9861-0.42220.27132.97040.17752.4779-0.438-0.3978-0.39930.22890.317-0.3195-0.33120.27660.0830.3013-0.01860.00320.4407-0.1350.1486-4.0556.3017-61.992
194.47890.6505-0.68031.6485-1.08443.2077-0.8028-0.54620.13120.1359-0.12530.47740.5436-0.57210.83721.1272-0.1738-0.19820.7074-0.23810.8545-47.1965-7.0626-92.1962
201.83570.430.43480.9924-0.21242.3652-0.1334-0.452-0.89320.0405-0.5350.2396-0.0706-1.2376-0.29570.47760.1036-0.36641.6826-0.4341.53236.9972-4.6255-7.2317
211.94950.093-0.07823.0763-1.28244.24980.098-1.6565-1.49530.5155-0.18930.79281.4231-0.48870.10021.0656-0.03510.42371.49180.49721.3305-18.051435.1583-52.1277
224.7753-0.60571.23683.24710.0322.73220.3415-0.5625-1.1439-0.509-0.1719-0.13260.04381.1875-0.09630.67570.00250.00150.8090.23990.8103-17.7606-11.2334-97.5855
231.0545-0.52680.73342.06160.7664.5475-0.15280.74910.7884-0.1670.19410.28220.4024-0.40810.07180.3084-0.3418-0.3720.91250.31040.758649.308347.2202-114.8069
244.81750.7614-1.87754.0405-0.89933.2463-0.6080.1884-1.83030.10670.0333-0.35320.4703-0.28670.47160.50160.0060.1770.57360.04140.902842.9515-14.7086-64.1468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:147)
2X-RAY DIFFRACTION2chain 'A' and (resseq 1025:1271)
3X-RAY DIFFRACTION3chain 'B' and (resseq -1:147)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1025:1271)
5X-RAY DIFFRACTION5chain 'C' and (resseq -1:147)
6X-RAY DIFFRACTION6chain 'C' and (resseq 1025:1271)
7X-RAY DIFFRACTION7chain 'D' and (resseq 1:76)
8X-RAY DIFFRACTION8chain 'E' and (resseq 1:76)
9X-RAY DIFFRACTION9chain 'F' and (resseq 1:76)
10X-RAY DIFFRACTION10chain 'G' and (resseq 1:76)
11X-RAY DIFFRACTION11chain 'H' and (resseq 1:76)
12X-RAY DIFFRACTION12chain 'I' and (resseq 1:76)
13X-RAY DIFFRACTION13chain 'J' and (resseq -1:147)
14X-RAY DIFFRACTION14chain 'K' and (resseq -1:147)
15X-RAY DIFFRACTION15chain 'J' and (resseq 1025:1271)
16X-RAY DIFFRACTION16chain 'K' and (resseq 1025:1271)
17X-RAY DIFFRACTION17chain 'L' and (resseq -1:147)
18X-RAY DIFFRACTION18chain 'L' and (resseq 1025:1271)
19X-RAY DIFFRACTION19chain 'M' and (resseq 1:76)
20X-RAY DIFFRACTION20chain 'N' and (resseq 1:76)
21X-RAY DIFFRACTION21chain 'O' and (resseq 1:76)
22X-RAY DIFFRACTION22chain 'P' and (resseq 1:76)
23X-RAY DIFFRACTION23chain 'Q' and (resseq 1:76)
24X-RAY DIFFRACTION24chain 'R' and (resseq 1:76)

+
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