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- PDB-5yj1: Mouse Cereblon thalidomide binding domain complexed with R-form t... -

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Basic information

Entry
Database: PDB / ID: 5yj1
TitleMouse Cereblon thalidomide binding domain complexed with R-form thalidomide
ComponentsProtein cereblon
KeywordsMETAL BINDING PROTEIN / Zinc binding protein
Function / homology
Function and homology information


negative regulation of large conductance calcium-activated potassium channel activity / negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination ...negative regulation of large conductance calcium-activated potassium channel activity / negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Peptide methionine sulfoxide reductase. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain ...Peptide methionine sulfoxide reductase. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-6EL / Protein cereblon
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMori, T. / Hakoshima, T.
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis of thalidomide enantiomer binding to cereblon
Authors: Mori, T. / Ito, T. / Liu, S. / Ando, H. / Sakamoto, S. / Yamaguchi, Y. / Tokunaga, E. / Shibata, N. / Handa, H. / Hakoshima, T.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
D: Protein cereblon
G: Protein cereblon
J: Protein cereblon
M: Protein cereblon
P: Protein cereblon
S: Protein cereblon
V: Protein cereblon
Y: Protein cereblon
b: Protein cereblon
e: Protein cereblon
h: Protein cereblon
k: Protein cereblon
n: Protein cereblon
q: Protein cereblon
t: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,42478
Polymers197,36416
Non-polymers8,06062
Water14,160786
1
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6220 Å2
MethodPISA
2
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
3
G: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6593
Polymers12,3351
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6340 Å2
MethodPISA
4
J: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area5680 Å2
MethodPISA
5
M: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9476
Polymers12,3351
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5790 Å2
MethodPISA
6
P: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7554
Polymers12,3351
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5650 Å2
MethodPISA
7
S: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5730 Å2
MethodPISA
8
V: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5850 Å2
MethodPISA
9
Y: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9476
Polymers12,3351
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5730 Å2
MethodPISA
10
b: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5710 Å2
MethodPISA
11
e: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5760 Å2
MethodPISA
12
h: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7554
Polymers12,3351
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5800 Å2
MethodPISA
13
k: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5870 Å2
MethodPISA
14
n: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9476
Polymers12,3351
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5680 Å2
MethodPISA
15
q: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7554
Polymers12,3351
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5730 Å2
MethodPISA
16
t: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8515
Polymers12,3351
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.615, 201.615, 123.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11t-504-

SO4

21t-504-

SO4

31t-611-

HOH

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Components

#1: Protein
Protein cereblon / Protein PiL


Mass: 12335.271 Da / Num. of mol.: 16 / Fragment: UNP residues 322-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crbn / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C7D2
#2: Chemical
ChemComp-6EL / 2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-dione


Mass: 258.229 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C13H10N2O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.0M ammonium sulfate 0.1M sodium acetate (pH5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 130317 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.6
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 12954 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WX2

3wx2


Resolution: 2→19.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22766 6364 5 %RANDOM
Rwork0.19882 ---
obs0.20025 120034 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11798 0 470 786 13054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212576
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.97517115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.01951468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.22723.704432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38152081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6171532
X-RAY DIFFRACTIONr_chiral_restr0.080.21903
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0219072
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.3633.0026016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3774.4637436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0033.3446560
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.99326.12419542
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 443 -
Rwork0.237 8790 -
obs--99.92 %

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