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- PDB-8bc6: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 8bc6
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide
Components
  • Cereblon isoform 4
  • GLN-MET-GLN-SNN
KeywordsSIGNALING PROTEIN / Protein Damage / Protein Ageing / Protein Chain Break / Aspartimide
Function / homologyCULT domain / CULT domain profile. / metal ion binding / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.72 Å
AuthorsHeim, C. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Identification and structural basis of C-terminal cyclic imides as natural degrons for cereblon.
Authors: Heim, C. / Spring, A.K. / Kirchgassner, S. / Schwarzer, D. / Hartmann, M.D.
History
DepositionOct 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cereblon isoform 4
B: Cereblon isoform 4
C: Cereblon isoform 4
D: GLN-MET-GLN-SNN
E: GLN-MET-GLN-SNN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,57213
Polymers41,9015
Non-polymers6718
Water2,090116
1
A: Cereblon isoform 4
D: GLN-MET-GLN-SNN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4846
Polymers14,1342
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-23 kcal/mol
Surface area5870 Å2
MethodPISA
2
B: Cereblon isoform 4
E: GLN-MET-GLN-SNN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3895
Polymers14,1342
Non-polymers2553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-17 kcal/mol
Surface area5680 Å2
MethodPISA
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6982
Polymers13,6331
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.966, 59.015, 88.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cereblon isoform 4


Mass: 13632.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0
#2: Protein/peptide GLN-MET-GLN-SNN


Mass: 501.556 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The last residue is a cyclized asparagine, which is called aminosuccinimide, or more commonly aspartimide
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.5 M (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.718→37.23 Å / Num. obs: 32513 / % possible obs: 99.6 % / Redundancy: 12.73 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.8
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 12.46 % / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 5140 / CC1/2: 0.632 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4V2Y

4v2y


Resolution: 1.72→37.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.727 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22261 1635 5 %RANDOM
Rwork0.19459 ---
obs0.196 30878 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.924 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0 Å2
2--0.93 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.72→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 44 116 2381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132333
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182103
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.6373152
X-RAY DIFFRACTIONr_angle_other_deg1.4051.594817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3515280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50420.08125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10215347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9291519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022675
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02630
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_it1.6632.2571135
X-RAY DIFFRACTIONr_mcbond_other1.6622.2561134
X-RAY DIFFRACTIONr_mcangle_it2.4853.3621404
X-RAY DIFFRACTIONr_mcangle_other2.4843.3631405
X-RAY DIFFRACTIONr_scbond_it2.4392.6131198
X-RAY DIFFRACTIONr_scbond_other2.4382.6131198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.743.8221747
X-RAY DIFFRACTIONr_long_range_B_refined6.62526.8912578
X-RAY DIFFRACTIONr_long_range_B_other6.62326.6752564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3078 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.72→1.763 Å
RfactorNum. reflection% reflection
Rfree0.361 131 -
Rwork0.396 2187 -
obs--98.39 %
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)
12.83810.21581.17042.66271.63925.37290.02860.0459-0.3012-0.0077-0.04920.14060.2183-0.04530.02060.01280.0059-0.00370.0462-0.02540.049119.155717.44652.6236
23.4727-2.1659-0.05813.9002-0.45213.8180.0711-0.0866-0.0354-0.1113-0.0414-0.1281-0.05180.1574-0.02960.0371-0.01970.01170.02390.00240.013432.20617.222223.6474
36.7920.86333.73611.91441.41633.28640.1246-0.576-0.3072-0.1264-0.02460.38690.1809-0.7234-0.09990.1906-0.0699-0.02160.43580.08160.239930.1094-2.3696-8.408
400000000000000-00.1416000.141600.1416000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 153
2X-RAY DIFFRACTION2B19 - 152
3X-RAY DIFFRACTION3C18 - 150

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