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- PDB-8c3h: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 8c3h
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex a long aspartimide degron peptide
Components
  • Cereblon isoform 4
  • P3(40)
KeywordsSIGNALING PROTEIN / Protein Damage / Protein Ageing / Protein Chain Break / Aspartimide
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / : / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / response to interleukin-1 / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / neuron cellular homeostasis / Golgi lumen / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / neuron projection development / positive regulation of tumor necrosis factor production / cell-cell junction / synaptic vesicle
Similarity search - Function
CULT domain / CULT domain profile. / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...CULT domain / CULT domain profile. / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Cereblon isoform 4 / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.71 Å
AuthorsHeim, C. / Spring, A.K. / Hartmann, M.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Cereblon neo-substrate binding mimics the recognition of the cyclic imide degron.
Authors: Heim, C. / Spring, A.K. / Kirchgassner, S. / Schwarzer, D. / Hartmann, M.D.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _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

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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: P3(40)
E: P3(40)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2028
Polymers43,0065
Non-polymers1963
Water1,31573
1
A: Cereblon isoform 4
D: P3(40)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7523
Polymers14,6872
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
E: P3(40)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7523
Polymers14,6872
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Unit cell
Length a, b, c (Å)56.256, 58.821, 88.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 20 - 123 / Label seq-ID: 20 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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 P3(40) / Aspartimide degron peptide / Amyloid-beta precursor protein


Mass: 1054.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 274 K / Method: vapor diffusion / 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: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.71→47.53 Å / Num. obs: 32554 / % possible obs: 99.7 % / Redundancy: 12.84 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.3
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 12.42 % / Rmerge(I) obs: 1.629 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5215 / CC1/2: 0.701 / % possible all: 98.8

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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: 1.71→47.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.138 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2104 1630 5.007 %
Rwork0.1794 30923 -
all0.181 --
obs-32553 99.7 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 40.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0 Å20 Å2
2--2.273 Å20 Å2
3----0.584 Å2
Refinement stepCycle: LAST / Resolution: 1.71→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 19 73 2231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132266
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182013
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6343074
X-RAY DIFFRACTIONr_angle_other_deg1.4511.5864603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68321.043115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50815320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2011514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022665
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02609
X-RAY DIFFRACTIONr_nbd_refined0.2410.2378
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21776
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21037
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21040
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.218
X-RAY DIFFRACTIONr_nbd_other0.220.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.211
X-RAY DIFFRACTIONr_mcbond_it1.8292.7251139
X-RAY DIFFRACTIONr_mcbond_other1.8292.7261138
X-RAY DIFFRACTIONr_mcangle_it2.5444.0671417
X-RAY DIFFRACTIONr_mcangle_other2.5434.0671418
X-RAY DIFFRACTIONr_scbond_it2.5042.9731127
X-RAY DIFFRACTIONr_scbond_other2.5042.9731127
X-RAY DIFFRACTIONr_scangle_it3.844.3631653
X-RAY DIFFRACTIONr_scangle_other3.8394.3621654
X-RAY DIFFRACTIONr_lrange_it5.69530.9012420
X-RAY DIFFRACTIONr_lrange_other5.6730.8182416
X-RAY DIFFRACTIONr_ncsr_local_group_10.1070.053144
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.106550.05008
12BX-RAY DIFFRACTIONLocal ncs0.106550.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.7530.331230.352218X-RAY DIFFRACTION97.8679
1.753-1.8010.3181110.3032174X-RAY DIFFRACTION99.4343
1.801-1.8540.2681100.2572140X-RAY DIFFRACTION99.6457
1.854-1.9110.2371050.2362067X-RAY DIFFRACTION99.7703
1.911-1.9730.231180.2022029X-RAY DIFFRACTION99.7677
1.973-2.0420.195960.1791937X-RAY DIFFRACTION99.9017
2.042-2.1190.1941010.1681888X-RAY DIFFRACTION99.8996
2.119-2.2060.196960.1651819X-RAY DIFFRACTION100
2.206-2.3030.203870.1481744X-RAY DIFFRACTION99.9454
2.303-2.4160.191870.151691X-RAY DIFFRACTION100
2.416-2.5460.209880.1611609X-RAY DIFFRACTION100
2.546-2.70.19830.171504X-RAY DIFFRACTION100
2.7-2.8860.201740.1641421X-RAY DIFFRACTION100
2.886-3.1160.216680.1591353X-RAY DIFFRACTION100
3.116-3.4120.18670.1611225X-RAY DIFFRACTION100
3.412-3.8120.161610.1641122X-RAY DIFFRACTION100
3.812-4.3980.18540.1511009X-RAY DIFFRACTION100
4.398-5.3750.238410.167869X-RAY DIFFRACTION100
5.375-7.5570.264380.254688X-RAY DIFFRACTION100
7.557-47.530.315220.232416X-RAY DIFFRACTION99.5455
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)
12.0568-0.02130.8852.13181.39925.05330.02210.0239-0.1715-0.0281-0.02550.16990.15030.01760.00340.01180.0109-0.01910.0257-0.01850.108818.617117.54622.3276
22.9391-1.41520.20413.6177-0.68773.4290.0464-0.0503-0.0686-0.0890.0063-0.0802-0.00610.0951-0.05270.0063-0.00580.00820.01410.00550.054631.88346.98523.5485
34.4802-1.01173.88214.44060.46985.5832-0.0254-0.3968-0.46410.03290.21040.7664-0.0593-0.7882-0.1850.12070.01760.05810.36920.0640.35931.2318-2.6142-8.2947
46.30910.37190.46962.3179-0.21191.02870.0460.4440.382-0.2476-0.0298-0.2773-0.32420.2206-0.01620.2316-0.03160.02540.1967-0.00530.151628.812722.2432-5.7771
51.42772.97551.03296.48372.53631.51640.167-0.14750.13040.1886-0.1910.1343-0.3279-0.08160.0240.33170.0413-0.01430.2219-0.05790.196926.432618.065930.8194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA20 - 123
2X-RAY DIFFRACTION2ALLB20 - 123
3X-RAY DIFFRACTION3ALLC18 - 123
4X-RAY DIFFRACTION4ALLD2 - 7
5X-RAY DIFFRACTION5ALLE2 - 7

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