PDB-8bc7: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl...

ID or keywords:

Entry

Database: PDB / ID: 8bc7

Title

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aminoglutarimide degron peptide

Components

Cereblon isoform 4
PHE-PHE-GLU-GLN-MET-GLN-QCI

Keywords

SIGNALING PROTEIN / Protein Damage / Protein Ageing / Protein Chain Break / Aminoglutarimide

Function / homology

CULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Cereblon isoform 4

Function and homology information

Biological species

Magnetospirillum gryphiswaldense (magnetotactic)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.719 Å

Authors

Heim, C. / Albrecht, R. / Spring, A.K. / Hartmann, M.D.

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	Oct 15, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bc7.cif.gz	135.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8bc7.ent.gz	101.7 KB	Display	PDB format
PDBx/mmJSON format	8bc7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8bc7_validation.pdf.gz	722 KB	Display	wwPDB validaton report
Full document	8bc7_full_validation.pdf.gz	726.1 KB	Display
Data in XML	8bc7_validation.xml.gz	14.7 KB	Display
Data in CIF	8bc7_validation.cif.gz	20 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bc/8bc7 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bc7	HTTPS FTP

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Related structure data

Related structure data	8bc6C 4v2yS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cereblon isoform 4

B: Cereblon isoform 4

C: Cereblon isoform 4

D: PHE-PHE-GLU-GLN-MET-GLN-QCI

hetero molecules

42.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cereblon isoform 4

hetero molecules

defined by author&software
Evidence: gel filtration
14 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cereblon isoform 4

D: PHE-PHE-GLU-GLN-MET-GLN-QCI

hetero molecules

defined by author&software
14.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Cereblon isoform 4

hetero molecules

defined by author&software
14 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.606, 59.450, 89.059
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	B
6	3	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	PRO	PRO	A	A	20 - 122	20 - 122
2	1	1	SER	SER	PRO	PRO	B	B	20 - 122	20 - 122
3	2	2	GLY	GLY	ALA	ALA	A	A	18 - 123	18 - 123
4	2	2	GLY	GLY	ALA	ALA	C	C	18 - 123	18 - 123
5	3	3	SER	SER	ALA	ALA	B	B	20 - 123	20 - 123
6	3	3	SER	SER	ALA	ALA	C	C	20 - 123	20 - 123

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#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	PHE-PHE-GLU-GLN-MET-GLN-QCI Mass: 1068.224 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The last residue is a cyclized glutamine, called aminoglutarimide 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-EF2 / S-Thalidomide Mass: 258.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₀N₂O₄ / Comment: medication*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.719→49.446 Å / Num. obs: 32675 / % possible obs: 100 % / Redundancy: 13.05 % / CC_1/2: 0.999 / R_merge(I) obs: 0.104 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.72→1.82 Å / Redundancy: 13.54 % / R_merge(I) obs: 1.91 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 5210 / CC_1/2: 0.632 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0266	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4V2Y

4v2y

Resolution: 1.719→49.446 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.955 / SU B: 6.199 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2111	1633	4.998 %
R_work	0.1743	31042	-
all	0.176	-	-
obs	-	32675	99.957 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 41.172 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.695 Å²	-0 Å²	0 Å²
2-	-	1.396 Å²	-0 Å²
3-	-	-	-0.701 Å²

Refinement step

Cycle: LAST / Resolution: 1.719→49.446 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2426	0	41	94	2561

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	2562
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2272
X-RAY DIFFRACTION	r_angle_refined_deg	1.76	1.625	3473
X-RAY DIFFRACTION	r_angle_other_deg	1.458	1.578	5199
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.055	5	306
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.414	19.93	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.195	15	361
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.528	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	299
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2986
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	698
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	430
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	1995
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1186
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1185
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	82
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.102	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.387	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.789	2.466	1236
X-RAY DIFFRACTION	r_mcbond_other	1.785	2.467	1235
X-RAY DIFFRACTION	r_mcangle_it	2.623	3.676	1535
X-RAY DIFFRACTION	r_mcangle_other	2.623	3.676	1536
X-RAY DIFFRACTION	r_scbond_it	2.784	2.859	1326
X-RAY DIFFRACTION	r_scbond_other	2.782	2.858	1327
X-RAY DIFFRACTION	r_scangle_it	4.34	4.168	1937
X-RAY DIFFRACTION	r_scangle_other	4.339	4.167	1938
X-RAY DIFFRACTION	r_lrange_it	6.249	28.598	2780
X-RAY DIFFRACTION	r_lrange_other	6.24	28.474	2772
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.125	0.05	3004
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.141	0.05	2445
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.143	0.05	2423

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.12475	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.12475	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.14148	0.05007
2	4	C	X-RAY DIFFRACTION	Local ncs	0.14148	0.05007
3	5	B	X-RAY DIFFRACTION	Local ncs	0.14291	0.05007
3	6	C	X-RAY DIFFRACTION	Local ncs	0.14291	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.719-1.764	0.351	119	0.369	2260	0.368	2384	0.492	0.44	99.7903	0.359
1.764-1.812	0.301	111	0.309	2216	0.309	2327	0.745	0.736	100	0.289
1.812-1.865	0.282	116	0.261	2136	0.262	2252	0.795	0.825	100	0.236
1.865-1.922	0.249	108	0.23	2079	0.231	2187	0.884	0.887	100	0.198
1.922-1.985	0.227	111	0.195	2012	0.196	2123	0.92	0.922	100	0.164
1.985-2.054	0.201	102	0.168	1978	0.17	2080	0.943	0.945	100	0.141
2.054-2.132	0.193	102	0.162	1878	0.164	1980	0.943	0.954	100	0.138
2.132-2.219	0.214	92	0.157	1818	0.16	1910	0.949	0.957	100	0.133
2.219-2.317	0.204	91	0.148	1743	0.15	1834	0.946	0.962	100	0.129
2.317-2.43	0.2	87	0.15	1683	0.153	1770	0.951	0.961	100	0.132
2.43-2.561	0.189	85	0.156	1618	0.158	1703	0.959	0.964	100	0.138
2.561-2.716	0.173	84	0.161	1504	0.161	1588	0.956	0.962	100	0.146
2.716-2.903	0.192	74	0.161	1422	0.162	1496	0.96	0.962	100	0.154
2.903-3.135	0.247	68	0.165	1358	0.169	1426	0.939	0.958	100	0.163
3.135-3.433	0.209	67	0.161	1229	0.163	1296	0.952	0.962	100	0.167
3.433-3.835	0.195	60	0.164	1126	0.165	1186	0.953	0.964	100	0.181
3.835-4.424	0.154	54	0.144	1008	0.144	1062	0.97	0.974	100	0.168
4.424-5.408	0.218	42	0.157	866	0.159	908	0.967	0.974	100	0.191
5.408-7.602	0.261	38	0.226	690	0.228	728	0.956	0.953	100	0.264
7.602-49.446	0.269	22	0.221	418	0.223	440	0.943	0.959	100	0.282

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.3238	-0.0723	0.6864	2.5686	1.3918	4.5002	0.06	0.0659	-0.2782	-0.0511	-0.036	0.1656	0.224	0.0274	-0.024	0.0327	0.0224	-0.0239	0.0753	-0.0246	0.0527	19.0461	17.6601	2.6101
2	3.1129	-1.1718	0.436	3.4346	-0.6561	2.4965	0.0253	-0.037	-0.0426	-0.0228	0.0351	0.0303	0.0162	0.0631	-0.0604	0.0212	-0.0099	0.0065	0.0349	-0.0022	0.0044	32.0231	7.4183	23.9835
3	3.8352	2.2015	1.3638	4.2176	0.7303	3.6325	0.056	-0.2385	-0.1449	0.051	0.0345	0.6484	0.3089	-0.76	-0.0904	0.1794	-0.0357	0.0352	0.4149	0.0509	0.2496	28.4794	-5.8924	-6.707
4	1.1884	3.1649	0.8068	8.5148	2.1753	0.5602	0.0431	-0.0602	0.1239	0.1282	-0.0903	0.1949	0.0017	-0.0081	0.0473	0.266	-0.0126	-0.0179	0.2436	-0.0177	0.2775	27.3557	19.3146	30.7708

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	16 - 123
2	X-RAY DIFFRACTION	1	ALL	A	201
3	X-RAY DIFFRACTION	2	ALL	B	20 - 123
4	X-RAY DIFFRACTION	2		B	201
5	X-RAY DIFFRACTION	3	ALL	C	18 - 123
6	X-RAY DIFFRACTION	3	ALL	C	201
7	X-RAY DIFFRACTION	4	ALL	D	2 - 8

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