[English] 日本語
Yorodumi
- PDB-6r1c: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r1c
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation
Function / homologyCULT domain / CULT domain profile. / metal ion binding / ASPARTIC ACID / S-Thalidomide / Chem-JOW / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHeim, C. / Hartmann, M.D.
CitationJournal: J.Med.Chem. / Year: 2019
Title: De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives.
Authors: Heim, C. / Pliatsika, D. / Mousavizadeh, F. / Bar, K. / Hernandez Alvarez, B. / Giannis, A. / Hartmann, M.D.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cereblon isoform 4
B: Cereblon isoform 4
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,65414
Polymers41,1113
Non-polymers1,54411
Water3,999222
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2555
Polymers13,7041
Non-polymers5524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3726
Polymers13,7041
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0273
Polymers13,7041
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.656, 59.020, 88.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALALAALAAA14 - 12315 - 124
21VALVALALAALABB14 - 12315 - 124
12GLYGLYPROPROAA18 - 12219 - 123
22GLYGLYPROPROCC18 - 12219 - 123
13GLYGLYPROPROBB18 - 12219 - 123
23GLYGLYPROPROCC18 - 12219 - 123

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Cereblon isoform 4


Mass: 13703.577 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0

-
Non-polymers , 7 types, 233 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#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
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-JOW / 4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid


Mass: 377.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.4 M Ammonium phosphate

-
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: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→49.12 Å / Num. obs: 48555 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.29
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 7572 / CC1/2: 0.87 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v2y

4v2y


Resolution: 1.5→49.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.253 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21537 2427 5 %RANDOM
Rwork0.19354 ---
obs0.19463 46128 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0 Å2
2--0.78 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 93 222 2855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192784
X-RAY DIFFRACTIONr_bond_other_d0.0030.022415
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9363790
X-RAY DIFFRACTIONr_angle_other_deg1.0152.9925575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77221.953128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6511521
X-RAY DIFFRACTIONr_chiral_restr0.1060.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02675
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_it1.011.7571330
X-RAY DIFFRACTIONr_mcbond_other1.0091.7551329
X-RAY DIFFRACTIONr_mcangle_it1.7792.6171661
X-RAY DIFFRACTIONr_mcangle_other1.7792.6191662
X-RAY DIFFRACTIONr_scbond_it1.0851.891454
X-RAY DIFFRACTIONr_scbond_other1.0841.8911455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8252.8012119
X-RAY DIFFRACTIONr_long_range_B_refined4.83220.3223166
X-RAY DIFFRACTIONr_long_range_B_other4.8120.3063165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A65500.14
12B65500.14
21A60020.15
22C60020.15
31B58540.17
32C58540.17
LS refinement shellResolution: 1.495→1.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 167 -
Rwork0.374 3156 -
obs--93.79 %
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)
10.8233-0.06440.64590.18970.09171.1140.036-0.0192-0.04610.00570.02590.0281-0.0074-0.0066-0.06190.01810.0032-0.00620.057-0.01870.025918.777817.32013.1246
20.815-0.5558-0.15880.535-0.20550.78180.0264-0.0402-0.0581-0.0314-0.01740.0479-0.03520.0659-0.0090.0423-0.00560.00250.04150.0040.019832.616.856823.5141
31.51570.76281.28191.31450.26651.23910.0893-0.2737-0.05870.0197-0.00680.0280.092-0.2802-0.08250.0109-0.036-0.0010.15410.00630.011627.6804-6.1757-7.0911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 392
2X-RAY DIFFRACTION2B14 - 391
3X-RAY DIFFRACTION3C18 - 339

+
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