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- PDB-7cng: Structure of CDK5R1 bound FEM1B -

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Basic information

Entry
Database: PDB / ID: 7cng
TitleStructure of CDK5R1 bound FEM1B
ComponentsProtein fem-1 homolog B,Peptide from Cyclin-dependent kinase 5 activator 1
KeywordsPEPTIDE BINDING PROTEIN / ubiquitination / E3 ligase / degron
Function / homology
Function and homology information


superior olivary nucleus maturation / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / contractile muscle fiber / Activated NTRK2 signals through CDK5 / neuron cell-cell adhesion / layer formation in cerebral cortex / regulation of synaptic vesicle cycle ...superior olivary nucleus maturation / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / contractile muscle fiber / Activated NTRK2 signals through CDK5 / neuron cell-cell adhesion / layer formation in cerebral cortex / regulation of synaptic vesicle cycle / branching involved in prostate gland morphogenesis / regulation of dendritic spine morphogenesis / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / CRMPs in Sema3A signaling / NGF-stimulated transcription / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / embryo development ending in birth or egg hatching / Cul2-RING ubiquitin ligase complex / regulation of neuron differentiation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / beta-tubulin binding / protein kinase activator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / alpha-tubulin binding / ubiquitin-like ligase-substrate adaptor activity / positive regulation of protein targeting to membrane / cyclin-dependent protein kinase holoenzyme complex / regulation of macroautophagy / ephrin receptor signaling pathway / positive regulation of microtubule polymerization / ionotropic glutamate receptor binding / NPAS4 regulates expression of target genes / ionotropic glutamate receptor signaling pathway / cerebellum development / protein serine/threonine kinase activator activity / ephrin receptor binding / axon guidance / hippocampus development / regulation of actin cytoskeleton organization / brain development / neuron migration / peptidyl-threonine phosphorylation / neuromuscular junction / G protein-coupled acetylcholine receptor signaling pathway / microtubule cytoskeleton organization / neuron differentiation / neuron projection development / positive regulation of neuron apoptotic process / rhythmic process / actin filament binding / presynapse / Neddylation / kinase activity / growth cone / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protease binding / dendritic spine / postsynaptic density / protein ubiquitination / neuron projection / protein kinase activity / cadherin binding / axon / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / dendrite / neuronal cell body / apoptotic process / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Cyclin-dependent kinase 5 activator 1 / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsChen, X. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase.
Authors: Chen, X. / Liao, S. / Makaros, Y. / Guo, Q. / Zhu, Z. / Krizelman, R. / Dahan, K. / Tu, X. / Yao, X. / Koren, I. / Xu, C.
History
DepositionJul 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 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 fem-1 homolog B,Peptide from Cyclin-dependent kinase 5 activator 1
B: Protein fem-1 homolog B,Peptide from Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9766
Polymers78,5922
Non-polymers3844
Water0
1
A: Protein fem-1 homolog B,Peptide from Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4883
Polymers39,2961
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-24 kcal/mol
Surface area15330 Å2
MethodPISA
2
B: Protein fem-1 homolog B,Peptide from Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4883
Polymers39,2961
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.812, 126.812, 144.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Protein fem-1 homolog B,Peptide from Cyclin-dependent kinase 5 activator 1 / FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic ...FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic pathway protein alpha / F1A-alpha / CDK5 activator 1 / Cyclin-dependent kinase 5 regulatory subunit 1 / TPKII regulatory subunit


Mass: 39295.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1B fused with CDK5R1 peptide, linked with linker residues GGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1B, F1AA, KIAA0396, CDK5R1, CDK5R, NCK5A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UK73, UniProt: Q15078
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 15530 / % possible obs: 100 % / Redundancy: 25.5 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.5
Reflection shellResolution: 3.49→3.63 Å / Rmerge(I) obs: 2.271 / Num. unique obs: 1510 / CC1/2: 0.725

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBF

6lbf


Resolution: 3.49→28.9 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1447 10 %
Rwork0.2204 13018 -
obs0.2251 14465 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.08 Å2 / Biso mean: 51.3575 Å2 / Biso min: 18.85 Å2
Refinement stepCycle: final / Resolution: 3.49→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 20 0 5124
Biso mean--58 --
Num. residues----686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.49-3.620.307820.257873481654
3.62-3.760.27271230.26491118124183
3.76-3.930.31061480.24151325147397
3.93-4.140.29561510.24413631514100
4.14-4.40.26441540.223813831537100
4.4-4.740.26411530.218213841537100
4.74-5.210.28351540.220913941548100
5.21-5.960.311570.226714021559100
5.96-7.480.25971590.221114351594100
7.49-28.90.20491660.17291480164698

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