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- PDB-6ldp: Structure of CDK5R1-bound FEM1C -

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Basic information

Entry
Database: PDB / ID: 6ldp
TitleStructure of CDK5R1-bound FEM1C
ComponentsProtein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1
KeywordsPROTEIN BINDING / ubiquitination E3 ligase
Function / homology
Function and homology information


superior olivary nucleus maturation / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / contractile muscle fiber / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / regulation of dendritic spine morphogenesis / CRMPs in Sema3A signaling / NGF-stimulated transcription ...superior olivary nucleus maturation / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / contractile muscle fiber / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / regulation of dendritic spine morphogenesis / CRMPs in Sema3A signaling / NGF-stimulated transcription / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / regulation of synaptic vesicle cycle / embryo development ending in birth or egg hatching / regulation of neuron differentiation / Cul2-RING ubiquitin ligase complex / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / beta-tubulin binding / protein kinase activator activity / ephrin receptor signaling pathway / positive regulation of protein targeting to membrane / alpha-tubulin binding / ubiquitin ligase complex / regulation of macroautophagy / ubiquitin-like ligase-substrate adaptor activity / cyclin-dependent protein kinase holoenzyme complex / ionotropic glutamate receptor binding / positive regulation of microtubule polymerization / ephrin receptor binding / NPAS4 regulates expression of target genes / ionotropic glutamate receptor signaling pathway / cerebellum development / protein serine/threonine kinase activator activity / axon guidance / hippocampus development / peptidyl-threonine phosphorylation / regulation of actin cytoskeleton organization / neuron migration / neuromuscular junction / brain development / neuron differentiation / microtubule cytoskeleton organization / G protein-coupled acetylcholine receptor signaling pathway / neuron projection development / actin filament binding / positive regulation of neuron apoptotic process / kinase activity / rhythmic process / presynapse / Neddylation / growth cone / peptidyl-serine phosphorylation / protease binding / Regulation of TP53 Activity through Phosphorylation / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / protein kinase activity / postsynaptic density / protein ubiquitination / neuron projection / cadherin binding / axon / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / neuronal cell body / dendrite / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cyclin-dependent kinase 5 activator protein / Cyclin-dependent kinase 5 activator / 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 / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Cyclin-dependent kinase 5 activator 1 / Protein fem-1 homolog C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, X. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China 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
DepositionNov 22, 2019Deposition 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 22, 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 / 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
Revision 1.5Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1
B: Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6116
Polymers91,2262
Non-polymers3844
Water1,38777
1
A: Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8053
Polymers45,6131
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-23 kcal/mol
Surface area17930 Å2
MethodPISA
2
B: Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8053
Polymers45,6131
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.930, 96.620, 146.520
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
11(chain A and ((resid 6 through 8 and (name N...
21(chain B and (resid 6 through 16 or (resid 17...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPHEPHE(chain A and ((resid 6 through 8 and (name N...AA6 - 88 - 10
12THRTHRARGARG(chain A and ((resid 6 through 8 and (name N...AA5 - 4167 - 418
13THRTHRARGARG(chain A and ((resid 6 through 8 and (name N...AA5 - 4167 - 418
14THRTHRARGARG(chain A and ((resid 6 through 8 and (name N...AA5 - 4167 - 418
15THRTHRARGARG(chain A and ((resid 6 through 8 and (name N...AA5 - 4167 - 418
21ALAALALEULEU(chain B and (resid 6 through 16 or (resid 17...BB6 - 168 - 18
22ARGARGLYSLYS(chain B and (resid 6 through 16 or (resid 17...BB17 - 2119 - 23
23ALAALAARGARG(chain B and (resid 6 through 16 or (resid 17...BB6 - 4168 - 418
24ALAALAARGARG(chain B and (resid 6 through 16 or (resid 17...BB6 - 4168 - 418
25ALAALAARGARG(chain B and (resid 6 through 16 or (resid 17...BB6 - 4168 - 418
26ALAALAARGARG(chain B and (resid 6 through 16 or (resid 17...BB6 - 4168 - 418

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Components

#1: Protein Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1 / FEM1c / FEM1-gamma / CDK5R1 peptide / CDK5 activator 1 / Cyclin-dependent kinase 5 regulatory ...FEM1c / FEM1-gamma / CDK5R1 peptide / CDK5 activator 1 / Cyclin-dependent kinase 5 regulatory subunit 1 / TPKII regulatory subunit


Mass: 45613.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1C fused with CDK5R1 peptide, linked with linker residues GGGSGGGSGGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785, CDK5R1, CDK5R, NCK5A / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0, UniProt: Q15078
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium sulfate, 0.1M Tris-Hcl pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→37.12 Å / Num. obs: 56771 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 1 / Net I/σ(I): 21.5
Reflection shellResolution: 2.35→2.41 Å / Num. unique obs: 5605 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBF

6lbf


Resolution: 2.35→34.346 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2714 4.78 %
Rwork0.2224 54057 -
obs0.2242 56771 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.42 Å2 / Biso mean: 74.3728 Å2 / Biso min: 46.04 Å2
Refinement stepCycle: final / Resolution: 2.35→34.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 20 77 5705
Biso mean--86.88 63.42 -
Num. residues----755
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2148X-RAY DIFFRACTION9.949TORSIONAL
12B2148X-RAY DIFFRACTION9.949TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.39270.35281470.32552803100
2.3927-2.43870.3551290.30352820100
2.4387-2.48850.32051340.27952795100
2.4885-2.54260.35261120.27292858100
2.5426-2.60170.33371320.26532818100
2.6017-2.66680.27941280.25492833100
2.6668-2.73880.29551620.25742772100
2.7388-2.81940.34361520.25292831100
2.8194-2.91030.32081430.27442808100
2.9103-3.01430.32021360.27872850100
3.0143-3.13490.30281490.25672817100
3.1349-3.27750.29761610.26822817100
3.2775-3.45010.29741360.26342840100
3.4501-3.66610.2571400.22372864100
3.6661-3.94870.21671420.20982851100
3.9487-4.34540.23261610.18992850100
4.3454-4.97260.26081580.1922875100
4.9726-6.25870.24841310.21562937100
6.2587-34.3460.20551610.1909301899

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