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- PDB-6xkc: Crystal structure of E3 ligase -

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Basic information

Entry
Database: PDB / ID: 6xkc
TitleCrystal structure of E3 ligase
ComponentsProtein fem-1 homolog C
KeywordsLIGASE / UPS / ubiquitin / E3 ligase / protein degradation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / negative regulation of non-canonical NF-kappaB signal transduction / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ubiquitin ligase complex / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleoplasm / cytosol
Similarity search - Function
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
Protein fem-1 homolog C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsYan, X. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J.R. / Dong, C. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Molecular basis for ubiquitin ligase CRL2 FEM1C -mediated recognition of C-degron.
Authors: Yan, X. / Wang, X. / Li, Y. / Zhou, M. / Li, Y. / Song, L. / Mi, W. / Min, J. / Dong, C.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
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 / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Protein fem-1 homolog C
B: Protein fem-1 homolog C
C: Protein fem-1 homolog C
D: Protein fem-1 homolog C
E: Protein fem-1 homolog C
F: Protein fem-1 homolog C


Theoretical massNumber of molelcules
Total (without water)159,7476
Polymers159,7476
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-60 kcal/mol
Surface area53990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.003, 97.003, 148.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Protein fem-1 homolog C / FEM1c / FEM1-gamma


Mass: 26624.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785 / Plasmid: pET15-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V3R / References: UniProt: Q96JP0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.24 % / Mosaicity: 0.673 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 16% Jeffamine M-600 pH 7.0 and 0.1 M HEPES 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 99464 / % possible obs: 97.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 38.36 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Rrim(I) all: 0.075 / Χ2: 1.424 / Net I/σ(I): 11 / Num. measured all: 521083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.073.60.83641940.5990.4410.951.16582.1
2.07-2.140.81945290.0070.4730.9561.58588.9
2.1-2.144.40.68347520.7290.3390.7651.14193.4
2.14-2.194.60.61148940.7940.3010.6841.13296.1
2.19-2.234.80.52549510.8780.2570.5871.15698.4
2.23-2.2950.50450800.870.2480.5631.64399.3
2.29-2.345.30.40751210.9340.1940.4521.144100
2.34-2.415.30.32350990.9540.1540.3591.19199.9
2.41-2.485.10.26550530.9670.130.2961.21199.5
2.48-2.565.20.22150090.9770.1070.2461.21397.8
2.56-2.655.80.19150630.9850.0870.211.225100
2.65-2.765.80.15750890.9870.0720.1731.29399.9
2.76-2.885.70.12551090.9920.0570.1381.215100
2.88-3.035.70.08950970.9960.0410.0981.30299.9
3.03-3.225.30.0750600.9970.0340.0781.3799.5
3.22-3.475.70.05250270.9980.0240.0581.59499.1
3.47-3.8260.04150930.9990.0180.0451.768100
3.82-4.375.80.03650990.9990.0160.0391.85999.9
4.37-5.515.50.03450420.9990.0160.0381.89399.3
5.51-505.80.03351030.9990.0150.0362.01599.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MA4

5ma4


Resolution: 2.03→49.45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.221 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4820 4.89 %RANDOM
Rwork0.218 ---
obs0.219 98614 97.8 %-
Displacement parametersBiso max: 151.62 Å2 / Biso mean: 48.96 Å2 / Biso min: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.3206 Å20 Å20 Å2
2--3.3206 Å20 Å2
3----6.6411 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.03→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10456 0 0 154 10610
Biso mean---41.58 -
Num. residues----1458
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4223SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2273HARMONIC5
X-RAY DIFFRACTIONt_it13120HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1864SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15358SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13120HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg17875HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion15.65
LS refinement shellResolution: 2.03→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2968 119 6.03 %
Rwork0.2356 1854 -
all0.2395 1973 -
obs--83.06 %
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)
13.42282.94291.26054.52152.32262.64840.4033-0.0999-0.36190.9381-0.1776-0.4320.9348-0.2167-0.22570.0188-0.0661-0.1012-0.44150.0208-0.081530.9771-32.811857.8247
20.6457-0.8783-0.11274.49530.61620.88290.033-0.0236-0.067-0.1048-0.07760.4138-0.0878-0.15080.0446-0.16070.01640.0142-0.1323-0.02960.157820.219320.527762.2003
31.3392-0.25390.07070.6963-0.12870.4896-0.00040.01260.1610.1006-0.0267-0.0876-0.010.21160.0271-0.0673-0.0515-0.0327-0.0785-0.02730.094274.25313.254561.5089
43.2962-2.8625-1.21194.42782.33632.08150.43810.09880.3634-1.0474-0.2045-0.4483-0.8923-0.1932-0.23350.06260.0830.1054-0.42690.016-0.060230.899332.845840.4929
50.61380.8930.10724.40910.59830.81320.02450.01910.06570.1132-0.07310.44310.0828-0.15520.0486-0.1718-0.0179-0.0191-0.1454-0.03170.158220.2222-20.411536.1041
61.80640.3578-0.06760.8438-0.19750.531-0.0081-0.0136-0.1837-0.1021-0.0332-0.1093-0.00330.21880.0412-0.0650.04960.0293-0.0888-0.02940.073174.3961-3.276236.784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|244 }A2 - 244
2X-RAY DIFFRACTION2{ B|2 - B|244 }B2 - 244
3X-RAY DIFFRACTION3{ C|2 - C|244 }C2 - 244
4X-RAY DIFFRACTION4{ D|2 - D|244 }D2 - 244
5X-RAY DIFFRACTION5{ E|2 - E|244 }E2 - 244
6X-RAY DIFFRACTION6{ F|2 - F|244 }F2 - 244

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