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- PDB-5wwz: Crystal structure of the KH2 domain of human RNA-binding E3 ubiqu... -

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Basic information

Entry
Database: PDB / ID: 5wwz
TitleCrystal structure of the KH2 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C
ComponentsRNA-binding E3 ubiquitin-protein ligase MEX3C
KeywordsRNA BINDING PROTEIN / KH2 / MEX-3C
Function / homology
Function and homology information


chondrocyte hypertrophy / regulation of fat cell differentiation / energy homeostasis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / Zinc finger, C3HC4 type (RING finger) / K Homology domain, type 1 superfamily ...: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / Zinc finger, C3HC4 type (RING finger) / K Homology domain, type 1 superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / K Homology domain / K homology RNA-binding domain / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding E3 ubiquitin-protein ligase MEX3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, L. / Wang, C. / Li, F. / Gong, Q.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity
Authors: Yang, L. / Wang, C. / Li, F. / Zhang, J. / Nayab, A. / Wu, J. / Shi, Y. / Gong, Q.
History
DepositionJan 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
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
B: RNA-binding E3 ubiquitin-protein ligase MEX3C
A: RNA-binding E3 ubiquitin-protein ligase MEX3C
C: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7017
Polymers29,3173
Non-polymers3844
Water72140
1
B: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8682
Polymers9,7721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area5860 Å2
MethodPISA
2
A: RNA-binding E3 ubiquitin-protein ligase MEX3C


Theoretical massNumber of molelcules
Total (without water)9,7721
Polymers9,7721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5560 Å2
MethodPISA
3
C: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0604
Polymers9,7721
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.321, 83.321, 78.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 29 or (resid 30...
21(chain B and (resid 4 through 43 or (resid 44...
31(chain C and (resid 4 through 44 or (resid 45...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 29 or (resid 30...A4 - 29
121(chain A and (resid 4 through 29 or (resid 30...A30
131(chain A and (resid 4 through 29 or (resid 30...A4 - 81
141(chain A and (resid 4 through 29 or (resid 30...A4 - 81
151(chain A and (resid 4 through 29 or (resid 30...A4 - 81
161(chain A and (resid 4 through 29 or (resid 30...A4 - 81
211(chain B and (resid 4 through 43 or (resid 44...B4 - 43
221(chain B and (resid 4 through 43 or (resid 44...B44 - 45
231(chain B and (resid 4 through 43 or (resid 44...B4 - 83
241(chain B and (resid 4 through 43 or (resid 44...B4 - 83
251(chain B and (resid 4 through 43 or (resid 44...B4 - 83
261(chain B and (resid 4 through 43 or (resid 44...B4 - 83
311(chain C and (resid 4 through 44 or (resid 45...C4 - 44
321(chain C and (resid 4 through 44 or (resid 45...C45
331(chain C and (resid 4 through 44 or (resid 45...C4 - 82
341(chain C and (resid 4 through 44 or (resid 45...C4 - 82
351(chain C and (resid 4 through 44 or (resid 45...C4 - 82
361(chain C and (resid 4 through 44 or (resid 45...C4 - 82

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Components

#1: Protein RNA-binding E3 ubiquitin-protein ligase MEX3C / RING finger and KH domain-containing protein 2 / RING finger protein 194 / RING-type E3 ubiquitin ...RING finger and KH domain-containing protein 2 / RING finger protein 194 / RING-type E3 ubiquitin transferase MEX3C


Mass: 9772.222 Da / Num. of mol.: 3 / Fragment: KH2 domain, UNP residues 320-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEX3C, RKHD2, RNF194, BM-013 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5U5Q3, RING-type E3 ubiquitin transferase
#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.: 40 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.6M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 10139 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.41 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Χ2: 0.483 / Net I/σ(I): 4.4 / Num. measured all: 70047
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.596.90.5639800.8880.230.6090.439100
2.59-2.697.30.4679850.9190.1840.5030.4799.9
2.69-2.827.20.3319890.9650.1310.3570.448100
2.82-2.967.20.2429950.9780.0960.2610.461100
2.96-3.156.90.1749860.9880.0710.1890.469100
3.15-3.396.60.10610100.9930.0440.1150.491100
3.39-3.737.30.08310100.9960.0320.0890.55100
3.73-4.277.10.05810100.9980.0230.0630.56999.8
4.27-5.386.50.04810470.9980.020.0530.537100
5.38-406.40.03911270.9990.0160.0420.38999.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WWW

5www


Resolution: 2.5→37.262 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 468 4.63 %
Rwork0.2263 9639 -
obs0.2284 10107 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.36 Å2 / Biso mean: 56.6324 Å2 / Biso min: 28.59 Å2
Refinement stepCycle: final / Resolution: 2.5→37.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 20 40 1855
Biso mean--64.07 46.64 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021859
X-RAY DIFFRACTIONf_angle_d0.432552
X-RAY DIFFRACTIONf_chiral_restr0.042293
X-RAY DIFFRACTIONf_plane_restr0.003338
X-RAY DIFFRACTIONf_dihedral_angle_d13.7041101
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1036X-RAY DIFFRACTION7.218TORSIONAL
12B1036X-RAY DIFFRACTION7.218TORSIONAL
13C1036X-RAY DIFFRACTION7.218TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4987-2.86010.34161470.248631393286
2.8601-3.6030.32941280.244631953323
3.603-37.26640.23661930.212333053498
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)
12.21170.0217-1.68666.61330.19672.8489-0.11660.1827-0.0460.59390.22480.32450.0128-0.3854-0.09620.41970.06030.04850.38090.03820.31743.5681-19.0599-31.6815
22.7982-1.0531.80713.4465-1.67258.6842-0.41120.0241-0.0902-0.3504-0.0006-0.29750.54740.16090.37430.4987-0.01930.2260.35440.01590.4559-2.5907-27.4472-9.2402
37.60491.4020.14990.9562-0.69270.68820.01410.1040.267-0.33780.0171-0.024-0.13260.0657-0.02230.6095-0.00630.02860.3579-0.03610.4028-16.9819-6.3621-16.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 314 through 393)B314 - 393
2X-RAY DIFFRACTION2(chain 'A' and resid 314 through 391)A314 - 391
3X-RAY DIFFRACTION3(chain 'C' and resid 314 through 392)C314 - 392

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