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

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Basic information

Entry
Database: PDB / ID: 5wwx
TitleCrystal structure of the KH2 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA
Components
  • RNA (5'-R(P*AP*GP*AP*GP*U)-3')
  • RNA-binding E3 ubiquitin-protein ligase MEX3C
KeywordsRNA BINDING PROTEIN/RNA / KH2 / MEX-3C / RNA / RNA BINDING PROTEIN-RNA complex
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
NICKEL (II) ION / RNA / RNA-binding E3 ubiquitin-protein ligase MEX3C
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Aug 30, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding E3 ubiquitin-protein ligase MEX3C
C: RNA (5'-R(P*AP*GP*AP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4413
Polymers11,3822
Non-polymers591
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint0 kcal/mol
Surface area6710 Å2
Unit cell
Length a, b, c (Å)74.611, 74.611, 32.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-401-

NI

21A-548-

HOH

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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.: 1 / 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: RNA chain RNA (5'-R(P*AP*GP*AP*GP*U)-3')


Mass: 1610.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.04M Magnesium acetate tetrahydrate, 0.05M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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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→40 Å / Num. obs: 6609 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 3.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.077.90.5340.904199.8
2.07-2.1580.3460.958199.8
2.15-2.257.70.3320.9311100
2.25-2.377.30.2390.9691100
2.37-2.527.50.2050.981100
2.52-2.718.10.1640.9851100
2.71-2.997.80.1220.993199.2
2.99-3.427.10.0840.995199.5
3.42-4.317.60.0540.997199.7
4.31-4070.0480.998198

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
MOSFLMdata reduction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WWW

5www


Resolution: 2→33.367 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.218 337 5.12 %
Rwork0.1701 --
obs0.1724 6586 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.81 Å2 / Biso mean: 23.0942 Å2 / Biso min: 8.76 Å2
Refinement stepCycle: final / Resolution: 2→33.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms672 110 1 62 845
Biso mean--25.67 32.7 -
Num. residues----89
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008848
X-RAY DIFFRACTIONf_angle_d0.9231179
X-RAY DIFFRACTIONf_chiral_restr0.051133
X-RAY DIFFRACTIONf_plane_restr0.005137
X-RAY DIFFRACTIONf_dihedral_angle_d16.63508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9992-2.51870.25211660.170730543220100
2.5187-33.37170.20411710.16983195336699

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