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- PDB-5zi6: The RING domain structure of MEX-3C -

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Basic information

Entry
Database: PDB / ID: 5zi6
TitleThe RING domain structure of MEX-3C
ComponentsRNA-binding E3 ubiquitin-protein ligase MEX3C
KeywordsLIGASE / E3 liagase / Ubiquitination / MEX-3C / RING domain
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
: / : / : / KH domain / K Homology domain, type 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. ...: / : / : / KH domain / K Homology domain, type 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
Similarity search - Domain/homology
RNA-binding E3 ubiquitin-protein ligase MEX3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMoududee, S.A. / Tang, Y.
CitationJournal: Protein Sci. / Year: 2018
Title: Structural and functional characterization of hMEX-3C Ring finger domain as an E3 ubiquitin ligase
Authors: Moududee, S.A. / Jiang, Y. / Gilbert, N. / Xie, G. / Xu, Z. / Wu, J. / Gong, Q. / Tang, Y. / Shi, Y.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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
B: RNA-binding E3 ubiquitin-protein ligase MEX3C
C: RNA-binding E3 ubiquitin-protein ligase MEX3C
D: RNA-binding E3 ubiquitin-protein ligase MEX3C
E: RNA-binding E3 ubiquitin-protein ligase MEX3C
F: RNA-binding E3 ubiquitin-protein ligase MEX3C
G: RNA-binding E3 ubiquitin-protein ligase MEX3C
H: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,48824
Polymers48,4418
Non-polymers1,04716
Water18010
1
A: RNA-binding E3 ubiquitin-protein ligase MEX3C
B: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA-binding E3 ubiquitin-protein ligase MEX3C
D: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA-binding E3 ubiquitin-protein ligase MEX3C
F: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RNA-binding E3 ubiquitin-protein ligase MEX3C
H: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.135, 44.567, 67.157
Angle α, β, γ (deg.)92.430, 90.500, 91.390
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
21(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
31(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
41(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
51(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
61(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
71(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
81(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))

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
11CYSCYSPHEPHE(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA608 - 6124 - 8
12ASNASNASNASN(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA61410
13VALVALLYSLYS(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA616 - 63912 - 35
14THRTHRSERSER(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA641 - 65937 - 55
21CYSCYSPHEPHE(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB608 - 6124 - 8
22ASNASNASNASN(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB61410
23VALVALLYSLYS(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB616 - 63912 - 35
24THRTHRSERSER(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB641 - 65937 - 55
31CYSCYSPHEPHE(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC608 - 6124 - 8
32ASNASNASNASN(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC61410
33VALVALLYSLYS(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC616 - 63912 - 35
34THRTHRSERSER(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC641 - 65937 - 55
41CYSCYSPHEPHE(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD608 - 6124 - 8
42ASNASNASNASN(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD61410
43VALVALLYSLYS(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD616 - 63912 - 35
44THRTHRSERSER(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD641 - 65937 - 55
51CYSCYSPHEPHE(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE608 - 6124 - 8
52ASNASNASNASN(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE61410
53VALVALLYSLYS(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE616 - 63912 - 35
54THRTHRSERSER(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE641 - 65937 - 55
61CYSCYSPHEPHE(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF608 - 6124 - 8
62ASNASNASNASN(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF61410
63VALVALLYSLYS(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF616 - 63912 - 35
64THRTHRSERSER(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF641 - 65937 - 55
71CYSCYSPHEPHE(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG608 - 6124 - 8
72ASNASNASNASN(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG61410
73VALVALLYSLYS(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG616 - 63912 - 35
74THRTHRSERSER(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG641 - 65937 - 55
81CYSCYSPHEPHE(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH608 - 6124 - 8
82ASNASNASNASN(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH61410
83VALVALLYSLYS(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH616 - 63912 - 35
84THRTHRSERSER(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH641 - 65937 - 55

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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: 6055.123 Da / Num. of mol.: 8 / Fragment: UNP residues 605-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEX3C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5U5Q3, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 25%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 20938 / % possible obs: 94.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 42.83 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.053 / Rrim(I) all: 0.103 / Χ2: 0.635 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.10.8989730.6080.5621.0620.43290.1
2.24-2.283.30.75310310.7290.4630.8850.45393.3
2.28-2.323.40.70810750.8360.4320.8310.4294.6
2.32-2.373.50.58910360.8970.3530.6880.44295.2
2.37-2.423.60.50110510.9060.2990.5850.44495.2
2.42-2.483.60.48711000.90.2910.5680.45296.1
2.48-2.543.60.40610350.8950.2430.4730.43196
2.54-2.613.60.37310910.9160.2230.4360.45896
2.61-2.693.70.28210530.9530.1680.3290.46394.5
2.69-2.773.50.21910060.970.1330.2570.591.9
2.77-2.873.50.17610110.9780.1080.2080.52988.1
2.87-2.993.80.14410650.9880.0850.1680.55197.6
2.99-3.123.80.12410770.9890.0730.1440.55297
3.12-3.293.70.10110560.9910.060.1180.60396.1
3.29-3.493.70.08110970.9930.0480.0940.68397.2
3.49-3.763.70.06110540.9970.0360.0710.74994.4
3.76-4.143.50.0619840.9950.0370.0720.87388.1
4.14-4.743.80.04910450.9970.0290.0570.99496
4.74-5.973.80.05310730.9960.0310.0621.08396.2
5.97-403.70.05210250.9980.0310.061.46791.7

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→36.384 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.57 / Phase error: 27.19
RfactorNum. reflection% reflection
Rfree0.2434 959 4.58 %
Rwork0.2072 --
obs0.2088 20922 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.25 Å2 / Biso mean: 51.7163 Å2 / Biso min: 27.79 Å2
Refinement stepCycle: final / Resolution: 2.2→36.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 16 10 3346
Biso mean--43.58 39.47 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093376
X-RAY DIFFRACTIONf_angle_d1.2814576
X-RAY DIFFRACTIONf_chiral_restr0.072552
X-RAY DIFFRACTIONf_plane_restr0.008592
X-RAY DIFFRACTIONf_dihedral_angle_d15.9612096
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1719X-RAY DIFFRACTION11.768TORSIONAL
12B1719X-RAY DIFFRACTION11.768TORSIONAL
13C1719X-RAY DIFFRACTION11.768TORSIONAL
14D1719X-RAY DIFFRACTION11.768TORSIONAL
15E1719X-RAY DIFFRACTION11.768TORSIONAL
16F1719X-RAY DIFFRACTION11.768TORSIONAL
17G1719X-RAY DIFFRACTION11.768TORSIONAL
18H1719X-RAY DIFFRACTION11.768TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.29760.31881040.3051269588
2.2976-2.44150.31961400.301291595
2.4415-2.62990.30311750.2714290896
2.6299-2.89450.2971480.2437274992
2.8945-3.31310.25341460.2362296097
3.3131-4.17320.22811100.1925285292
4.1732-36.3840.19871360.1558288495

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