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Basic information

Entry
Database: PDB / ID: 2xeu
TitleRing domain
ComponentsRING FINGER PROTEIN 4
KeywordsTRANSCRIPTION / ZINC-FINGER / METAL-BINDING
Function / homology
Function and homology information


regulation of spindle assembly / regulation of kinetochore assembly / microtubule end / SUMO polymer binding / protein K6-linked ubiquitination / response to arsenic-containing substance / protein K11-linked ubiquitination / negative regulation of protein localization to chromatin / protein K63-linked ubiquitination / nucleosome binding ...regulation of spindle assembly / regulation of kinetochore assembly / microtubule end / SUMO polymer binding / protein K6-linked ubiquitination / response to arsenic-containing substance / protein K11-linked ubiquitination / negative regulation of protein localization to chromatin / protein K63-linked ubiquitination / nucleosome binding / protein autoubiquitination / protein K48-linked ubiquitination / nuclear receptor coactivator activity / RING-type E3 ubiquitin transferase / PML body / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RNF4, RING finger, HC subclass / : / Zinc finger, C3HC4 type (RING finger) / Ring finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...RNF4, RING finger, HC subclass / : / Zinc finger, C3HC4 type (RING finger) / Ring finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / E3 ubiquitin-protein ligase RNF4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsPlechanovova, A. / McMahon, S.A. / Johnson, K.A. / Navratilova, I. / Naismith, J.H. / Hay, R.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Mechanism of Ubiquitylation by Dimeric Ring Ligase Rnf4
Authors: Plechanovova, A. / Jaffray, E.G. / Mcmahon, S.A. / Johnson, K.A. / Navratilova, I. / Naismith, J.H. / Hay, R.T.
History
DepositionMay 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Other ...Database references / Other / Refinement description / Version format compliance
Revision 1.2Sep 14, 2011Group: Database references / Other / Refinement description
Revision 1.3Oct 3, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: RING FINGER PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8816
Polymers7,2151
Non-polymers6655
Water97354
1
A: RING FINGER PROTEIN 4
hetero molecules

A: RING FINGER PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,76112
Polymers14,4312
Non-polymers1,33010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_564z+1/4,-y+5/4,x-1/41
Buried area2420 Å2
ΔGint-60.3 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.616, 72.616, 72.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-2012-

HOH

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Components

#1: Protein RING FINGER PROTEIN 4


Mass: 7215.458 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 130-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P78317
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.91 Å3/Da / Density % sol: 35.17 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.28
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.5→18 Å / Num. obs: 10402 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→18.15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.011 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19727 525 4.8 %RANDOM
Rwork0.16836 ---
obs0.16972 10391 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.475 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 35 54 587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021558
X-RAY DIFFRACTIONr_bond_other_d0.0010.02382
X-RAY DIFFRACTIONr_angle_refined_deg1.4392.026749
X-RAY DIFFRACTIONr_angle_other_deg0.9383.015930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.17822.85721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3221596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.871154
X-RAY DIFFRACTIONr_chiral_restr0.0750.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02102
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.67433051
X-RAY DIFFRACTIONr_sphericity_free6.755554
X-RAY DIFFRACTIONr_sphericity_bonded3.9555924
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 48 -
Rwork0.155 727 -
obs--100 %
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)
12.44542.2465-0.13933.9592-1.60365.3180.1676-0.1487-0.44320.0495-0.1774-0.62870.06410.32020.00980.03070.00680.01670.04880.05370.20955.88936.53130.378
27.2990.0526-2.01158.36720.00133.72840.00750.2419-0.0155-0.1413-0.115-0.0240.0521-0.10750.10750.0070.00240.00740.01150.00040.011344.93639.37126.291
312.06792.39744.0996.11171.36779.03110.10850.7446-0.654-0.4368-0.1394-0.20480.35110.30970.03090.07370.02870.03990.0655-0.03540.101747.51230.90821.489
42.7530.4222-1.679510.36344.00888.9368-0.03070.2325-0.7-0.30710.32930.1710.61770.1458-0.29860.11740.0069-0.09690.0487-0.07470.300840.17929.72724.128
53.24511.1263-6.38881.38310.460922.6128-0.11410.4758-0.064-0.15410.25820.27690.4135-0.5198-0.14420.1608-0.0266-0.20810.1027-0.05160.510134.74233.48323.059
67.29494.79390.66119.96470.35632.7477-0.33230.39620.0297-0.82530.18480.37630.0435-0.17550.14750.085-0.006-0.01070.047-0.00020.051744.44541.87920.291
70.0054-0.00020.00160.02670.00780.00730.00320.010.00220.0145-0.00050.00110.0054-0.0019-0.00280.02740.01390.0410.03260.05240.231652.03432.41728.407
80.00050.0003-0.00070.0008-0.00090.004-0.00250.0015-0.0026-0.0002-0.00080.0010.006-0.00520.00330.0285-0.00630.04370.02070.00290.079938.05736.87828.953
97.0767-6.562-8.208410.93037.51979.52290.0949-0.31140.125-0.10180.0461-0.2394-0.10780.3658-0.1410.0075-0.01210.02120.0444-0.03440.075357.5145.34621.62
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2A22 - 34
3X-RAY DIFFRACTION3A35 - 41
4X-RAY DIFFRACTION4A42 - 50
5X-RAY DIFFRACTION5A51 - 55
6X-RAY DIFFRACTION6A56 - 64
7X-RAY DIFFRACTION7A1065
8X-RAY DIFFRACTION8A1066
9X-RAY DIFFRACTION9A1067

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