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- PDB-4ppe: human RNF4 RING domain -

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Basic information

Entry
Database: PDB / ID: 4ppe
Titlehuman RNF4 RING domain
ComponentsE3 ubiquitin-protein ligase RNF4
KeywordsLIGASE / RING domain / Ubiquitin Ligase
Function / homology
Function and homology information


regulation of spindle assembly / regulation of kinetochore assembly / microtubule end / SUMO polymer binding / protein K6-linked ubiquitination / protein K11-linked ubiquitination / response to arsenic-containing substance / negative regulation of protein localization to chromatin / protein K63-linked ubiquitination / protein autoubiquitination ...regulation of spindle assembly / regulation of kinetochore assembly / microtubule end / SUMO polymer binding / protein K6-linked ubiquitination / protein K11-linked ubiquitination / response to arsenic-containing substance / negative regulation of protein localization to chromatin / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / nucleosome binding / 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
E3 ubiquitin-protein ligase RNF4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPerry, J.J. / Arvai, A.S. / Hitomi, C. / Tainer, J.A.
CitationJournal: Embo Rep. / Year: 2014
Title: RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response.
Authors: Groocock, L.M. / Nie, M. / Prudden, J. / Moiani, D. / Wang, T. / Cheltsov, A. / Rambo, R.P. / Arvai, A.S. / Hitomi, C. / Tainer, J.A. / Luger, K. / Perry, J.J. / Lazzerini-Denchi, E. / Boddy, M.N.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF4
B: E3 ubiquitin-protein ligase RNF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7956
Polymers16,5332
Non-polymers2624
Water1,26170
1
A: E3 ubiquitin-protein ligase RNF4
hetero molecules

B: E3 ubiquitin-protein ligase RNF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7956
Polymers16,5332
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2360 Å2
ΔGint-10 kcal/mol
Surface area8410 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase RNF4
B: E3 ubiquitin-protein ligase RNF4
hetero molecules

A: E3 ubiquitin-protein ligase RNF4
B: E3 ubiquitin-protein ligase RNF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,59012
Polymers33,0664
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7580 Å2
ΔGint-49 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.938, 86.987, 22.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein E3 ubiquitin-protein ligase RNF4 / RING finger protein 4 / Small nuclear ring finger protein / Protein SNURF


Mass: 8266.574 Da / Num. of mol.: 2 / Fragment: hRNF4 RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RES4-26, RNF4, SNURF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL
References: UniProt: P78317, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.8 Å3/Da / Density % sol: 31.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.5 % (w/v) MPEG 2000, 100 mM hepes pH 6.5, 5 % (w/v), MgSO4, 0.5 % (w/v) beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2011 / Details: mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 9939 / Num. obs: 9024 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.335 Å / SU ML: 0.31 / σ(F): 0.07 / Phase error: 30.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 368 5.02 %Random
Rwork0.2296 ---
obs0.2321 7333 85.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.786 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4447 Å20 Å2-0 Å2
2--5.5249 Å2-0 Å2
3----0.0802 Å2
Refinement stepCycle: LAST / Resolution: 2→28.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 4 70 1112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041058
X-RAY DIFFRACTIONf_angle_d1.0521427
X-RAY DIFFRACTIONf_dihedral_angle_d15.868405
X-RAY DIFFRACTIONf_chiral_restr0.074160
X-RAY DIFFRACTIONf_plane_restr0.003183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.28940.34561010.31691884X-RAY DIFFRACTION70
2.2894-2.88390.30751300.2432504X-RAY DIFFRACTION94

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