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- PDB-3h8h: Structure of the C-terminal domain of human RNF2/RING1B; -

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Basic information

Entry
Database: PDB / ID: 3h8h
TitleStructure of the C-terminal domain of human RNF2/RING1B;
ComponentsE3 ubiquitin-protein ligase RING2
KeywordsTRANSCRIPTION / UBIQUITIN FOLD / LIGASE / RING1B / POLYCOMB / E3-LIGASE / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / TRANSCRIPTION REGULATION / METAL-BINDING / PROTO-ONCOGENE / CHROMATIN REGULATOR / UBL CONJUGATION PATHWAY / REPRESSOR / TRANSCRIPTION REGULATION COMPLEX / Nucleus / Phosphoprotein / Zinc-finger / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / MLL1 complex / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / RING-type E3 ubiquitin transferase / euchromatin / negative regulation of DNA-binding transcription factor activity / ubiquitin protein ligase activity / mitotic cell cycle / gene expression / Oxidative Stress Induced Senescence / nuclear body / protein ubiquitination / chromatin remodeling / chromatin binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsWalker, J.R. / Bezsonova, I. / Bacik, J. / Duan, S. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Biochemistry / Year: 2009
Title: Ring1B contains a ubiquitin-like docking module for interaction with Cbx proteins.
Authors: Bezsonova, I. / Walker, J.R. / Bacik, J.P. / Duan, S. / Dhe-Paganon, S. / Arrowsmith, C.H.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2845
Polymers12,6461
Non-polymers6384
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase RING2
hetero molecules

A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,56910
Polymers25,2922
Non-polymers1,2768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2580 Å2
ΔGint-65 kcal/mol
Surface area10790 Å2
MethodPISA
3
A: E3 ubiquitin-protein ligase RING2
hetero molecules

A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,56910
Polymers25,2922
Non-polymers1,2768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2050 Å2
ΔGint-25 kcal/mol
Surface area10950 Å2
MethodPISA
4
A: E3 ubiquitin-protein ligase RING2
hetero molecules

A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,56910
Polymers25,2922
Non-polymers1,2768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1940 Å2
ΔGint-23 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.169, 72.169, 90.966
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein E3 ubiquitin-protein ligase RING2 / RING finger protein 2 / RING finger protein 1B / RING1b / RING finger protein BAP-1 / DinG protein ...RING finger protein 2 / RING finger protein 1B / RING1b / RING finger protein BAP-1 / DinG protein / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3


Mass: 12646.210 Da / Num. of mol.: 1 / Fragment: RESIDUES 220-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAP1, DING, HIPI3, RING1B, RNF2 / Plasmid: PET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus
References: UniProt: Q99496, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.93 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 2 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 7, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→27.28 Å / Num. obs: 9884 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rsym value: 0.112 / Net I/σ(I): 28.58
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.67 / Rsym value: 0.724 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SOLVEphasing
RESOLVEmodel building
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.699 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 471 4.8 %RANDOM
Rwork0.2 ---
obs0.202 9415 99.2 %-
all-9884 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 25 59 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9991062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.877595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33623.44829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84515130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.021153
X-RAY DIFFRACTIONr_chiral_restr0.120.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021562
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9241.5476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6482769
X-RAY DIFFRACTIONr_scbond_it2.5033309
X-RAY DIFFRACTIONr_scangle_it3.94.5293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 38 -
Rwork0.239 617 -
obs--92.78 %
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)
14.6260.1967-7.1444.9217-3.975517.0331-0.1039-0.60150.0030.77230.1331-0.0020.01770.0157-0.02930.2576-0.0591-0.03850.34290.00540.213419.377915.474214.5417
23.54560.64962.92813.48060.99949.2891-0.0551-0.1720.08760.20390.0378-0.1039-0.09220.07720.01730.11390.00880.00680.11420.00140.146921.153717.6368-1.4682
38.50086.7937-2.548910.35471.03616.02690.2172-0.17570.06440.115-0.0109-0.9498-0.67840.8204-0.20630.2715-0.0322-0.06380.2494-0.01780.38621.370921.3737-7.2758
46.48530.2397-3.40778.491-2.38219.74380.2324-0.224-0.14590.01180.014-0.2944-0.25651.0604-0.24640.146-0.0268-0.070.2112-0.02770.216124.817920.79767.2116
56.41162.87776.49326.5519-0.92019.6860.3835-0.47140.01910.5805-0.26930.23970.2586-0.2371-0.11420.20620.03960.03510.1924-0.01680.103711.849319.427213.575
69.91934.3011-0.361911.7495-1.55199.7643-0.0694-0.14050.00110.33670.14040.203-0.127-0.2885-0.0710.13270.0142-0.00760.1196-0.01140.128210.434624.87516.8846
79.69220.6032-1.0583.8521-0.82420.7167-0.14880.2874-0.082-0.3670.16970.0387-0.00910.1743-0.02090.2468-0.0452-0.01250.1757-0.0410.173518.774229.90513.4612
812.22084.67423.79826.8082.92665.1960.17490.08620.0395-0.08430.0094-0.1423-0.18910.281-0.18420.26820.0160.00180.25780.01720.250616.98832.0032-1.0833
94.238-1.33972.03029.3746-4.40295.634-0.06630.19590.38440.1332-0.3056-0.2074-0.25590.09890.37190.1105-0.0248-0.04020.09950.00140.120612.197920.1293-1.041
103.48881.5413-1.83283.55772.69968.74940.0060.3028-0.0949-0.1257-0.0279-0.25490.2074-0.18270.02180.14890.0167-0.00570.1492-0.02030.159516.53646.688-3.384
110.08640.37710.01913.18852.39456.48780.0429-0.00090.0571-0.1785-0.35170.67540.0908-0.64130.30880.17930.045-0.08220.1629-0.07560.25467.353515.10122.7821
1214.05961.33424.00228.75612.32524.856-0.1413-0.509-0.19750.45070.14760.11810.1039-0.1624-0.00620.1515-0.00480.01870.14950.00520.13918.603613.765811.446
136.47-1.6131-2.543315.51920.94645.547-0.0533-0.1632-0.3680.37290.04260.22340.2765-0.13380.01060.134-0.00050.01060.13940.00730.155910.56158.31218.7133
142.6983-4.51160.83848.0596-0.12583.42050.1940.0576-0.0915-0.2711-0.15210.13830.2145-0.0912-0.04190.1638-0.0161-0.05220.15670.02670.209519.9936.88799.6431
153.3267-0.22921.42321.5413-1.42249.26480.0272-0.1785-0.2027-0.10320.12670.29790.05290.0213-0.15390.11710.0081-0.01580.106-0.01840.13818.471416.47060.9077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A224 - 229
2X-RAY DIFFRACTION2A230 - 235
3X-RAY DIFFRACTION3A236 - 239
4X-RAY DIFFRACTION4A243 - 249
5X-RAY DIFFRACTION5A250 - 256
6X-RAY DIFFRACTION6A257 - 261
7X-RAY DIFFRACTION7A262 - 272
8X-RAY DIFFRACTION8A285 - 289
9X-RAY DIFFRACTION9A290 - 295
10X-RAY DIFFRACTION10A296 - 302
11X-RAY DIFFRACTION11A303 - 308
12X-RAY DIFFRACTION12A309 - 313
13X-RAY DIFFRACTION13A314 - 318
14X-RAY DIFFRACTION14A319 - 324
15X-RAY DIFFRACTION15A325 - 330

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