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- PDB-4r8p: Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation m... -

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Basic information

Entry
Database: PDB / ID: 4r8p
TitleCrystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle
Components
  • (DNA (147-mer)) x 2
  • E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Polycomb complex protein BMI-1
KeywordsStructural Protein/DNA / RING domain / Arginine anchor / Ubiquitin ligase / Histone modification enzyme / Structural Protein-DNA complex
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / regulation of adaxial/abaxial pattern formation ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / regulation of adaxial/abaxial pattern formation / sex chromatin / PcG protein complex / positive regulation of immature T cell proliferation in thymus / Signaling by BMP / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / protein K11-linked ubiquitination / SUMOylation of RNA binding proteins / anterior/posterior axis specification / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / germ cell development / ubiquitin conjugating enzyme activity / humoral immune response / hemopoiesis / MLL1 complex / negative regulation of apoptotic signaling pathway / cellular response to interleukin-1 / protein monoubiquitination / negative regulation of BMP signaling pathway / ubiquitin ligase complex / cellular response to dexamethasone stimulus / negative regulation of DNA-binding transcription factor activity / protein K48-linked ubiquitination / SUMOylation of DNA damage response and repair proteins / heterochromatin / protein autoubiquitination / positive regulation of B cell proliferation / SUMOylation of transcription cofactors / TICAM1, RIP1-mediated IKK complex recruitment / SUMOylation of chromatin organization proteins / epigenetic regulation of gene expression / IKK complex recruitment mediated by RIP1 / Regulation of PTEN gene transcription / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / apoptotic signaling pathway / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / euchromatin / Inactivation of CSF3 (G-CSF) signaling / brain development / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / positive regulation of fibroblast proliferation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / structural constituent of chromatin / Antigen processing: Ubiquitination & Proteasome degradation / nucleosome / heterochromatin formation / mitotic cell cycle / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / regulation of gene expression / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / gene expression / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / nuclear body / chromatin remodeling / protein heterodimerization activity / DNA repair / apoptotic process / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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) / Histone, subunit A / Histone, subunit A / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) ...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) / Histone, subunit A / Histone, subunit A / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polycomb complex protein BMI-1 / Ubiquitin-conjugating enzyme E2 D3 / Histone H4 / Histone H3.2 / Histone H2A / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Synthetic DNA (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2846 Å
AuthorsMcGinty, R.K. / Henrici, R.C. / Tan, S.
CitationJournal: Nature / Year: 2014
Title: Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome.
Authors: McGinty, R.K. / Henrici, R.C. / Tan, S.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 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 / 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: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (147-mer)
J: DNA (147-mer)
K: Polycomb complex protein BMI-1
L: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
M: Polycomb complex protein BMI-1
N: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,84122
Polymers284,31814
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.923, 180.049, 375.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 6 types, 12 molecules AEBFCGDHKMLN

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: histone H3.2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: histone H4 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: histone H2B 1.1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281
#7: Protein Polycomb complex protein BMI-1 / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 12595.749 Da / Num. of mol.: 2 / Fragment: Residues 2-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P35226
#8: Protein E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG ...Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG / RING finger protein 1B / RING1b / RING finger protein 2 / RING finger protein BAP-1 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 30118.637 Da / Num. of mol.: 2
Fragment: Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
Source method: isolated from a genetically manipulated source
Details: Ring1B(2-116) fragment linked to UBE2D3/UbcH5c (2-148) through a linker encodin g the GSGSRS sequence
Source: (gene. exp.) Homo sapiens (human)
Gene: BAP1, DING, HIPI3, RING1B, Ring1B-UbcH5c fusion, RNF2, UBC5C, UBCH5C, UBE2D3
Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q99496, UniProt: P61077, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), ubiquitin-protein ligase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-mer)


Mass: 45138.770 Da / Num. of mol.: 1 / Fragment: Widom 601 147-mer (+ strand)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic DNA (others) / Gene: Widom 601 nucleosome positioning sequence / Plasmid: pST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
#6: DNA chain DNA (147-mer)


Mass: 45610.043 Da / Num. of mol.: 1 / Fragment: Widom 601 147-mer (- strand)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic DNA (others) / Gene: Widom 601 nucleosome positioning sequence / Plasmid: pST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

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Non-polymers , 1 types, 8 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 294 K / Method: modified micro batch under oil / pH: 7.5
Details: 25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2013
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2846→45 Å / Num. all: 54219 / Num. obs: 54142 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.9 % / Biso Wilson estimate: 105.01 Å2 / Rsym value: 0.063 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2846-3.463.90.641.23103478770.6499.8
3.46-3.673.90.3522.12931074410.35299.8
3.67-3.933.90.1973.82739869830.19799.7
3.93-4.2440.1226.12590565510.12299.8
4.24-4.653.90.07310.32371960320.07399.8
4.65-5.193.90.05214.42161755050.05299.7
5.19-63.80.04815.71849748130.04899.5
6-7.343.80.03123.21550441210.03199.4
7.34-10.393.80.01639.61213932180.01698.8
10.39-453.50.01253.8589616780.01291.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.28 Å45 Å
Translation3.28 Å45 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.5phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine models of PDB entries 3RPG and 3LZ0

3rpg

3lz0


Resolution: 3.2846→45 Å / SU ML: 0.43 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 2750 5.08 %random
Rwork0.197 ---
all0.1993 54142 --
obs0.1993 54119 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 368.24 Å2 / Biso mean: 137.4911 Å2 / Biso min: 44.46 Å2
Refinement stepCycle: LAST / Resolution: 3.2846→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11201 5925 8 0 17134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318059
X-RAY DIFFRACTIONf_angle_d0.50425766
X-RAY DIFFRACTIONf_chiral_restr0.022981
X-RAY DIFFRACTIONf_plane_restr0.0022282
X-RAY DIFFRACTIONf_dihedral_angle_d21.7157054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.2846-3.34120.3571520.328325172669266999
3.3412-3.4020.34511410.3129253726782678100
3.402-3.46740.3711300.311925882718271899
3.4674-3.53810.33911510.2895251826692669100
3.5381-3.6150.29081210.2661259227132713100
3.615-3.69910.32471270.266256426912691100
3.6991-3.79150.28211430.2403252526682668100
3.7915-3.8940.28981420.2348257027122712100
3.894-4.00850.26541370.232725762713271399
4.0085-4.13780.27711460.2104251326592659100
4.1378-4.28560.2461270.2258027072707100
4.2856-4.4570.24711260.1846257226982698100
4.457-4.65970.18521530.1794256027132713100
4.6597-4.90510.22811330.1783259027232723100
4.9051-5.2120.23711370.184726142751275199
5.212-5.61370.20961270.198725682695269599
5.6137-6.17730.28151650.209725862751275199
6.1773-7.06830.23771350.204526022737273799
7.0683-8.8940.21761510.15225952746274698
8.894-45.00380.17241060.134826022708270893
Refinement TLS params.Method: refined / Origin x: 29.28 Å / Origin y: 30.3205 Å / Origin z: -47.343 Å
111213212223313233
T0.4614 Å20.0161 Å20.0646 Å2-0.3592 Å2-0.0613 Å2--0.8379 Å2
L1.282 °20.2116 °20.1594 °2-0.8885 °20.1365 °2--3.955 °2
S0.0224 Å °0.0905 Å °0.1001 Å °0.3016 Å °-0.065 Å °0.181 Å °0.1288 Å °-0.1509 Å °-0.0273 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA37 - 134
2X-RAY DIFFRACTION1allB17 - 102
3X-RAY DIFFRACTION1allC16 - 119
4X-RAY DIFFRACTION1allD31 - 125
5X-RAY DIFFRACTION1allE38 - 134
6X-RAY DIFFRACTION1allF21 - 102
7X-RAY DIFFRACTION1allG12 - 118
8X-RAY DIFFRACTION1allH31 - 125
9X-RAY DIFFRACTION1allI-71 - 72
10X-RAY DIFFRACTION1allJ-72 - 72
11X-RAY DIFFRACTION1allK3 - 107
12X-RAY DIFFRACTION1allL15 - 347
13X-RAY DIFFRACTION1allM6 - 102
14X-RAY DIFFRACTION1allN16 - 347
15X-RAY DIFFRACTION1allK501 - 502
16X-RAY DIFFRACTION1allL401 - 504
17X-RAY DIFFRACTION1allM201 - 506
18X-RAY DIFFRACTION1allN401 - 508

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