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- PDB-3ntw: Structure of the MLLE domain of EDD in complex with a PAM2 peptid... -

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Basic information

Entry
Database: PDB / ID: 3ntw
TitleStructure of the MLLE domain of EDD in complex with a PAM2 peptide from Paip1
Components
  • E3 ubiquitin-protein ligase UBR5
  • Polyadenylate-binding protein-interacting protein 1
KeywordsPROTEIN BINDING / protein-protein complex / MLLE domain / PABC domain
Function / homology
Function and homology information


heterochromatin boundary formation / mCRD-mediated mRNA stability complex / ubiquitin-dependent protein catabolic process via the N-end rule pathway / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / nuclear protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination ...heterochromatin boundary formation / mCRD-mediated mRNA stability complex / ubiquitin-dependent protein catabolic process via the N-end rule pathway / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / nuclear protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation by host of viral process / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / negative regulation of interleukin-17 production / protein K11-linked ubiquitination / mRNA stabilization / regulation of translational initiation / ubiquitin-ubiquitin ligase activity / DNA repair-dependent chromatin remodeling / protein K48-linked ubiquitination / progesterone receptor signaling pathway / ubiquitin binding / negative regulation of smoothened signaling pathway / translational initiation / regulation of protein stability / positive regulation of protein import into nucleus / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / viral translation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / DNA damage response / positive regulation of gene expression / chromatin / perinuclear region of cytoplasm / protein-containing complex / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / E3 ubiquitin ligase EDD, ubiquitin-associated domain / : / E3 ubiquitin ligase EDD / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. ...: / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / E3 ubiquitin ligase EDD, ubiquitin-associated domain / : / E3 ubiquitin ligase EDD / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5 / Polyadenylate-binding protein-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J. Biol. Chem. / Year: 2015
Title: The MLLE domain of the ubiquitin ligase UBR5 binds to its catalytic domain to regulate substrate binding.
Authors: Munoz-Escobar, J. / Matta-Camacho, E. / Kozlov, G. / Gehring, K.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UBR5
B: Polyadenylate-binding protein-interacting protein 1
C: E3 ubiquitin-protein ligase UBR5
D: Polyadenylate-binding protein-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)19,0624
Polymers19,0624
Non-polymers00
Water1448
1
A: E3 ubiquitin-protein ligase UBR5
B: Polyadenylate-binding protein-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)9,5312
Polymers9,5312
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area4530 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase UBR5
D: Polyadenylate-binding protein-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)9,5312
Polymers9,5312
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-8 kcal/mol
Surface area4280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.794, 95.794, 82.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA2382 - 24369 - 63
21ALAALAVALVALCC2382 - 24369 - 63
12LYSLYSSERSERBB127 - 1385 - 16
22LYSLYSSERSERDD127 - 1385 - 16

NCS ensembles :
ID
1
2

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Components

#1: Protein E3 ubiquitin-protein ligase UBR5 / E3 ubiquitin-protein ligase / HECT domain-containing 1 / Hyperplastic discs protein homolog / 100 kDa protein


Mass: 7103.293 Da / Num. of mol.: 2 / Fragment: UNP residues 515-574, MLLE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ubr5, Dd5, Edd, Edd1, Hyd / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q62671, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Polyadenylate-binding protein-interacting protein 1 / Poly(A)-binding protein-interacting protein 1 / PABP-interacting protein 1 / PAIP-1


Mass: 2427.706 Da / Num. of mol.: 2 / Fragment: UNP residues 123-144, PAM2 motif / Source method: obtained synthetically / Details: Chemically synthesized peptide / References: UniProt: Q9H074
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M ammonium sulfate, 0.2 M lithium sulfate, 10% glycerol and 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 7012 / Num. obs: 6999 / % possible obs: 99.81 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.2
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 6.6 / Num. unique all: 503 / % possible all: 99.81

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1i2t

1i2t


Resolution: 2.6→41.49 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.867 / SU B: 27.522 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28994 341 4.6 %RANDOM
Rwork0.227 ---
all0.228 6999 --
obs0.22988 6999 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 0 8 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221118
X-RAY DIFFRACTIONr_angle_refined_deg2.062.0241510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6823.40944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.01715203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0921510
X-RAY DIFFRACTIONr_chiral_restr0.1270.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02816
X-RAY DIFFRACTIONr_nbd_refined0.2470.2500
X-RAY DIFFRACTIONr_nbtor_refined0.3360.2766
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3550.23
X-RAY DIFFRACTIONr_mcbond_it0.671.5732
X-RAY DIFFRACTIONr_mcangle_it1.19921144
X-RAY DIFFRACTIONr_scbond_it2.463420
X-RAY DIFFRACTIONr_scangle_it4.1844.5365
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A219tight positional0.160.05
2B48tight positional0.090.05
1A195loose positional0.665
2B47loose positional0.825
1A219tight thermal0.160.5
2B48tight thermal0.140.5
1A195loose thermal1.5710
2B47loose thermal1.8910
LS refinement shellResolution: 2.596→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 16 -
Rwork0.356 503 -
obs--99.81 %
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)
14.82421.8874-1.81995.70471.98162.1475-0.16230.1053-0.20920.6712-0.14360.09830.34050.10020.30590.48350.14150.0650.3789-0.01090.4704-31.1476-31.95811.7666
26.0147-0.0428-3.62647.92034.28744.47940.0090.0873-0.04020.1724-0.1382-0.2643-0.120.28020.12920.41130.1160.02310.4778-0.00280.4133-25.0877-31.1492-4.3561
37.38514.49813.57774.13193.11312.3598-0.55850.35150.5006-0.38610.5033-1.0713-0.84691.39280.05520.48960.03530.03990.5711-0.04420.486-20.9549-20.7356-1.8013
435.5027-10.9573-20.779819.7195-9.229727.1402-2.53062.70160.6418-0.69941.3176-0.31460.1570.1081.2130.55710.099-0.03660.6024-0.16650.4566-29.1008-20.1212-7.7347
542.359410.77640.9092.74160.23130.01950.1311-0.99510.35061.2871-0.2611.6286-0.27120.16810.12990.60930.20640.25530.3355-0.01850.495-37.6471-26.66462.4932
67.058-2.0256-0.02392.66295.34413.6849-0.1180.5392-0.7250.3375-0.41510.40030.4074-0.55550.53310.58090.04360.07870.2071-0.01160.5166-44.3257-13.16335.3861
74.0454-0.3483-3.00843.24971.23044.67620.08730.1264-0.09560.041-0.1634-0.00720.1070.08670.07610.58850.03370.02080.29140.02540.4009-39.7418-9.07639.9998
813.4506-3.6321-13.346322.83235.990113.50340.3089-0.66650.7662-0.04350.3199-1.0238-0.39671.4446-0.62880.5103-0.0277-0.00560.3154-0.00510.4262-29.8912-7.79156.5119
912.7244-10.91484.081416.1008-4.26981.39690.2568-0.95330.36492.1748-0.4139-0.30590.23441.15640.15710.70020.0990.05670.4688-0.04230.3845-30.1261-13.616414.6128
107.82823.0145-4.187614.581-0.550820.05860.60471.0937-0.18260.7033-0.34880.44490.4574-0.1655-0.25590.82560.02050.10810.21-0.10970.5807-40.977-22.81567.1939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2377 - 2398
2X-RAY DIFFRACTION2A2399 - 2426
3X-RAY DIFFRACTION3A2427 - 2437
4X-RAY DIFFRACTION4B127 - 133
5X-RAY DIFFRACTION5B134 - 138
6X-RAY DIFFRACTION6C2382 - 2395
7X-RAY DIFFRACTION7C2396 - 2426
8X-RAY DIFFRACTION8C2427 - 2437
9X-RAY DIFFRACTION9D126 - 133
10X-RAY DIFFRACTION10D134 - 139

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