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- PDB-5lp8: Crystal structure of an asymmetric dimer of the ubiquitin ligase HUWE1 -

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Basic information

Entry
Database: PDB / ID: 5lp8
TitleCrystal structure of an asymmetric dimer of the ubiquitin ligase HUWE1
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / ubiquitin ligase / E3 enzyme / HECT
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / positive regulation of mitophagy in response to mitochondrial depolarization / histone ubiquitin ligase activity / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...negative regulation of mitochondrial fusion / positive regulation of mitophagy in response to mitochondrial depolarization / histone ubiquitin ligase activity / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain ...HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSander, B. / Lorenz, S.G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationLO 2003/1-1 Germany
CitationJournal: Elife / Year: 2017
Title: A conformational switch regulates the ubiquitin ligase HUWE1.
Authors: Sander, B. / Xu, W. / Eilers, M. / Popov, N. / Lorenz, S.
History
DepositionAug 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Data collection
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase HUWE1
A: E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)105,9042
Polymers105,9042
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-26 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.464, 177.464, 106.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein E3 ubiquitin-protein ligase HUWE1 / ARF-binding protein 1 / ARF-BP1 / HECT / UBA and WWE domain-containing protein 1 / Homologous to ...ARF-binding protein 1 / ARF-BP1 / HECT / UBA and WWE domain-containing protein 1 / Homologous to E6AP carboxyl terminus homologous protein 9 / HectH9 / Large structure of UREB1 / LASU1 / Mcl-1 ubiquitin ligase E3 / Mule / Upstream regulatory element-binding protein 1 / URE-binding protein 1


Mass: 52951.945 Da / Num. of mol.: 2 / Fragment: UNP residues 3951-4374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1, KIAA0312, KIAA1578, UREB1, HSPC272 / Plasmid: pBADM11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7Z6Z7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 4.56 Å3/Da / Density % sol: 73.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Hepes pH 7, PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.7→46.15 Å / Num. obs: 52053 / % possible obs: 99.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.2
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4483 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h1d

3h1d


Resolution: 2.7→46.15 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.225 2549 4.9 %
Rwork0.194 --
obs0.195 52026 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6983 0 0 32 7015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037129
X-RAY DIFFRACTIONf_angle_d0.7439615
X-RAY DIFFRACTIONf_dihedral_angle_d12.2522657
X-RAY DIFFRACTIONf_chiral_restr0.031024
X-RAY DIFFRACTIONf_plane_restr0.0031250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.75210.32571250.31372706X-RAY DIFFRACTION98
2.7521-2.80820.31631620.2862732X-RAY DIFFRACTION99
2.8082-2.86930.29731480.25412745X-RAY DIFFRACTION100
2.8693-2.9360.2981480.24252727X-RAY DIFFRACTION100
2.936-3.00940.24651440.23272775X-RAY DIFFRACTION100
3.0094-3.09080.26431290.25192744X-RAY DIFFRACTION100
3.0908-3.18170.29531380.25152784X-RAY DIFFRACTION100
3.1817-3.28440.31511250.24622769X-RAY DIFFRACTION100
3.2844-3.40170.28071490.22262720X-RAY DIFFRACTION100
3.4017-3.53790.23771260.21092759X-RAY DIFFRACTION99
3.5379-3.69880.24231690.20322744X-RAY DIFFRACTION99
3.6988-3.89370.24631250.20632729X-RAY DIFFRACTION99
3.8937-4.13750.20641320.18152760X-RAY DIFFRACTION99
4.1375-4.45680.18211470.15262739X-RAY DIFFRACTION99
4.4568-4.90480.17591270.14642742X-RAY DIFFRACTION99
4.9048-5.61350.21361390.15822724X-RAY DIFFRACTION97
5.6135-7.06830.18091560.17932767X-RAY DIFFRACTION100
7.0683-46.1530.18111600.1592811X-RAY DIFFRACTION99
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)
10.0046-0.00540.01030.0075-0.01160.01040.05410.02180.0014-0.0549-0.05530.06320.0094-0.0505-0.00010.4595-0.0556-0.09590.3019-0.03250.4344-25.4005101.826115.9637
20.15920.1885-0.03070.1859-0.00970.014-0.60740.07650.4066-0.58880.25280.2503-0.3883-0.1532-0.12310.9191-0.2826-0.63020.0553-0.14020.5652-29.72131.87216.2738
30.0036-0.0018-0.00590.00030.00110.0268-0.01520.07450.12670.0142-0.0009-0.0462-0.1843-0.0266-01.0482-0.41340.03080.8138-0.08080.5353-21.3095115.68-21.5098
40.11180.01520.06650.04060.04220.0773-0.2110.11070.0968-0.1033-0.02570.2384-0.3156-0.0919-0.16880.6887-0.2984-0.27980.2003-0.16590.3522-37.1946109.6542-1.4874
50.01020.00340.00180.003-0.0110.00910.00050.0525-0.0818-0.0544-0.1129-0.0037-0.02370.0205-00.4128-0.06460.0640.3669-0.0450.3611-19.854796.235415.282
60.0301-0.0109-0.0180.020.01960.0108-0.0683-0.0579-0.0098-0.1235-0.0687-0.0746-0.02440.124100.2599-0.04760.06610.48930.03650.3952-7.342482.287434.2311
70.23130.13810.04420.1976-0.02530.2515-0.0898-0.1444-0.0450.0154-0.0288-0.03490.0969-0.0572-0.08640.1656-0.06640.05760.40970.0390.2484-26.680678.192643.6239
80.30570.11140.25810.09790.0070.5018-0.17880.06320.0617-0.0570.05520.1049-0.0469-0.1538-0.06540.2527-0.12920.0160.4148-0.00110.282-40.189673.434326.3208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 3950 THROUGH 3993 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 3994 THROUGH 4150 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 4151 THROUGH 4216 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 4217 THROUGH 4374 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 3936 THROUGH 3993 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 3994 THROUGH 4025 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 4026 THROUGH 4275 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 4276 THROUGH 4372 )

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