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- PDB-6pfl: Crystal structure of Human HUWE1 WWE domain in complex with ADPR -

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Basic information

Entry
Database: PDB / ID: 6pfl
TitleCrystal structure of Human HUWE1 WWE domain in complex with ADPR
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsTRANSFERASE / HUWE1 / WWE domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / protein monoubiquitination / Golgi organization / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / protein monoubiquitination / Golgi organization / 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 / cytoplasm / cytosol
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
ADENOSINE-5-DIPHOSPHORIBOSE / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHalabelian, L. / Zeng, H. / Dong, A. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of Human HUWE1 WWE domain in complex with ADPR
Authors: Halabelian, L. / Zeng, H. / Dong, A. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1587
Polymers21,0392
Non-polymers1,1195
Water48627
1
A: E3 ubiquitin-protein ligase HUWE1
B: E3 ubiquitin-protein ligase HUWE1
hetero molecules

A: E3 ubiquitin-protein ligase HUWE1
B: E3 ubiquitin-protein ligase HUWE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,31614
Polymers42,0784
Non-polymers2,23710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area8610 Å2
ΔGint-45 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.423, 50.423, 128.412
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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 / HECT-type E3 ...ARF-binding protein 1 / ARF-BP1 / HECT / UBA and WWE domain-containing protein 1 / HECT-type E3 ubiquitin transferase HUWE1 / 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: 10519.563 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1, KIAA0312, KIAA1578, UREB1, HSPC272 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pRARE2
References: UniProt: Q7Z6Z7, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.09 % / Mosaicity: 0.25 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4M NaCitrate, and 0.1M Tris-HCL pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→43.67 Å / Num. obs: 11221 / % possible obs: 97.8 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 11.3 / Num. measured all: 67269 / Scaling rejects: 25
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.528 / Num. measured all: 5537 / Num. unique obs: 904 / CC1/2: 0.847 / Rpim(I) all: 0.221 / Rrim(I) all: 0.575 / Net I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MIW

6miw


Resolution: 2.1→43.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.359 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 550 4.9 %RANDOM
Rwork0.208 ---
obs0.2106 10669 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.32 Å2 / Biso mean: 41.156 Å2 / Biso min: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.25 Å2-0 Å2
2---0.51 Å20 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 2.1→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 57 27 1289
Biso mean--48.51 44.88 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121300
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181072
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.6591782
X-RAY DIFFRACTIONr_angle_other_deg1.2481.5792458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3625153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55619.73776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4171515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 31 -
Rwork0.287 777 -
all-808 -
obs--98.9 %

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