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- PDB-6xz1: Conjugate of the HECT domain of HUWE1 with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6xz1
TitleConjugate of the HECT domain of HUWE1 with ubiquitin
Components
  • HECT, UBA and WWE domain containing 1, isoform CRA_a
  • Polyubiquitin-B
KeywordsLIGASE / ubiquitin ligase / E3 enzyme / ubiquitin-propargylamide / activity-based probe
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin-protein transferase activity / DNA repair / nucleus
Similarity search - Function
HUWE1, UBA domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic 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) / WWE domain ...HUWE1, UBA domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic 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) / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / UBA/TS-N domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin associated domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Pectin lyase fold / Pectin lyase fold/virulence factor / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Armadillo-type fold / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / PHOSPHATE ION / HECT-type E3 ubiquitin transferase / Tail fiber
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, B. / Seenivasan, A. / Nair, R. / Chen, D. / Lowe, E.D. / Lorenz, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2243 Germany
German Research Foundation (DFG)LO 2003/1-1 Germany
German Research Foundation (DFG)LO 2003/1-2 Germany
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Reconstitution and Structural Analysis of a HECT Ligase-Ubiquitin Complex via an Activity-Based Probe.
Authors: Nair, R.M. / Seenivasan, A. / Liu, B. / Chen, D. / Lowe, E.D. / Lorenz, S.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 13, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HECT, UBA and WWE domain containing 1, isoform CRA_a
C: Polyubiquitin-B
B: HECT, UBA and WWE domain containing 1, isoform CRA_a
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82711
Polymers107,2384
Non-polymers5897
Water2,918162
1
A: HECT, UBA and WWE domain containing 1, isoform CRA_a
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8665
Polymers53,6192
Non-polymers2473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-13 kcal/mol
Surface area21120 Å2
MethodPISA
2
B: HECT, UBA and WWE domain containing 1, isoform CRA_a
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9616
Polymers53,6192
Non-polymers3424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-20 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.552, 142.171, 103.512
Angle α, β, γ (deg.)90.000, 129.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HECT, UBA and WWE domain containing 1, isoform CRA_a


Mass: 45099.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1, hCG_2000770 / Plasmid: pSKB2 / Production host: Escherichia coli (E. coli) / Variant (production host): LOBSTR / References: UniProt: A0A024R9Y3
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pTXB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2019 / Details: X-ray
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→79.752 Å / Num. obs: 135622 / % possible obs: 99.68 % / Redundancy: 5.3 % / Biso Wilson estimate: 51.59 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.08074 / Rrim(I) all: 0.1879 / Net I/σ(I): 7.14
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 6927 / CC1/2: 0.482 / CC star: 0.807 / Rpim(I) all: 0.9056 / % possible all: 99.65

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 3H1D

1ubq

3h1d


Resolution: 2.3→79.752 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.07
RfactorNum. reflection% reflection
Rfree0.2545 3464 2.55 %
Rwork0.2257 --
obs0.2265 135622 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.47 Å2 / Biso mean: 59.3223 Å2 / Biso min: 30.84 Å2
Refinement stepCycle: final / Resolution: 2.3→79.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7367 0 33 162 7562
Biso mean--85.02 56.79 -
Num. residues----918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.33150.46521520.4312520097
2.3315-2.36480.44241390.4283517097
2.3648-2.40010.42161150.4152522598
2.4001-2.43760.42611670.3928536999
2.4376-2.47760.41741470.3791527099
2.4776-2.52030.40731020.3723530299
2.5203-2.56620.3771520.3622527599
2.5662-2.61550.37111380.3476533099
2.6155-2.66890.33031280.3435534199
2.6689-2.72690.34381500.3395527799
2.7269-2.79040.31621140.3264529899
2.7904-2.86020.39261460.3171522498
2.8602-2.93750.35861380.2946531698
2.9375-3.02390.20741410.27525599
3.0239-3.12150.32311300.2648534899
3.1215-3.23310.33131320.2555322100
3.2331-3.36260.37631450.247527799
3.3626-3.51560.2121460.2058533299
3.5156-3.70090.19051410.1893532199
3.7009-3.93280.22981360.1807524999
3.9328-4.23650.21491440.16255308100
4.2365-4.66270.18371490.1475341100
4.6627-5.33730.17031280.1605532899
5.3373-6.7240.19291380.1871529899

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