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- PDB-7bii: Crystal structure of Nematocida HUWE1 -

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Basic information

Entry
Database: PDB / ID: 7bii
TitleCrystal structure of Nematocida HUWE1
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / HECT E3 ligase / ubiquitin / protein quality control
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / Golgi organization / base-excision repair / protein polyubiquitination / ubiquitin protein ligase activity / membrane fusion / Golgi membrane / nucleus
Similarity search - Function
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) / 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
Similarity search - Domain/homology
HECT-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesNematocida sp. ERTm5 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.037 Å
AuthorsGrabarczyk, D.B. / Petrova, O.A. / Meinhart, A. / Kessler, D. / Clausen, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain.
Authors: Grabarczyk, D.B. / Petrova, O.A. / Deszcz, L. / Kurzbauer, R. / Murphy, P. / Ahel, J. / Vogel, A. / Gogova, R. / Faas, V. / Kordic, D. / Schleiffer, A. / Meinhart, A. / Imre, R. / Lehner, A. ...Authors: Grabarczyk, D.B. / Petrova, O.A. / Deszcz, L. / Kurzbauer, R. / Murphy, P. / Ahel, J. / Vogel, A. / Gogova, R. / Faas, V. / Kordic, D. / Schleiffer, A. / Meinhart, A. / Imre, R. / Lehner, A. / Neuhold, J. / Bader, G. / Stolt-Bergner, P. / Bottcher, J. / Wolkerstorfer, B. / Fischer, G. / Grishkovskaya, I. / Haselbach, D. / Kessler, D. / Clausen, T.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)575,7472
Polymers575,7472
Non-polymers00
Water00
1
A: E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)287,8731
Polymers287,8731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)287,8731
Polymers287,8731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.519, 96.218, 199.655
Angle α, β, γ (deg.)92.220, 100.450, 95.330
Int Tables number1
Space group name H-MP1

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Components

#1: Protein E3 ubiquitin-protein ligase HUWE1


Mass: 287873.375 Da / Num. of mol.: 2 / Mutation: C2457A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nematocida sp. ERTm5 (fungus) / Gene: NEIG_01557 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A177ELV2

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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: 60.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 10.4% PEG 4000, 100mM MgCl2, 100mM HEPES pH 6.6, 6mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.037→196.03 Å / Num. obs: 75499 / % possible obs: 89.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Net I/σ(I): 5.6
Reflection shellResolution: 3.037→3.393 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3785 / CC1/2: 0.741

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G1N

3g1n


Resolution: 3.037→196.03 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.551
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3733 4.94 %RANDOM
Rwork0.2024 ---
obs0.2039 75499 56.3 %-
Displacement parametersBiso max: 232.11 Å2 / Biso mean: 104.76 Å2 / Biso min: 42.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.8852 Å2-3.6826 Å2-2.818 Å2
2---0.9401 Å2-5.8693 Å2
3---1.8254 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3.037→196.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34901 0 0 0 34901
Num. residues----4287
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d12857SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5912HARMONIC5
X-RAY DIFFRACTIONt_it35577HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4759SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact29088SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d35577HARMONIC20.006
X-RAY DIFFRACTIONt_angle_deg47991HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion18.73
LS refinement shellResolution: 3.04→3.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2921 81 5.36 %
Rwork0.252 1429 -
all0.2543 1510 -
obs--5.9 %
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)
14.7337-0.87371.47334.3943-1.49536.4691-0.46020.19740.5489-0.40820.22750.2263-0.5312-0.64010.2327-0.2605-0.1017-0.305-0.38270.183-0.1577-22.66318.897116.7441
20.7963-0.024-0.5360.8984-0.65311.02830.0109-0.03130.0308-0.3459-0.2398-0.2835-0.04860.31840.229-0.1216-0.1991-0.0975-0.0413-0.0062-0.252622.214317.788895.842
33.8664-2.16060.90783.4517-3.031912.8202-0.2572-0.21580.2040.11440.46210.1273-0.6238-1.0386-0.2049-0.2910.3313-0.0229-0.3103-0.072-0.2226-20.421355.22135.1559
42.55710.5481-0.45571.9984-0.54552.45930.0841-0.2540.1106-0.0182-0.1145-0.1486-0.47010.15460.0304-0.16010.02940.0343-0.339-0.0688-0.015711.901239.9153166.6392
55.3086-1.0544-1.18553.75051.00086.94240.2483-0.6330.37080.1465-0.46120.4261-0.5311-0.41690.2129-0.3987-0.14330.1479-0.3019-0.3273-0.111260.5905109.9496198.7247
60.4526-0.41930.13922.8356-2.85113.0411-0.0173-0.145-0.0385-0.1273-0.3444-0.24520.4010.17270.36160.164-0.19510.0014-0.2963-0.1213-0.277684.488761.7299208.0625
70.8124-0.77880.49241.4901-1.17323.16310.0931-0.3129-0.09420.31090.10560.4868-0.1226-0.3691-0.1987-0.47-0.00810.10640.046-0.14960.006332.942281.3494214.166
82.33630.252-0.32193.08-0.34832.3534-0.17820.03350.0038-0.3074-0.00960.35190.1612-0.42230.1878-0.43260.0014-0.0447-0.0964-0.0733-0.016642.909874.3507148.4613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|364 }A2 - 364
2X-RAY DIFFRACTION2{ A|365 - A|1777 }A365 - 1777
3X-RAY DIFFRACTION3{ A|1778 - A|2038 }A1778 - 2038
4X-RAY DIFFRACTION4{ A|2039 - A|2482 }A2039 - 2482
5X-RAY DIFFRACTION5{ B|2 - B|364 }B2 - 364
6X-RAY DIFFRACTION6{ B|365 - B|1018 }B365 - 1018
7X-RAY DIFFRACTION7{ B|1019 - B|2038 }B1019 - 2038
8X-RAY DIFFRACTION8{ B|2039 - B|2482 }B2039 - 2482

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