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- PDB-6j1y: Semi-open conformation E3 ligase -

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Basic information

Entry
Database: PDB / ID: 6j1y
TitleSemi-open conformation E3 ligase
ComponentsNEDD4-like E3 ubiquitin-protein ligase WWP1
KeywordsLIGASE / E3 ligase / Semi-open conformation / Auto-inhibition
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / ubiquitin ligase complex / Downregulation of ERBB4 signaling / monoatomic ion transmembrane transport / central nervous system development / Stimuli-sensing channels / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...HECT-type E3 ubiquitin transferase / ubiquitin ligase complex / Downregulation of ERBB4 signaling / monoatomic ion transmembrane transport / central nervous system development / Stimuli-sensing channels / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / symbiont entry into host cell / negative regulation of DNA-templated transcription / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
NEDD4-like E3 ubiquitin-protein ligase WWP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLiu, Z.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670730 China
National Natural Science Foundation of China31871394 China
National Natural Science Foundation of China31422015 China
CitationJournal: Nat Commun / Year: 2019
Title: A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases.
Authors: Wang, Z. / Liu, Z. / Chen, X. / Li, J. / Yao, W. / Huang, S. / Gu, A. / Lei, Q.Y. / Mao, Y. / Wen, W.
History
DepositionDec 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP1
B: NEDD4-like E3 ubiquitin-protein ligase WWP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4083
Polymers122,3162
Non-polymers921
Water18010
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP1


Theoretical massNumber of molelcules
Total (without water)61,1581
Polymers61,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19350 Å2
MethodPISA
2
B: NEDD4-like E3 ubiquitin-protein ligase WWP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2502
Polymers61,1581
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.019, 59.370, 85.075
Angle α, β, γ (deg.)99.39, 92.29, 108.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NEDD4-like E3 ubiquitin-protein ligase WWP1 / Atrophin-1-interacting protein 5 / AIP5 / HECT-type E3 ubiquitin transferase WWP1 / TGIF- ...Atrophin-1-interacting protein 5 / AIP5 / HECT-type E3 ubiquitin transferase WWP1 / TGIF-interacting ubiquitin ligase 1 / Tiul1 / WW domain-containing protein 1


Mass: 61158.039 Da / Num. of mol.: 2 / Fragment: WWP1 semi-open conformation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9H0M0, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium malonate pH 5.0, 12% w/v Polyethyleneglycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 33955 / % possible obs: 95.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 32.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3493 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XMC

5xmc


Resolution: 2.55→42.572 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1649 4.86 %
Rwork0.2081 --
obs0.2104 33949 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→42.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6327 0 6 10 6343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086502
X-RAY DIFFRACTIONf_angle_d0.9358841
X-RAY DIFFRACTIONf_dihedral_angle_d10.7323739
X-RAY DIFFRACTIONf_chiral_restr0.053970
X-RAY DIFFRACTIONf_plane_restr0.0061130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.62510.31481450.26852789X-RAY DIFFRACTION98
2.6251-2.70980.34721550.25812756X-RAY DIFFRACTION98
2.7098-2.80660.29651590.23592752X-RAY DIFFRACTION98
2.8066-2.91890.27781470.23422752X-RAY DIFFRACTION98
2.9189-3.05180.31751320.23582790X-RAY DIFFRACTION98
3.0518-3.21260.31661160.22852807X-RAY DIFFRACTION99
3.2126-3.41380.29261390.22022793X-RAY DIFFRACTION99
3.4138-3.67720.27391210.22482056X-RAY DIFFRACTION73
3.6772-4.0470.23411290.20192528X-RAY DIFFRACTION90
4.047-4.6320.20751340.17852798X-RAY DIFFRACTION98
4.632-5.83350.22171500.18682768X-RAY DIFFRACTION99
5.8335-42.57830.22941220.19882711X-RAY DIFFRACTION96
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)
10.6133-0.36610.4913.3601-0.48913.89480.0988-0.0168-0.1172-0.3692-0.06330.57790.023-0.3243-0.10180.35170.0323-0.10040.2945-0.01110.541149.8439-3.3165-19.1957
22.82531.18771.20641.31381.7632.4640.0966-0.0292-0.04710.22770.04890.08210.11980.0881-0.16050.41370.0425-0.11720.24920.04280.510763.20420.8192-11.6617
36.95411.8829-1.18784.8218-0.36184.53570.0502-0.62671.0052-0.0797-0.0158-0.1608-0.40830.0664-0.03420.396-0.0184-0.10210.3615-0.13490.635882.06718.9062-8.5092
40.21690.53220.2741.3250.60720.4592-0.08560.1098-0.1741-0.160.0715-0.06510.10090.08850.03710.48690.0513-0.03660.31450.04250.583968.663310.8539-16.79
52.2353-0.9961-0.49946.3059-1.72474.54540.178-0.0141-0.0206-0.3073-0.2022-0.27410.22550.11190.0370.29560.0418-0.05290.1929-0.00120.462555.047628.4203-12.687
61.117-1.8654-2.06486.58155.94148.71170.56840.4242-0.4446-0.6103-0.206-0.3678-0.7005-1.5253-0.56790.3645-0.0106-0.00180.6521-0.13150.788780.530335.732514.4033
72.0621-0.70161.57475.7330.36913.6104-0.32920.15820.2780.31950.22980.42720.0861-0.5250.120.3269-0.07550.00290.5548-0.01780.468872.490928.554749.2738
83.75830.5734-0.77331.3509-0.16072.45210.1989-0.28570.12960.06470.0186-0.2731-0.04050.1208-0.17230.25660.0158-0.02930.4208-0.10140.39891.434727.904221.0118
94.26560.8355-0.94739.21061.27285.059-0.06340.2236-0.311-0.5712-0.01470.60720.2963-0.2060.05120.425-0.0138-0.1540.3521-0.04120.389176.1762-2.41029.0443
100.84231.8948-0.00445.52691.71642.2362-0.0276-0.2139-0.16110.02890.1747-0.3222-0.21060.2582-0.10540.2882-0.0042-0.09170.4918-0.03850.476485.3114.284121.8993
115.96932.33620.57513.7317-1.40376.75030.1069-0.6909-0.0190.03-0.1404-0.31510.0758-0.04920.04770.250.0387-0.0730.3418-0.05510.410460.684622.695216.9642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 430 through 624 )
2X-RAY DIFFRACTION2chain 'A' and (resid 625 through 692 )
3X-RAY DIFFRACTION3chain 'A' and (resid 693 through 738 )
4X-RAY DIFFRACTION4chain 'A' and (resid 739 through 815 )
5X-RAY DIFFRACTION5chain 'A' and (resid 816 through 916 )
6X-RAY DIFFRACTION6chain 'B' and (resid 417 through 448 )
7X-RAY DIFFRACTION7chain 'B' and (resid 449 through 546 )
8X-RAY DIFFRACTION8chain 'B' and (resid 547 through 692 )
9X-RAY DIFFRACTION9chain 'B' and (resid 693 through 752 )
10X-RAY DIFFRACTION10chain 'B' and (resid 753 through 802 )
11X-RAY DIFFRACTION11chain 'B' and (resid 803 through 916 )

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