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- PDB-9eqk: WWP1 WW2-2,3-linker-WW3-WW4-HECT (WWP1-2L34H) with ordered WW2 domain -

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Basic information

Entry
Database: PDB / ID: 9eqk
TitleWWP1 WW2-2,3-linker-WW3-WW4-HECT (WWP1-2L34H) with ordered WW2 domain
ComponentsNEDD4-like E3 ubiquitin-protein ligase WWP1
KeywordsLIGASE / Ubiquitin
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: 3 Å
AuthorsDudey, A.P. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateResearch Grant 19-14R United Kingdom
CitationJournal: To Be Published
Title: Expanding the Inhibitor Space of the WWP1 and WWP2 HECT E3 Ligases
Authors: Dudey, A.P. / Rigby, J.M. / Hughes, G.R. / Stephenson, G.R. / Storr, T.E. / Chantry, A. / Hemmings, A.M.
History
DepositionMar 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)130,1452
Polymers130,1452
Non-polymers00
Water30617
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP1


Theoretical massNumber of molelcules
Total (without water)65,0721
Polymers65,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEDD4-like E3 ubiquitin-protein ligase WWP1


Theoretical massNumber of molelcules
Total (without water)65,0721
Polymers65,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)226.984, 59.719, 108.258
Angle α, β, γ (deg.)90.000, 99.410, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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: 65072.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RP
References: UniProt: Q9H0M0, HECT-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.73 % / Description: Flat-rod Clusters
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Tris.HCl pH 6.5, 17.5 % reagent alcohol (90 % ethanol, 5 % methanol, 5 % isopropanol).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Feb 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 3→106.823 Å / Num. obs: 29046 / % possible obs: 94.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.37 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.159 / Rrim(I) all: 0.42 / Net I/av σ(I): 1.42 / Net I/σ(I): 4.7
Reflection shellResolution: 3.171→8.605 Å / Redundancy: 7 % / Num. unique obs: 1181 / CC1/2: 0.368 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→84.49 Å / SU ML: 0.504 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2744 1492 5.14 %
Rwork0.2054 27554 -
obs0.2089 29046 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 3→84.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8661 0 0 17 8678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01028903
X-RAY DIFFRACTIONf_angle_d1.188912075
X-RAY DIFFRACTIONf_chiral_restr0.05351252
X-RAY DIFFRACTIONf_plane_restr0.00931567
X-RAY DIFFRACTIONf_dihedral_angle_d7.16011165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.40971240.34012383X-RAY DIFFRACTION95.5
3.09-3.20.33251370.30292457X-RAY DIFFRACTION99.88
3.2-3.330.37291360.30082510X-RAY DIFFRACTION99.89
3.33-3.480.36221550.26012479X-RAY DIFFRACTION99.85
3.48-3.670.28751290.22392504X-RAY DIFFRACTION99.96
3.67-3.90.30091350.21542498X-RAY DIFFRACTION99.96
3.9-4.20.30941270.21222509X-RAY DIFFRACTION100
4.2-4.620.2321450.16712508X-RAY DIFFRACTION100
4.62-5.290.24741310.16122529X-RAY DIFFRACTION100
5.29-6.660.23571130.18142589X-RAY DIFFRACTION99.93
6.67-84.490.20491600.16192588X-RAY DIFFRACTION99.24
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)
12.30733437057-0.793055467377-2.448841348510.5805895519151.369916951164.97306687615-0.3572125762220.0687577891784-0.3931773532970.0180131607495-0.103555839399-0.2378814875560.360665936348-0.1666759787570.3452273412810.655018012158-0.009753575385360.1216911043760.404267156797-0.03541173535880.76362148070141.7103172786-19.456086718817.5605176157
22.31216847060.262709088603-1.233806460752.81471677673-3.129338215957.303478685370.0656929266765-0.6571753504040.446992653610.5481222195110.318930428095-0.0658518713865-0.249562319947-0.10149624041-0.4579192159580.688262253030.108795284329-0.001740899200860.717315128373-0.1363142511320.60896501181116.7215687801-1.8803061108944.3449685018
32.23905578979-0.272011550207-0.07328123738352.410261060510.8467394901971.20102880581-0.0423541443447-0.0815378882016-0.09030408874710.04375998624460.0404646352818-0.2227073783250.0358529380762-0.0865857371389-0.01213092500130.4084613891430.02796151272650.03200867582960.3026103158420.00406139806060.4400836086534.958108263-17.536267766518.6416347951
43.850409556530.1781164201771.995288729473.16076560334-0.9403528186495.37392942295-0.186711475980.05350682682260.399057910217-0.776037465284-0.1614277885680.3779543892910.1339353375110.1778649581940.317418925780.7296720533520.03485722000130.05405781558580.3851114966180.05332217103710.69155102794541.025377642711.48918660251.97602763251
52.775512218850.4311724456680.6439511156581.661180536370.4808317231962.078224990390.0895313738558-0.3608471385870.4277479315220.2440059601780.0913444839094-0.127000109953-0.07469122538650.0943799877274-0.1717450936920.4733279011270.02021957654510.06223679531080.341298718588-0.0978735651050.4844946069244.6495477453-0.65545523873329.1660197882
62.13349501032-0.0614436837-0.07367490861433.091517620190.2950823491134.646490397860.2700793563940.1182621380020.06955105338150.00970077523276-0.130513338533-0.3513259013420.0423519754989-0.26014320496-0.100512251370.728073723245-0.02596672160330.09015827775730.7762299341650.0276727736190.67014718512228.656844456-8.5564769075-24.7773043668
73.22529979957-3.121435749990.01715714956283.144599094120.2232613512310.8566492970140.458411685113-0.4973868720011.588816059220.0707136982728-0.363630991796-0.7605271871380.02478414091680.010710371126-0.2369674754870.699080209189-0.08985290139190.1657590255330.777645762675-0.01233199910770.824637861722-1.5205938041716.6389541705-12.3944986711
83.566322605510.804751057005-0.5052131837292.51873757111-0.5001255596172.54412047502-0.03831711952620.302986161358-0.2815862537540.118428936488-0.197475356069-0.1663390436910.09879075962540.7156012461250.1320224502480.8828591579380.1006850433690.15743738210.945149478690.1246735439581.01032940747-9.9036931343827.5385087962-23.2216206782
91.78791413134-0.225431410897-0.03220112327533.84515974241-0.4157825756421.704368483410.116038605610.028792217296-0.040563600165-0.00918563116518-0.03727932932970.8757982751560.177811242769-0.187154270756-0.05437210683770.514997687507-0.179402448778-0.09573273080350.7326460295810.008065790699920.57805772122410.82007409196.81143446048-25.4574291421
102.193678001490.97411095115-0.5026559160291.69695236038-0.8258419085840.395325291823-0.04262013898360.3233830705850.364963254361-0.251971258832-0.0557135655378-0.007088120674640.1312575542310.06777388599930.1131606710550.629251821826-0.0614941226048-0.04503243935570.8998279234720.1620238878380.62752875423929.834762000322.2491272385-36.1419197469
111.822111470910.2009011025320.6889529377721.864851907530.9116046988173.50420848880.09336103801560.1672696270120.00445035263413-0.006295427111960.03718594098160.0500486060675-0.0156112748454-0.308484526268-0.1238961988780.57694279117-0.06731789296590.03088155961870.5441819761050.01592412016320.54871764816119.568633973728.8958942738-9.16132358005
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 103 )AA3 - 1031 - 101
22chain 'A' and (resid 104 through 159 )AA104 - 159102 - 151
33chain 'A' and (resid 160 through 328 )AA160 - 328152 - 315
44chain 'A' and (resid 329 through 394 )AA329 - 394316 - 377
55chain 'A' and (resid 395 through 548 )AA395 - 548378 - 531
66chain 'B' and (resid 9 through 59 )BB9 - 591 - 51
77chain 'B' and (resid 60 through 89 )BB60 - 8952 - 77
88chain 'B' and (resid 90 through 174 )BB90 - 17478 - 155
99chain 'B' and (resid 175 through 328 )BB175 - 328156 - 309
1010chain 'B' and (resid 329 through 421 )BB329 - 421310 - 402
1111chain 'B' and (resid 422 through 544 )BB422 - 544403 - 525

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