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- PDB-8jwu: PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker -

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Basic information

Entry
Database: PDB / ID: 8jwu
TitlePHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker
ComponentsPHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin / RING ligase / PHD / linker
Function / homology
Function and homology information


negative regulation of osteoclast proliferation / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy ...negative regulation of osteoclast proliferation / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / nuclear speck / protein ubiquitination / Golgi apparatus / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PHF7/G2E3, PHD domain / PHF7/G2E3, ePHD domain / : / PHD-like zinc-binding domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...PHF7/G2E3, PHD domain / PHF7/G2E3, ePHD domain / : / PHD-like zinc-binding domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase PHF7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsLee, H.S. / Bang, I. / Choi, H.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Genes Dev. / Year: 2023
Title: Molecular basis for PHF7-mediated ubiquitination of histone H3.
Authors: Lee, H.S. / Bang, I. / You, J. / Jeong, T.K. / Kim, C.R. / Hwang, M. / Kim, J.S. / Baek, S.H. / Song, J.J. / Choi, H.J.
History
DepositionJun 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
B: PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
C: PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,81126
Polymers154,3063
Non-polymers1,50423
Water00
1
A: PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9599
Polymers51,4351
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8938
Polymers51,4351
Non-polymers4587
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9599
Polymers51,4351
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.540, 102.050, 78.640
Angle α, β, γ (deg.)90.000, 95.922, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-508-

ZN

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Components

#1: Protein PHD finger protein 7,Ubiquitin-conjugating enzyme E2 D2 / Testis development protein NYD-SP6 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ...Testis development protein NYD-SP6 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 51435.457 Da / Num. of mol.: 3 / Mutation: S346R,C409K
Source method: isolated from a genetically manipulated source
Details: Fusion chimera construct composed of Rho1D4-tag, mouse PHF7 (28-307),(GSGG)3 linker, human UBE2D2(1-147)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Phf7, UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q9DAG9, UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn
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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG8000, DMSO, MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 3.58→29.89 Å / Num. obs: 19600 / % possible obs: 99.32 % / Redundancy: 6.9 % / Biso Wilson estimate: 115.31 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 11.16
Reflection shellResolution: 3.58→3.708 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1918 / CC1/2: 0.819 / CC star: 0.949 / % possible all: 99.69

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WEQ,8JWS,6HPR,Alphafold

1weq

8jws

6hpr


Resolution: 3.58→29.89 Å / SU ML: 0.4757 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 1951 9.98 %
Rwork0.216 17590 -
obs0.2209 19541 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149.07 Å2
Refinement stepCycle: LAST / Resolution: 3.58→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9326 0 23 0 9349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00579573
X-RAY DIFFRACTIONf_angle_d0.947613036
X-RAY DIFFRACTIONf_chiral_restr0.05581406
X-RAY DIFFRACTIONf_plane_restr0.0071732
X-RAY DIFFRACTIONf_dihedral_angle_d10.13893407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.670.34081400.33011258X-RAY DIFFRACTION99.86
3.67-3.770.34081360.29311237X-RAY DIFFRACTION99.56
3.77-3.880.37921360.27871232X-RAY DIFFRACTION99.49
3.88-40.31731390.26751258X-RAY DIFFRACTION99.64
4-4.150.30271390.24831254X-RAY DIFFRACTION99
4.15-4.310.28581380.22921241X-RAY DIFFRACTION99.21
4.31-4.510.25961370.22381230X-RAY DIFFRACTION99.42
4.51-4.740.25481410.1981266X-RAY DIFFRACTION99.86
4.75-5.040.25461400.20161255X-RAY DIFFRACTION99.71
5.04-5.430.26341380.20331265X-RAY DIFFRACTION99.86
5.43-5.970.29711410.21551265X-RAY DIFFRACTION99.86
5.97-6.830.27771420.22311270X-RAY DIFFRACTION99.86
6.83-8.570.23921400.19841278X-RAY DIFFRACTION99.65
8.57-29.890.20191440.17521281X-RAY DIFFRACTION98.68
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)
13.45915758378-2.608760089330.3293115704256.53518271481-0.2786651852742.175304260780.7097893193190.2723963663230.93245845014-0.266203635257-0.384513282735-0.57482292111-0.7303807121310.0841616072549-0.3341283564311.34324520408-0.1726358897710.1919763854381.024445787350.1061873182231.05752666233-47.40444.68544.461
23.62730186806-0.4274865912710.8753834425373.15466874372-0.04160408824693.40591717901-0.6061084161750.283783200456-0.3098787008840.4956163454610.5901744638830.154251730954-0.510930794096-0.2746195171410.07154511174691.18763139593-0.1607029045430.012241274980.8097413764120.03901068449960.839016055594-56.38326.21552.738
31.38526961145-2.22325361241.339400140863.55119322323-2.598497887932.72700567795-0.200491414892-0.7681157681310.3473808545730.1125328295160.377513390942-1.00621995238-0.02848675623060.361287413237-0.2484329404841.25223108082-0.331456738732-0.2822246542771.613743653210.06734748436981.02781878185-36.54820.42470.586
40.476651386934-0.2221236954270.577389197181.371377270980.675440818832.29134509164-0.463392134246-1.527561902660.1303944772291.488774283641.0020690949-0.951999230128-0.4785116120380.0516860424929-0.6484751777671.829886252510.431374980197-0.274134397732.47933982170.1570905098231.58522915706-22.3914.93384.966
53.27669744742-0.556499492015-2.517621899022.20240420057-1.461612922586.11741619701-0.522237499313-0.0347561881255-0.2178767237410.5988958157050.146828751726-0.2537587144330.797784215841-0.02367631111530.3550829988161.21910083158-0.0198436930151-0.07734058405490.705691552961-0.1192469073530.82230054715-49.95611.54675.441
64.247942059192.02215898840.8204220477761.929817754481.399009631222.149900548230.358990693963-0.811700965218-0.3706886480651.4836527192-0.131237649361-1.222014595320.6554301456050.929678285591-0.3401897196951.770990716450.266922576176-0.6492333077971.737154853610.08434250021881.53008402402-20.04513.17154.368
73.694902399672.283863014010.3300180543665.73695254949-0.0601259731013.979768282440.7457345928270.328717938453-0.2224747878230.142726729515-0.7330394946680.2160491152540.9690737856970.464957683403-0.05528535234561.60366691410.269062309802-0.1125891121931.227790853690.003465319435510.95944275472-38.7176.86143.828
84.00481912449-1.61101587703-1.001098613762.488924818490.1386752774456.19321741843-0.1997353902580.406097279164-0.09260281761560.10164106530.1060651085290.1310976363111.05594321826-0.2390007553250.09765102585210.92970471704-0.158738506235-0.0705378440960.7472773205150.003468402255470.843034224057-50.10918.3120.828
93.976459478851.75979555319-0.8657932102541.89078111811-0.3134809956832.32486775167-0.422027439271-0.536824021026-0.7006459854660.3230407711410.2077361732480.6835656403920.657673500721-0.7085001305410.2580584051121.3792968276-0.3018564478890.2447807181681.56155033342-0.002928078473911.59490436212-29.31359.05179.969
103.12979241644-0.419581626339-0.8609148146584.124678156070.7286182165025.26671339607-0.001262921972090.2210147597240.1370405832410.314867792786-0.0613230179088-0.0485965917379-0.42003253339-1.585427014180.07523113674060.6635829241970.0345494409303-0.02958780616571.256370702430.030140575531.13372584685-20.30477.95171.586
114.02939542879-1.143428530880.2605432756622.516570939410.2084932640687.37562448398-0.4075118282190.4171856840340.117999717492-0.4588242025110.459096926601-0.194298545509-0.7126883988670.180780793235-0.02370417607780.901102219475-0.219231564927-0.01708372724470.988799819874-0.07516095870770.974920359412-0.33380.62951.795
124.68214579103-0.6966903097672.94545409943.93583705393-2.047235315496.898602610450.0396771132880.1617824874810.3399899560230.433670153897-1.10059658074-1.810807098590.9659493525751.176657569230.9169456574231.25818865250.0141241887548-0.1708335035711.124700366330.1229042664291.00064231736-40.01129.89727.855
135.99956777087-1.694071768690.3774687771874.10807732967-2.434016390045.2921360940.4018572460570.1708711138241.53991535783-0.53070080419-0.3635574232010.1458290158460.4590807045391.00077177164-0.04777909123861.470469772210.1492919323210.01495010420240.9502668361070.04107715606011.23189456061-51.46746.77412.663
140.0731849371855-0.4347702670020.1982585898242.078019436820.334547732994.82119718847-0.331133522951.58078101526-0.8953965871630.794996060696-0.198968622036-0.359481759034-0.928696491914-1.462265545710.2885014069061.061572232260.0709277444620.4802675047241.171271341580.07680102577491.49847218681.05664.84558.292
152.83995926827-0.344417461060.8238969675983.79361604923-0.7845128861462.287838848790.6580597825351.05484870415-0.3189408207350.353484969319-0.4442103672520.4569693670420.0137305309030.224393368144-0.3594576963641.24790766510.4035797178330.2598336081932.226473504490.00481249064471.475651925423.24561.64149.071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:136 )A18 - 136
2X-RAY DIFFRACTION2( CHAIN A AND RESID 146:216 )A146 - 216
3X-RAY DIFFRACTION3( CHAIN A AND RESID 217:233 )A217 - 233
4X-RAY DIFFRACTION4( CHAIN A AND RESID 234:288 )A234 - 288
5X-RAY DIFFRACTION5( CHAIN A AND RESID 999:1147 )A999 - 1147
6X-RAY DIFFRACTION6( CHAIN B AND RESID 18:136 )B18 - 136
7X-RAY DIFFRACTION7( CHAIN B AND RESID 146:216 )B146 - 216
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1000:1147 )B1000 - 1147
9X-RAY DIFFRACTION9( CHAIN C AND RESID 18:136 )C18 - 136
10X-RAY DIFFRACTION10( CHAIN C AND RESID 146:216 )C146 - 216
11X-RAY DIFFRACTION11( CHAIN C AND RESID 311:458 )C311 - 458
12X-RAY DIFFRACTION12( CHAIN B AND RESID 217:233 )B217 - 233
13X-RAY DIFFRACTION13( CHAIN B AND RESID 234:288 )B234 - 288
14X-RAY DIFFRACTION14( CHAIN C AND RESID 217:233 )C217 - 233
15X-RAY DIFFRACTION15( CHAIN C AND RESID 234:288 )C234 - 288

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