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- PDB-8jwj: PHD Finger Protein 7 (PHF7) in complex with UBE2D2 -

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Basic information

Entry
Database: PDB / ID: 8jwj
TitlePHD Finger Protein 7 (PHF7) in complex with UBE2D2
Components
  • PHD finger protein 7
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin / RING ligase / PHD / complex
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: 2.96 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
B: Ubiquitin-conjugating enzyme E2 D2
C: PHD finger protein 7
D: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,69326
Polymers101,9804
Non-polymers1,71322
Water00
1
A: PHD finger protein 7
B: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54410
Polymers50,9902
Non-polymers5548
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-30 kcal/mol
Surface area21410 Å2
MethodPISA
2
C: PHD finger protein 7
D: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14916
Polymers50,9902
Non-polymers1,15914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-53 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.304, 106.825, 145.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein PHD finger protein 7 / Testis development protein NYD-SP6


Mass: 33741.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Phf7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9DAG9
#2: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(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: 17248.855 Da / Num. of mol.: 2 / Mutation: S22R, C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme

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Non-polymers , 4 types, 22 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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Details

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: 3.91 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: MPD, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97403 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97403 Å / Relative weight: 1
ReflectionResolution: 2.96→47.35 Å / Num. obs: 32768 / % possible obs: 96.52 % / Redundancy: 4.5 % / Biso Wilson estimate: 91.1 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06656 / Rpim(I) all: 0.03397 / Rrim(I) all: 0.07505 / Net I/σ(I): 14.5
Reflection shellResolution: 2.961→3.067 Å / Redundancy: 4.6 % / Num. unique obs: 3144 / CC1/2: 0.716 / CC star: 0.914 / % possible all: 94.39

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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,6HPR,AlphaFold

1weq

6hpr


Resolution: 2.96→47.35 Å / SU ML: 0.4556 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 1993 6.08 %
Rwork0.1941 30765 -
obs0.1959 32758 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.78 Å2
Refinement stepCycle: LAST / Resolution: 2.96→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 64 0 6695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696846
X-RAY DIFFRACTIONf_angle_d0.94989262
X-RAY DIFFRACTIONf_chiral_restr0.0559964
X-RAY DIFFRACTIONf_plane_restr0.00811220
X-RAY DIFFRACTIONf_dihedral_angle_d10.39722573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.040.39961540.40772049X-RAY DIFFRACTION92.95
3.04-3.120.38391220.33452225X-RAY DIFFRACTION97.51
3.12-3.210.28621460.26952173X-RAY DIFFRACTION97.52
3.21-3.310.28881380.23912191X-RAY DIFFRACTION97.61
3.31-3.430.26891410.2222202X-RAY DIFFRACTION97.67
3.43-3.570.2781450.2352193X-RAY DIFFRACTION97.82
3.57-3.730.31450.23692194X-RAY DIFFRACTION97.78
3.73-3.930.21031460.18092213X-RAY DIFFRACTION97
3.93-4.170.19961410.16522196X-RAY DIFFRACTION97.78
4.17-4.490.18951440.15412210X-RAY DIFFRACTION96.75
4.49-4.950.17791430.14662207X-RAY DIFFRACTION96.39
4.95-5.660.17981460.16122193X-RAY DIFFRACTION95.63
5.66-7.130.22671370.19952222X-RAY DIFFRACTION95.16
7.13-47.350.19841450.18932297X-RAY DIFFRACTION94.1
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)
17.54906273535-0.414266682772-4.407660938072.227048249510.3605199712836.64378492052-0.5434567687410.120304224173-1.111227456240.2604432838760.04719295007310.824348487760.0477351467564-0.3939622270380.4189419975460.6798269279480.2250217906310.07666226898220.748301471739-0.169551753471.0061441167858.2698654747-13.537325582527.8101960214
23.75277645284-0.839799550435-0.519951069714.677475336731.94664845273.95686362043-0.958800453263-1.01951023399-1.047485309290.627679071482-0.02061633499380.6305658684410.709354741327-0.1281681008450.7654771801980.8195525736490.4912004964780.3739392360911.20216188452-0.1121614201711.1714529550541.2973515813-9.3289155807241.7961969316
32.534084651223.20341115963.121131822319.163408100361.314336878538.201437309080.19230494070.3981730133111.37399285613-0.186237207361-1.715355010450.898739638334-0.5735702814311.730246487551.314970396020.8942467049070.01532146362480.2269718612591.31332806722-0.08577249686921.4134790232952.221032602413.748863554352.0722557702
41.293140785070.170853227038-2.398186147784.41507299187-1.947277929765.046071645730.152334219378-0.3536824695771.28161847938-0.163841349605-0.379282869858-0.478023676638-1.254469863211.359183273460.2590991096431.08541156259-0.291438726234-0.5745326546651.352218757720.1438859937641.7559763320459.142784170130.4132025667.3691368146
54.4555632468-1.417360582611.9155104758.25606767412.28204929588.470060912960.0490614423123-0.0604581877228-0.05497195883490.220510454647-0.394510017471-0.01519743798660.09331003546110.1903460229020.3031670860390.3799751706380.09358647820170.009159499164890.5202539758420.1185336520680.5626085052536.188325612314.630111320455.9326433866
64.144669252381.31494520938-0.2695613829893.16802922429-1.417862568293.93491235871-0.317458346742-0.4180006073960.5252973879461.14784359674-0.121556596825-1.00107820949-0.7987088402190.3849207018340.3780899225990.713030016630.110558079719-0.3245596654220.584099910271-0.08504843178570.8722086658712.45081216366.482791509357.24685577
75.155120317911.57132582658-4.406296052458.2064421663-0.7327916280445.29105662058-0.3234702092930.1131798125610.3883927147130.4285684447410.2153308507340.09702943447840.394681032868-0.06298782159660.07737087061640.5674212031180.133696870593-0.08385322750740.490330016960.01023498762640.4313994984235.78165958246.173762850957.1656841886
84.93044987525-5.18661705026-4.503675541675.675391049284.883636154574.22112178860.1143897696041.359527140180.66964054626-1.570348652990.365386915667-1.12377168227-0.8113760340760.0454892644567-0.1375431371490.950404577593-0.1845901083750.1446940836940.849327233258-0.03627462701340.70376596101916.153361590837.905933798431.6859902884
92.851277327890.644741928163-1.730424738812.78743307726-2.6391307062.963823289430.1391213169320.9652145966950.417591818687-1.43435411860.119709036414-0.994813179843-0.4545447273231.16065231533-0.1857017413621.45808816801-0.4375693829390.5472264678291.35036072317-0.3042679596290.80519947846721.252414311922.91637227612.4219745417
103.930470314182.051964818773.606895929064.945955805293.94853861637.42852263455-0.1540753802930.196105313759-0.349837013530.0697536579210.293470672646-0.01415182875550.4677239999930.258476964739-0.1385398287940.4157668023330.01680742610530.05705004707470.4129188183220.08944422205660.52397313876813.972234823424.229752104240.7880759539
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 158)AA30 - 1581 - 122
22chain 'A' and (resid 159 through 229)AA159 - 229123 - 193
33chain 'A' and (resid 230 through 246)AA230 - 246194 - 210
44chain 'A' and (resid 247 through 301)AA247 - 301211 - 265
55chain 'B' and (resid -3 through 147)BI-3 - 1471 - 151
66chain 'C' and (resid 30 through 158)CJ30 - 1581 - 129
77chain 'C' and (resid 159 through 229)CJ159 - 229130 - 200
88chain 'C' and (resid 230 through 246)CJ230 - 246201 - 217
99chain 'C' and (resid 247 through 301)CJ247 - 301218 - 272
1010chain 'D' and (resid -2 through 147)DR-2 - 1472 - 151

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