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- PDB-2hth: Structural basis for ubiquitin recognition by the human EAP45/ESC... -

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Basic information

Entry
Database: PDB / ID: 2hth
TitleStructural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain
Components
  • Ubiquitin
  • Vacuolar protein sorting protein 36Vacuole
KeywordsPROTEIN TRANSPORT / GLUE domain / PH domain / Protein sorting / viral budding / Ubiquitin complex
Function / homology
Function and homology information


ESCRT II complex / : / : / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein modification process => GO:0036211 / membrane fission / multivesicular body assembly / phosphatidylinositol-3-phosphate binding / Peptide chain elongation / Selenocysteine synthesis ...ESCRT II complex / : / : / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein modification process => GO:0036211 / membrane fission / multivesicular body assembly / phosphatidylinositol-3-phosphate binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / cytosolic ribosome / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / HCMV Late Events / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD
Similarity search - Function
Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ribosomal L40e family / Ribosomal_L40e ...Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / PH-like domain superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Vacuolar protein-sorting-associated protein 36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsAlam, S.L. / Whitby, F.G. / Hill, C.P. / Sundquist, W.I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain.
Authors: Alam, S.L. / Langelier, C. / Whitby, F.G. / Koirala, S. / Robinson, H. / Hill, C.P. / Sundquist, W.I.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: Vacuolar protein sorting protein 36


Theoretical massNumber of molelcules
Total (without water)24,8342
Polymers24,8342
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.727, 102.727, 54.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA52, UBB, UBC / Plasmid: pet3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL codon Plus / References: UniProt: P62988, UniProt: P0CG48*PLUS
#2: Protein Vacuolar protein sorting protein 36 / Vacuole / ELL-associated protein of 45 kDa


Mass: 16257.649 Da / Num. of mol.: 1 / Fragment: EAP45 Glue domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS36, C13orf9, EAP45 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL codon plus / References: UniProt: Q86VN1

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG8000; 10% Ethylene glycol; 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.10000, 0.97910
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97911
ReflectionAv σ(I) over netI: 8.1 / Number: 187787 / Rmerge(I) obs: 0.123 / Χ2: 1.01 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 12326 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.675099.910.0851.023
5.36.6799.910.1020.879
4.635.310010.1051.065
4.214.6310010.1111.085
3.914.2110010.1391.392
3.683.9110010.1521.408
3.493.6810010.2051.072
3.343.4910010.2540.876
3.213.3410010.3760.685
3.13.2110010.530.586
ReflectionResolution: 2.7→50 Å / Num. obs: 8264 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
2.7-2.80.53681.4
2.8-2.910.46595.9
2.91-3.040.32799.8
3.04-3.20.237100
3.2-3.40.181100
3.4-3.660.14100
3.66-4.030.115100
4.03-4.620.103100
4.62-5.810.093100
5.81-500.0899.6

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Sm600.4810.1680.0730.331
2Sm55.6430.8120.2870.230.235
Phasing dmFOM : 0.71 / FOM acentric: 0.73 / FOM centric: 0.66 / Reflection: 5648 / Reflection acentric: 4418 / Reflection centric: 1230
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.4-39.9730.930.970.9286147139
5.9-9.40.830.870.74793553240
4.7-5.90.80.840.67944731213
4.1-4.70.810.830.74955762193
3.5-4.10.670.690.5616481367281
3.3-3.50.460.470.41022858164

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.7→37.32 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.873 / SU B: 13.718 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP RESIDUES 32-36, 53-57, 74-78 AND 90-103 ARE SET AT ZERO OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28872 810 9.8 %RANDOM
Rwork0.24775 ---
obs0.25184 7426 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.345 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20 Å2
2---1.73 Å20 Å2
3---3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 0 1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9531930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97223.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg141512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021038
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2937
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.212
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0321.5877
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81421385
X-RAY DIFFRACTIONr_scbond_it2.3333601
X-RAY DIFFRACTIONr_scangle_it3.684.5545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 49 -
Rwork0.367 440 -
obs--79.64 %
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)
119.634-16.977117.277648.4984-33.283731.71270.42561.12510.3466-2.03710.15490.07190.5117-0.5583-0.58040.1442-0.05610.16750.362300.6009-5.3993-25.0366-25.8532
211.14283.00651.712923.55-2.66717.9247-0.06350.72221.6764-0.29050.3520.4973-0.8265-0.4311-0.28850.18730.04370.18340.34390.06070.638-4.9871-18.8278-22.1207
310.611-4.9379-2.241210.8899-6.009712.4347-0.6711-0.51650.73231.0050.9580.2475-0.6627-0.6338-0.28690.1711-0.00850.12430.12630.00680.6151-4.5547-22.1567-14.1221
414.7253-12.0584-12.721116.97048.789354.8173-0.3704-1.26151.59010.62080.9662-0.1425-0.90352.3249-0.59580.1854-0.1288-0.03590.386-0.07890.84714.719-24.0905-16.9787
519.7679-0.82984.006114.4189-3.12641.4202-0.50571.25661.0785-0.8916-0.206-0.7966-0.73341.05420.71180.3623-0.12630.15960.32490.1550.76236.729-17.3533-25.1469
69.48-4.4441.253211.2689-5.87927.60550.31571.29110.7637-0.7296-0.5377-0.3306-0.38480.31450.2220.1396-0.01470.13270.27090.06270.53641.0983-20.9967-26.2825
75.9458-0.1076-1.82996.87194.275611.2208-0.1844-0.1297-0.59640.3415-0.33630.29740.4668-0.46070.52070.2069-0.00060.01570.13020.00430.636918.3435-43.9012-33.3588
87.9222-0.0113-1.22088.66767.66216.9583-0.5329-0.4755-0.72731.14870.5099-0.16850.9604-0.21360.02290.26650.0373-0.00310.19060.00890.657318.3896-42.119-29.7728
94.0699-0.2853-0.71936.30164.41735.3232-0.1245-0.4479-0.52310.49370.0356-0.11420.7660.14380.08890.1617-0.04350.07650.25860.07140.529915.7534-39.4118-27.1543
1013.7454-9.2369-4.36117.82782.92299.67190.3480.1735-1.18050.0254-0.29110.75870.3725-0.9308-0.05690.2663-0.0590.06050.21990.04650.626311.9839-37.392-22.1819
1112.77853.2136-1.086920.1873-2.27712.7771-0.3526-0.6829-0.26310.98760.0945-1.16370.11070.56120.25810.13960.0657-0.03640.2017-0.01310.427125.243-33.6986-26.2715
1229.7743-4.28928.26288.3266-12.716519.5273-0.66130.77670.1505-1.11140.75610.93830.6111-0.4472-0.09480.1483-0.0171-0.11320.18840.02520.601314.3316-29.3624-36.305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 81 - 8
2X-RAY DIFFRACTION2AA9 - 269 - 26
3X-RAY DIFFRACTION3AA27 - 3827 - 38
4X-RAY DIFFRACTION4AA39 - 4439 - 44
5X-RAY DIFFRACTION5AA45 - 5545 - 55
6X-RAY DIFFRACTION6AA56 - 7356 - 73
7X-RAY DIFFRACTION7BB5 - 297 - 31
8X-RAY DIFFRACTION8BB30 - 4732 - 49
9X-RAY DIFFRACTION9BB48 - 8350 - 85
10X-RAY DIFFRACTION10BB84 - 11286 - 114
11X-RAY DIFFRACTION11BB113 - 124115 - 126
12X-RAY DIFFRACTION12BB125 - 131127 - 133

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