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- PDB-9h1j: Crystal structure of the p62 UBA domain bound to VHH 6C10 -

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Basic information

Entry
Database: PDB / ID: 9h1j
TitleCrystal structure of the p62 UBA domain bound to VHH 6C10
Components
  • Sequestosome-1
  • VHH 6C10
KeywordsPROTEIN TRANSPORT / Autophagy / Macroautophagy / ubiquitin binding proteins
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / response to mitochondrial depolarisation / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / Lewy body / amphisome / regulation of protein complex stability ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / response to mitochondrial depolarisation / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / Lewy body / amphisome / regulation of protein complex stability / endosome organization / pexophagy / autophagy of mitochondrion / membraneless organelle assembly / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of mitochondrion organization / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / aggresome / endosomal transport / intracellular membraneless organelle / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of ferroptosis / temperature homeostasis / cellular response to stress / autolysosome / molecular sequestering activity / immune system process / mitophagy / energy homeostasis / sperm midpiece / signaling adaptor activity / inclusion body / negative regulation of protein ubiquitination / ionotropic glutamate receptor binding / positive regulation of autophagy / SH2 domain binding / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Pexophagy / protein kinase C binding / autophagosome / NRIF signals cell death from the nucleus / protein sequestering activity / sarcomere / response to ischemia / ubiquitin binding / positive regulation of long-term synaptic potentiation / PINK1-PRKN Mediated Mitophagy / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / protein catabolic process / molecular condensate scaffold activity / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / intracellular protein localization / late endosome / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsGutmann, S. / Villard, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Development of a p62 biodegrader for autophagy targeted degradation
Authors: Thiel, Z. / Marcellin, D. / Manneville, C. / Goretzki, B. / Egger, L. / Maher, R. / Siccardi, N. / Sandig, G. / Torres, L. / Probst, A. / Mueller, C.S. / George, N. / Vogel, M. / Lavoisier, ...Authors: Thiel, Z. / Marcellin, D. / Manneville, C. / Goretzki, B. / Egger, L. / Maher, R. / Siccardi, N. / Sandig, G. / Torres, L. / Probst, A. / Mueller, C.S. / George, N. / Vogel, M. / Lavoisier, A. / Choi, J.Y. / Forcellino, L. / Hauck, P. / Be, C. / Villard, F. / Gutmann, S. / Meyer, M. / Freuler, F. / Patoor, M. / Mitchell, G. / Nyfeler, B.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VHH 6C10
B: VHH 6C10
C: VHH 6C10
D: VHH 6C10
E: Sequestosome-1
F: Sequestosome-1
G: Sequestosome-1
H: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)75,7288
Polymers75,7288
Non-polymers00
Water10,431579
1
A: VHH 6C10
E: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)18,9322
Polymers18,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VHH 6C10
F: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)18,9322
Polymers18,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: VHH 6C10
G: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)18,9322
Polymers18,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: VHH 6C10
H: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)18,9322
Polymers18,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.886, 73.613, 89.785
Angle α, β, γ (deg.)90.000, 90.219, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody
VHH 6C10


Mass: 13274.704 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Lama glama (llama)
#2: Protein
Sequestosome-1


Mass: 5657.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13501
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1M Lithium Chloride, 0.1M Citric Acid, 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00007 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00007 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 1.73→19.89 Å / Num. obs: 84831 / % possible obs: 99 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rpim(I) all: 0.04 / Net I/σ(I): 7.2
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 4196 / CC1/2: 0.379 / Rpim(I) all: 1.337

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→19.66 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 4242 5.01 %
Rwork0.214 80510 -
obs0.2252 84752 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.19 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 0 579 5483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00155039
X-RAY DIFFRACTIONf_angle_d0.36796830
X-RAY DIFFRACTIONf_chiral_restr0.0365755
X-RAY DIFFRACTIONf_plane_restr0.0025875
X-RAY DIFFRACTIONf_dihedral_angle_d15.27241786
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)
11.6921327227-0.189335064988-1.118949239521.48951323626-0.08989313130021.28748803794-0.07216843503210.118603946459-0.1419184109050.0334178063880.01107732150820.117776379545-0.0443066780737-0.09808462587580.0537433872120.220807188210.02384222826770.008956302504250.498863129851-0.01903567628580.175044669692-4.1741564415126.812373607538.2855304159
21.687224255060.2036666292610.6737278931581.428320866750.1404333021640.6760746730040.0160439638380.01773736546220.155942987491-0.033006625729-0.09601498381810.03552284268760.0445842650876-0.05102787928190.06733753115440.246366180545-0.0189382344553-0.004677555318840.479468053216-0.009664908623640.1508118265964.556199081039.452897094916.52787195775
32.468602547280.282961701644-0.9509102997541.683763575570.02455285921721.32878707468-0.0807834448654-0.0881056732533-0.28848725642-0.0169682644625-0.0202546591119-0.07245719062810.05124105512590.03484675468180.09287570107820.218753679101-0.01933228710460.02887270415750.4408862620650.01705158435750.20248105303827.006521496726.67849335260.327755484615
42.2089918914-0.201416335680.9947218780171.46934459592-0.08844754801260.792180467752-0.1435590341140.1156117444190.3214929201580.00207270129923-0.0205091108969-0.123315143256-0.0115495032122-0.03206031714030.1392664749410.2555574661080.0102247362632-0.03888671994840.5599136184170.02147140530040.20996585841335.10230924639.8620870242144.9436745988
51.422389092850.2848588832290.1302616017571.412564148910.3723790448891.53054391650.04368581764280.01335997288240.1075115944750.0705104614678-0.1371962781190.04059510284420.0216655958927-0.1508099304090.08076184063920.2230631362590.0148022753288-0.01249936288790.527192397775-0.01537827599460.13630393466710.038599773139.870343474728.1595227846
61.394750982210.0261091737138-0.2877275437041.47276406329-0.1142585675131.40091344313-0.0497905126995-0.100040838655-0.0892911792899-0.01993185865350.08274985128910.02230048072340.01544865025310.0785629227351-0.02940990989310.212015544357-0.002051739396670.01591706185450.514766902103-0.01438807498690.1269277358218.9618790866-3.399113484216.9166844958
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA1 - 1161 - 116
22chain BBB2 - 1151 - 114
33chain CCC1 - 1151 - 115
44chain DDD1 - 1161 - 116
55chain EEE391 - 4351 - 45
66chain FFF390 - 4341 - 45

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