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- PDB-7oat: Structural basis for targeted p97 remodelling by ASPL as prerequi... -

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Basic information

Entry
Database: PDB / ID: 7oat
TitleStructural basis for targeted p97 remodelling by ASPL as prerequisite for p97 trimethylation by METTL21D
Components
  • Protein-lysine methyltransferase METTL21D
  • Tether containing UBX domain for GLUT4
  • Transitional endoplasmic reticulum ATPase
KeywordsTRANSFERASE / p97 / AAA+ ATPase / ASPL / METTL21D / VCP-KMT / VCP / methylation / remodelling
Function / homology
Function and homology information


positive regulation of protein modification process / peptidyl-lysine methylation / peptidyl-lysine trimethylation / regulation of D-glucose import / negative regulation of ATP-dependent activity / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control ...positive regulation of protein modification process / peptidyl-lysine methylation / peptidyl-lysine trimethylation / regulation of D-glucose import / negative regulation of ATP-dependent activity / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / positive regulation of protein K63-linked deubiquitination / protein-lysine N-methyltransferase activity / positive regulation of oxidative phosphorylation / : / mitotic spindle disassembly / aggresome assembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / vesicle membrane / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / stress granule disassembly / positive regulation of ATP biosynthetic process / histone methyltransferase activity / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / proteasomal protein catabolic process / ATP metabolic process / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / Attachment and Entry / lipid droplet / endoplasmic reticulum-Golgi intermediate compartment membrane / endomembrane system / proteasome complex / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / establishment of protein localization / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic side of plasma membrane / positive regulation of protein catabolic process / cytoplasmic stress granule / Aggrephagy / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / glucose homeostasis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ATPase binding / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry
Similarity search - Function
TUG ubiquitin-like domain / TUG ubiquitin-like domain / Lysine methyltransferase / Lysine methyltransferase / UBX domain / UBX domain / UBX domain profile. / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain ...TUG ubiquitin-like domain / TUG ubiquitin-like domain / Lysine methyltransferase / Lysine methyltransferase / UBX domain / UBX domain / UBX domain profile. / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / Transitional endoplasmic reticulum ATPase / Tether containing UBX domain for GLUT4 / Protein N-lysine methyltransferase METTL21D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsPetrovic, S. / Heinemann, U. / Roske, Y.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB740 TPB1 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D.
Authors: Petrovic, S. / Roske, Y. / Rami, B. / Phan, M.H.Q. / Panakova, D. / Heinemann, U.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tether containing UBX domain for GLUT4
B: Transitional endoplasmic reticulum ATPase
C: Protein-lysine methyltransferase METTL21D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,51010
Polymers100,3463
Non-polymers1,1647
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-RALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-26 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.258, 69.622, 140.175
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Tether containing UBX domain for GLUT4 / Alveolar soft part sarcoma chromosomal region candidate gene 1 protein / Alveolar soft part sarcoma ...Alveolar soft part sarcoma chromosomal region candidate gene 1 protein / Alveolar soft part sarcoma locus / Renal papillary cell carcinoma protein 17 / UBX domain-containing protein 9


Mass: 21606.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPSCR1, ASPL, RCC17, TUG, UBXD9, UBXN9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZE9
#2: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 53506.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#3: Protein Protein-lysine methyltransferase METTL21D / Methyltransferase-like protein 21D / VCP lysine methyltransferase / VCP-KMT / Valosin-containing ...Methyltransferase-like protein 21D / VCP lysine methyltransferase / VCP-KMT / Valosin-containing protein lysine methyltransferase


Mass: 25232.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCPKMT, C14orf138, METTL21D / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H867, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 65 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 8000, 0.2 M calcium acetate, 0.1 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.995→49.32 Å / Num. obs: 20828 / % possible obs: 98.1 % / Redundancy: 6.17 % / Biso Wilson estimate: 96.23 Å2 / CC1/2: 0.986 / Rrim(I) all: 0.273 / Net I/σ(I): 6.65
Reflection shellResolution: 3→3.15 Å / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3167 / CC1/2: 0.324 / Rrim(I) all: 1.983

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFS

5ifs


Resolution: 2.995→49.32 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.442
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 1042 5 %RANDOM
Rwork0.2253 ---
obs0.2275 20828 98.1 %-
Displacement parametersBiso max: 139.78 Å2 / Biso mean: 78.66 Å2 / Biso min: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.9857 Å20 Å20.5502 Å2
2---12.9286 Å20 Å2
3---9.9429 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 2.995→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6426 0 74 58 6558
Biso mean--76.64 50.39 -
Num. residues----816
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2369SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1147HARMONIC5
X-RAY DIFFRACTIONt_it6614HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion859SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4760SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6614HARMONIC20.006
X-RAY DIFFRACTIONt_angle_deg8949HARMONIC60.4
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion20
LS refinement shellResolution: 3→3.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3027 21 5.04 %
Rwork0.2729 396 -
all0.2744 417 -
obs--73.4 %
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)
10.98481.0917-1.15481.4796-1.6683.78980.00530.11490.12160.14910.0190.0698-0.31090.05-0.0243-0.0891-0.01480.0006-0.0289-0.0205-0.152317.684127.155-48.067
21.09910.9064-0.8531.5475-1.0692.77290.0016-0.0856-0.1010.0667-0.1461-0.09130.19740.26390.1445-0.25630.1198-0.0018-0.03750.0265-0.16227.8403-2.8869-41.1784
35.46310.48931.25984.2775-0.9135.4278-0.05-0.2132-0.0190.00090.0393-0.00420.2615-0.13840.0106-0.1479-0.00320.0369-0.23120.0092-0.2361-16.4719-20.3186-1.5916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|319 - A|496 }A319 - 496
2X-RAY DIFFRACTION2{ B|23 - B|461 B|501 - B|503 }B23 - 461
3X-RAY DIFFRACTION2{ B|23 - B|461 B|501 - B|503 }B501 - 503
4X-RAY DIFFRACTION3{ C|13 - C|223 C|301 - C|302 }C13 - 223
5X-RAY DIFFRACTION3{ C|13 - C|223 C|301 - C|302 }C301 - 302

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