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- PDB-7oas: Structural basis for targeted p97 remodeling by ASPL as prerequis... -

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Basic information

Entry
Database: PDB / ID: 7oas
TitleStructural basis for targeted p97 remodeling by ASPL as prerequisite for p97 trimethylation by METTL21D
ComponentsS-adenosyl-L-methionine-dependent methyltransferases superfamily protein
KeywordsTRANSFERASE / AtMETTL21D / lysine methylatransferase / Rossmann fold / AtCDC48
Function / homologyLysine methyltransferase / Lysine methyltransferase / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 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: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5873
Polymers25,1411
Non-polymers4462
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint3 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.295, 58.295, 142.851
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

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Components

#1: Protein S-adenosyl-L-methionine-dependent methyltransferases superfamily protein


Mass: 25140.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g08125 / Production host: Escherichia coli (E. coli) / References: UniProt: F4HUD6
#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20 %v/v EtOH 0.1 M Tris 8.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.819→41.303 Å / Num. obs: 22897 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 25.77 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.36
Reflection shellResolution: 1.82→1.93 Å / Num. unique obs: 3628 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LG1

4lg1


Resolution: 1.819→41.221 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1141 5 %
Rwork0.1973 21668 -
obs0.1994 22809 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.42 Å2 / Biso mean: 54.642 Å2 / Biso min: 27.13 Å2
Refinement stepCycle: final / Resolution: 1.819→41.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 30 171 1880
Biso mean--43.68 58.36 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071781
X-RAY DIFFRACTIONf_angle_d0.9182420
X-RAY DIFFRACTIONf_chiral_restr0.048277
X-RAY DIFFRACTIONf_plane_restr0.005304
X-RAY DIFFRACTIONf_dihedral_angle_d7.2621475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8192-1.9020.40291390.388261799
1.902-2.00220.34581400.3337266499
2.0022-2.12770.34331380.269263099
2.1277-2.29190.24061420.2259269099
2.2919-2.52260.27461420.2189267699
2.5226-2.88750.26951420.20482728100
2.8875-3.63760.24421460.1867275799
3.6376-41.2210.19431520.1618290699
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)
13.059-0.13183.15990.1919-0.69496.80260.5335-0.8618-0.1608-0.3439-0.09670.10751.5762-0.8726-0.36190.7458-0.07850.0160.526-0.01250.6159-9.0513.192822.4071
23.77420.91560.69413.16730.15694.60410.2117-0.4066-0.97190.31310.05660.08050.9842-0.0141-0.13740.6164-0.0130.01270.39890.08110.4039-6.182320.05331.0153
32.26770.3145-0.21051.5772-0.64522.9926-0.20350.146-0.3105-0.15710.0576-0.03960.47120.08820.12310.44590.03280.05690.3517-0.00020.3825-2.20323.343318.8418
42.27960.0936-0.63331.7525-0.70963.2464-0.1138-0.00950.0107-0.0187-0.0148-0.11410.0190.40190.11450.3224-0.0009-0.01990.33320.03210.32731.340632.358626.2638
51.2061-0.45111.02611.7841-1.23844.7707-0.2465-0.21460.47590.05710.1947-0.0298-0.9186-0.50720.05330.43510.0638-0.04070.3343-0.01030.4269-8.380441.3335.7603
62.75950.64460.19332.81160.31292.43040.09740.2814-0.7758-1.5771-0.56221.17270.6299-1.18410.37341.03510.2171-0.0160.7501-0.01440.8176-20.010426.497329.2889
74.912.1599-1.20766.1753-2.14175.2150.1552-0.24040.49820.20330.0250.4374-0.6311-0.3363-0.27990.310.10390.00930.3862-0.02510.4219-9.52439.311728.423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 18 )A4 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 43 )A19 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 107 )A44 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 176 )A108 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 196 )A177 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 209 )A197 - 209
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 219 )A210 - 219

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