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- PDB-8hl7: Crystal structure of p97 N/D1 in complex with a valosin-containin... -

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Basic information

Entry
Database: PDB / ID: 8hl7
TitleCrystal structure of p97 N/D1 in complex with a valosin-containing protein methyltransferase
Components
  • Protein N-lysine methyltransferase METTL21D
  • Transitional endoplasmic reticulum ATPase
KeywordsPROTEIN BINDING / VCPKMT / methyltransferase / trimethylated lysine / ASPL / ASPSCR1 / UBXD9 / TUG
Function / homology
Function and homology information


peptidyl-lysine methylation / peptidyl-lysine trimethylation / negative regulation of ATP-dependent activity / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-lysine N-methyltransferase activity / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control ...peptidyl-lysine methylation / peptidyl-lysine trimethylation / negative regulation of ATP-dependent activity / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-lysine N-methyltransferase activity / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / aggresome assembly / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein localization to chromatin / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / positive regulation of mitochondrial membrane potential / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / histone methyltransferase activity / ATPase complex / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / RHOH GTPase cycle / autophagosome maturation / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / viral genome replication / proteasome complex / lipid droplet / Transferases; Transferring one-carbon groups; Methyltransferases / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / site of double-strand break / cellular response to heat / ATPase binding / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / lipid binding / glutamatergic synapse / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane
Similarity search - Function
Lysine methyltransferase / Lysine methyltransferase / 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 ...Lysine methyltransferase / Lysine methyltransferase / 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 / 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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / FORMIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Transitional endoplasmic reticulum ATPase / Protein N-lysine methyltransferase METTL21D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKang, W. / Yang, J.K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A6A1A10044154 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1C1C1004221 Korea, Republic Of
CitationJournal: Iscience / Year: 2023
Title: Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase.
Authors: Nguyen, T.Q. / Koh, S. / Kwon, J. / Jang, S. / Kang, W. / Yang, J.K.
History
DepositionNov 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein N-lysine methyltransferase METTL21D
B: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,76911
Polymers72,2922
Non-polymers1,4779
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-12 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.780, 60.780, 473.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein N-lysine methyltransferase METTL21D / Methyltransferase-like protein 21D


Mass: 23500.980 Da / Num. of mol.: 1 / Mutation: I130V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21D / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H867, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 48791.023 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

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Non-polymers , 7 types, 19 molecules

#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 % (w/v) polyethylene glycol (PEG) 3350, 0.1M Na-HEPES (pH 7.5), 2 % (v/v) Tacsimate (pH 7.0), and 3 % (w/v) 6-aminohexanoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 26103 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 60.32 Å2 / CC1/2: 0.974 / Rpim(I) all: 0.058 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2787 / CC1/2: 0.89 / Rpim(I) all: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.57 Å / SU ML: 0.4305 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.0368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2609 1121 4.81 %
Rwork0.2172 22163 -
obs0.2194 23284 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 96 10 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944743
X-RAY DIFFRACTIONf_angle_d1.346448
X-RAY DIFFRACTIONf_chiral_restr0.066764
X-RAY DIFFRACTIONf_plane_restr0.0102824
X-RAY DIFFRACTIONf_dihedral_angle_d18.6011708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.39341180.31142721X-RAY DIFFRACTION100
2.93-3.080.36421010.28012758X-RAY DIFFRACTION100
3.08-3.270.34331520.25492659X-RAY DIFFRACTION99.96
3.27-3.530.28321500.24412715X-RAY DIFFRACTION99.97
3.53-3.880.25071330.20982756X-RAY DIFFRACTION100
3.88-4.440.23381410.18582761X-RAY DIFFRACTION99.97
4.44-5.590.22891460.18222843X-RAY DIFFRACTION100
5.59-29.570.24061800.2152950X-RAY DIFFRACTION97.93
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)
14.45754160865-1.11720529423-0.7815017621433.036998183672.380192056193.94892090873-0.175437059547-0.3557656003560.3167215746880.2635978357760.256734884115-0.0265098618510.107034491780.45254604287-0.08037850933270.8010893125620.06926898413990.1022858193690.306721779691-0.1495301196880.43930869678666.6983121959120.61036309954.3676860277
20.174682029105-1.19144394246-0.1549713795578.528280345852.439090782485.17904594067-0.537524874743-0.305973523051-0.2983497477520.9207022169430.2084168553061.265446406130.712481571743-0.5624670037370.3361634729830.914237889775-0.0563886640540.3359155631620.508443058798-0.07062216876220.62816870538356.1830057657116.10647136862.9502465765
33.53563956098-1.03722716692-1.377506093885.242493794311.169285257347.17593070659-0.2015982080130.687572142145-0.1678986508940.0389074030834-0.187198008441.125801185080.261344647908-1.911940343690.3514235233720.534361826952-0.02782175706250.07274543718660.667497755693-0.1888213338350.67779408045450.8423202751120.23368486346.5940950411
42.63230693916-1.00989081554-0.2882098445877.633976303612.06301772243.63307728772-0.03556897310720.628775653756-0.504774583418-0.6383187894050.0818793686210.5844149876490.0230201696977-0.1948903185380.002497866563820.736643821996-0.0890567694491-0.009480694991370.339218837362-0.1894436852260.5173833774981.423014058586.710455689219.6545999528
52.81592522776-0.5740135680831.038536082523.215557811930.9082037597373.621053488740.1341433047070.322578944145-0.05141245958650.3361487423610.0756984467536-0.6225236010760.09790549785120.582057441672-0.2390834626150.681146629832-0.1043303197610.007492470742070.347656458881-0.2063831079890.53846370386693.2308286888.889643580331.2556204825
60.402645216469-0.210210420165-0.05579455545271.785159012440.4069192430310.09276055593540.2777545532070.02538104758470.160213683329-0.519568282990.0599425578507-0.0563964097448-0.3461510083240.132725932109-0.061027165621.19980243007-0.09624475557590.1758196512020.415529567306-0.1913481790030.6725243221286.6181564687119.99762530125.3457038734
71.42907974965-0.501014611657-0.9663601178173.256241677821.747391674224.144840089270.107079081811-0.09322408216420.0744519495688-0.1874727863360.209881913077-0.2039256460970.003777145652850.675111161729-0.5570608730830.839686091104-0.09469512924360.09412574612440.368310814946-0.2305687951030.50765838165581.2909720825113.57081649428.4364976337
84.69584214806-0.352814237402-1.883733645125.971843498032.459776713926.530865045580.03661630679190.0937309685480.175608740658-0.152744769239-0.3350262820820.5841357629020.0816811222296-0.4478054339620.372962574070.728414880989-0.03050766778390.08980826883380.30760863772-0.1854498291840.38789846353470.2550338969115.14786533534.5112922987
92.17843555732-1.13101608273-1.711985149031.599319056061.900125891185.096573681260.6039716502310.849688574965-0.0211802476014-0.890738994861-0.5529358098050.048407961043-1.35361320445-0.174896578844-0.08816514354921.0390400694-0.03606258339630.08124153956370.703425216987-0.1882203186430.41656613043883.1946512301109.3586771882.06679963601
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 114 )AA15 - 1141 - 95
22chain 'A' and (resid 115 through 138 )AA115 - 13896 - 116
33chain 'A' and (resid 139 through 222 )AA139 - 222117 - 200
44chain 'B' and (resid 23 through 80 )BC23 - 801 - 58
55chain 'B' and (resid 81 through 176 )BC81 - 17659 - 154
66chain 'B' and (resid 177 through 239 )BC177 - 239155 - 207
77chain 'B' and (resid 240 through 309 )BC240 - 309208 - 277
88chain 'B' and (resid 310 through 358 )BC310 - 358278 - 326
99chain 'B' and (resid 359 through 458 )BC359 - 458327 - 416

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