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- PDB-5kiy: p97 ND1-A232E in complex with VIMP -

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Basic information

Entry
Database: PDB / ID: 5kiy
Titlep97 ND1-A232E in complex with VIMP
Components
  • Selenoprotein S
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE/MEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP / HYDROLASE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / low-density lipoprotein particle / very-low-density lipoprotein particle / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process ...regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / low-density lipoprotein particle / very-low-density lipoprotein particle / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / 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 / negative regulation of glucose import / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / NADH metabolic process / vesicle-fusing ATPase / cellular response to misfolded protein / : / ERAD pathway / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / response to redox state / regulation of aerobic respiration / regulation of gluconeogenesis / ATPase complex / regulation of synapse organization / antioxidant activity / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / ER overload response / ubiquitin-like protein ligase binding / autophagosome maturation / negative regulation of interleukin-6 production / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / negative regulation of tumor necrosis factor production / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / cytoplasmic microtubule / interstrand cross-link repair / negative regulation of smoothened signaling pathway / response to glucose / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Attachment and Entry / ATP metabolic process / : / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / cell redox homeostasis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteasomal protein catabolic process / ADP binding / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / negative regulation of inflammatory response / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to insulin stimulus / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / 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 / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / site of double-strand break / cellular response to oxidative stress / cellular response to heat
Similarity search - Function
Selenoprotein S / Selenoprotein S (SelS) / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain ...Selenoprotein S / Selenoprotein S (SelS) / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / 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. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase / Selenoprotein S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsTang, W.K. / Xia, D.
CitationJournal: Cell Discov / Year: 2017
Title: Structural basis for nucleotide-modulated p97 association with the ER membrane.
Authors: Tang, W.K. / Zhang, T. / Ye, Y. / Xia, D.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Selenoprotein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6344
Polymers62,1032
Non-polymers5312
Water37821
1
A: Transitional endoplasmic reticulum ATPase
B: Selenoprotein S
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)375,80224
Polymers372,61912
Non-polymers3,18312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area37980 Å2
ΔGint-203 kcal/mol
Surface area130530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.998, 144.998, 119.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 52373.859 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-460 / Mutation: A232E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Bacteria (eubacteria) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein Selenoprotein S / SelS / VCP-interacting membrane protein


Mass: 9729.287 Da / Num. of mol.: 1 / Fragment: residues 49-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SELENOS, SELS, VIMP, AD-015, SBBI8 / Production host: Bacteria (eubacteria) / References: UniProt: Q9BQE4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH 8, 6-7 % ethanol, 100 mM NaCl, 3.6-4.2 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 18688 / % possible obs: 98.3 % / Redundancy: 4 % / Net I/σ(I): 22.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KO8

4ko8


Resolution: 2.79→125.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 39.044 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R: 0.735 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25649 933 5 %RANDOM
Rwork0.1928 ---
obs0.19609 17735 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.393 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å20 Å2
2--1.44 Å20 Å2
3----4.68 Å2
Refinement stepCycle: 1 / Resolution: 2.79→125.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 32 21 3887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193921
X-RAY DIFFRACTIONr_bond_other_d0.0030.023791
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9925291
X-RAY DIFFRACTIONr_angle_other_deg1.1238798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6055485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92424.378185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.03615740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1111536
X-RAY DIFFRACTIONr_chiral_restr0.090.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02737
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it6.3989.8511946
X-RAY DIFFRACTIONr_mcbond_other6.3489.8491945
X-RAY DIFFRACTIONr_mcangle_it9.67214.7742429
X-RAY DIFFRACTIONr_mcangle_other9.67714.7792430
X-RAY DIFFRACTIONr_scbond_it6.52110.4621974
X-RAY DIFFRACTIONr_scbond_other6.5210.4561972
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.32315.4392861
X-RAY DIFFRACTIONr_long_range_B_refined16.11215870
X-RAY DIFFRACTIONr_long_range_B_other16.11215870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.793→2.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 53 -
Rwork0.432 1069 -
obs--82.44 %
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)
11.8413-0.07132.18131.6895-0.694.7197-0.17150.31640.5491-0.1093-0.15950.2256-0.3952-0.01020.33090.5378-0.0664-0.08440.26610.09390.512418.731361.111435.4165
22.832-0.07131.48795.68091.59845.56660.0081-0.20740.23770.4608-0.24130.0489-0.0325-0.11230.23330.3398-0.1374-0.0330.0748-0.01390.047526.464754.981149.7477
34.0204-0.4164-1.12741.9074-0.41552.3876-0.0126-0.1313-0.17330.1059-0.11660.3626-0.251-0.23630.12930.06890.0268-0.02640.0632-0.04550.10540.225931.025127.029
43.9432-0.4358-0.67612.08170.48442.39750.21660.36290.3499-0.0176-0.231-0.7259-0.24640.43550.01440.222-0.1028-0.00740.2080.14980.284533.224436.081315.1384
55.3198-0.0196-6.32941.88090.023210.25390.0658-0.16340.42780.13590.19270.0481-0.24480.3911-0.25850.2862-0.0706-0.11320.06640.00290.230227.896573.822738.4265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 124
2X-RAY DIFFRACTION2A125 - 190
3X-RAY DIFFRACTION3A203 - 371
4X-RAY DIFFRACTION4A372 - 460
5X-RAY DIFFRACTION5B76 - 108

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