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- PDB-5kiw: p97 ND1-L198W in complex with VIMP -

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Basic information

Entry
Database: PDB / ID: 5kiw
Titlep97 ND1-L198W in complex with VIMP
Components
  • Selenoprotein S
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE/MEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP / p97 / 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 / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation ...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 / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / negative regulation of glucose import / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / low-density lipoprotein particle / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / response to redox state / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / regulation of gluconeogenesis / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ER overload response / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / cytoplasmic microtubule / antioxidant activity / negative regulation of interleukin-6 production / RHOH GTPase cycle / negative regulation of tumor necrosis factor production / autophagosome maturation / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / response to glucose / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / lipid droplet / viral genome replication / proteasome complex / Josephin domain DUBs / cell redox homeostasis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / negative regulation of inflammatory response / cytoplasmic stress granule / Aggrephagy / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / cellular response to insulin stimulus / 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 / signaling receptor activity / site of double-strand break / cellular response to heat / cellular response to oxidative stress / ATPase binding
Similarity search - Function
Selenoprotein S / Selenoprotein S (SelS) / 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 ...Selenoprotein S / Selenoprotein S (SelS) / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
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: 3.41 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 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Transitional endoplasmic reticulum ATPase
C: Selenoprotein S
D: Selenoprotein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,2978
Polymers124,2364
Non-polymers1,0614
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.772, 153.772, 240.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15C
25D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A12 - 120
2111B12 - 120
1121A134 - 190
2121B134 - 190
1131A205 - 371
2131B205 - 371
1141A372 - 460
2141B372 - 460
1151C76 - 108
2151D76 - 108

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.431972, 0.901724, 0.017163), (0.84104, 0.409626, -0.353353), (-0.325657, -0.138204, -0.935333)-4.9996, 17.32784, 138.54843
3given(1), (1), (1)
4given(-0.424497, 0.905125, 0.023483), (0.845487, 0.40554, -0.347403), (-0.323966, -0.127617, -0.937422)-5.61974, 17.19986, 138.03265
5given(1), (1), (1)
6given(-0.537787, 0.843067, -0.004736), (0.842982, 0.53763, -0.018321), (-0.0129, -0.013845, -0.999821)0.26192, 0.72825, 127.96423
7given(1), (1), (1)
8given(-0.551825, 0.833942, -0.005437), (0.833672, 0.551452, -0.02984), (-0.021887, -0.020999, -0.99954)0.96382, 1.08793, 128.41875
9given(1), (1), (1)
10given(-0.464213, 0.885035, 0.034928), (0.821474, 0.44495, -0.356652), (-0.33119, -0.13687, -0.933584)-2.61542, 16.50478, 138.62082

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Components

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


Mass: 52388.875 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-460 / Mutation: L198W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein Selenoprotein S / SelS / VCP-interacting membrane protein


Mass: 9729.287 Da / Num. of mol.: 2 / Fragment: residues 49-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIMP, SELS, AD-015, SBBI8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BQE4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, pH 8, 15 % ethanol, 100 mM NaCl, 7 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.41→50 Å / Num. obs: 22714 / % possible obs: 95.9 % / Redundancy: 4 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KO8

4ko8


Resolution: 3.41→49.268 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.852 / SU B: 70.624 / SU ML: 0.489 / Cross valid method: THROUGHOUT / ESU R Free: 0.616 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29394 1135 4.9 %RANDOM
Rwork0.23328 ---
obs0.2362 21880 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 134.956 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0.61 Å20 Å2
2---1.22 Å20 Å2
3---3.95 Å2
Refinement stepCycle: 1 / Resolution: 3.41→49.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7780 0 64 1 7845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197962
X-RAY DIFFRACTIONr_bond_other_d0.0040.027883
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.98910754
X-RAY DIFFRACTIONr_angle_other_deg1.214318139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9035982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15424.18378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22151486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1551575
X-RAY DIFFRACTIONr_chiral_restr0.1020.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218900
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021713
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_it6.10110.0263943
X-RAY DIFFRACTIONr_mcbond_other6.10110.0253942
X-RAY DIFFRACTIONr_mcangle_it10.18515.0244920
X-RAY DIFFRACTIONr_mcangle_other10.18515.0254921
X-RAY DIFFRACTIONr_scbond_it6.46110.9684019
X-RAY DIFFRACTIONr_scbond_other6.4610.9694020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.26816.1085835
X-RAY DIFFRACTIONr_long_range_B_refined17.09377.9349097
X-RAY DIFFRACTIONr_long_range_B_other17.09277.9419098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A162210.27
22A91623.08
33A263213.45
44A134115.93
55C56416.16
LS refinement shellResolution: 3.407→3.496 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 68 -
Rwork0.477 1278 -
obs--78.39 %
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)
11.50880.14711.47020.285-0.413.10640.038-0.02620.1067-0.12360.05490.1094-0.05940.0644-0.09290.553-0.1796-0.05860.31980.00490.045623.517761.0577100.9538
21.11520.02770.59851.3709-0.33830.5151-0.3451-0.15820.0202-0.53230.1325-0.3082-0.27020.02430.21260.7609-0.294-0.12320.22970.12360.192836.762448.913320.2971
30.6724-0.2115-0.95561.3201-0.06411.6096-0.02410.0817-0.18440.0824-0.1985-0.0096-0.211-0.05260.22260.42450.0213-0.10220.3113-0.12220.2592-0.136731.035890.6492
40.92060.28220.3320.30150.4520.9075-0.1693-0.0519-0.1802-0.0362-0.00560.1627-0.14490.20250.17490.2629-0.06720.04410.33910.03970.415526.265416.490936.8436
52.7484-1.08872.25311.7988-0.64962.48150.224-0.0635-0.218-0.2442-0.2079-0.1264-0.33070.1733-0.01620.4732-0.236-0.09370.34530.09240.222132.801137.122878.7828
62.0997-0.51551.33231.6451-0.92861.2727-0.2548-0.1650.14760.01310.138-0.06-0.14440.00120.11690.5243-0.0715-0.10940.2043-0.00460.251713.593347.473148.5113
70.24950.53240.07331.21120.19950.0881-0.069-0.01960.1849-0.05110.00050.31740.08920.06450.06860.5215-0.1431-0.06320.3013-0.00690.295229.863775.995795.0656
81.22972.7590.505210.96714.17352.1534-0.19390.15760.3374-0.31160.37820.3295-0.04070.0667-0.18430.21370.0908-0.09090.36320.05920.427641.573519.517-17.3705
91.2095-0.47760.56130.1975-0.22780.2702-0.0948-0.03560.21380.0206-0.0302-0.14060.022-0.03330.1250.4787-0.27940.11320.26590.09870.403648.72960.205319.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 190
2X-RAY DIFFRACTION2B24 - 190
3X-RAY DIFFRACTION3A203 - 370
4X-RAY DIFFRACTION4B203 - 370
5X-RAY DIFFRACTION5A371 - 460
6X-RAY DIFFRACTION6B371 - 460
7X-RAY DIFFRACTION7C73 - 110
8X-RAY DIFFRACTION8D43 - 65
9X-RAY DIFFRACTION9D71 - 109

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