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- PDB-5kiu: VCP-interacting membrane protein (VIMP) -

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Basic information

Entry
Database: PDB / ID: 5kiu
TitleVCP-interacting membrane protein (VIMP)
ComponentsSelenoprotein S
KeywordsMEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP
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 / low-density lipoprotein particle / very-low-density lipoprotein particle / negative regulation of glucose import / Derlin-1 retrotranslocation complex ...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 / low-density lipoprotein particle / very-low-density lipoprotein particle / negative regulation of glucose import / Derlin-1 retrotranslocation complex / response to redox state / retrograde protein transport, ER to cytosol / regulation of gluconeogenesis / ER overload response / ubiquitin-specific protease binding / : / cytoplasmic microtubule / antioxidant activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / response to glucose / endoplasmic reticulum unfolded protein response / cell redox homeostasis / establishment of protein localization / negative regulation of inflammatory response / cellular response to insulin stimulus / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / cellular response to oxidative stress / ATPase binding / cellular response to lipopolysaccharide / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / Selenoprotein S / Selenoprotein S (SelS) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Selenoprotein S


Theoretical massNumber of molelcules
Total (without water)9,7291
Polymers9,7291
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.729, 17.973, 33.993
Angle α, β, γ (deg.)90.00, 95.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Selenoprotein S / SelS / VCP-interacting membrane protein


Mass: 9729.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIMP, SELS, AD-015, SBBI8 / Production host: Bacteria (eubacteria) / References: UniProt: Q9BQE4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES, pH 6.0, 20 % 2-propanol, 20 % PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→60.58 Å / Num. obs: 3854 / % possible obs: 92 % / Redundancy: 3 % / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2F

2q2f


Resolution: 2.2→60.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 17.438 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24434 173 4.5 %RANDOM
Rwork0.18576 ---
obs0.1885 3681 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.188 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å23.07 Å2
2---1.55 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms631 0 0 17 648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019636
X-RAY DIFFRACTIONr_bond_other_d0.0020.02664
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.964845
X-RAY DIFFRACTIONr_angle_other_deg1.05931520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19323.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53215143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.862159
X-RAY DIFFRACTIONr_chiral_restr0.1270.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02705
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02146
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_it2.1143.388303
X-RAY DIFFRACTIONr_mcbond_other2.0363.367302
X-RAY DIFFRACTIONr_mcangle_it3.2215.041377
X-RAY DIFFRACTIONr_mcangle_other3.2215.064378
X-RAY DIFFRACTIONr_scbond_it3.7764.301333
X-RAY DIFFRACTIONr_scbond_other3.7714.317334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2456.178469
X-RAY DIFFRACTIONr_long_range_B_refined7.99126.768720
X-RAY DIFFRACTIONr_long_range_B_other8.09226.745716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 15 -
Rwork0.262 251 -
obs--87.5 %
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)
12.99023.0446-2.16577.4322-2.60323.02930.01460.1908-0.011-0.1688-0.0491-0.3506-0.0588-0.02230.03450.07920.019-0.03060.03850.02150.085833.616214.615147.3202
22.60932.2754-3.71244.174-1.91996.0995-0.1659-0.1096-0.0625-0.14190.00480.08310.2510.26490.16110.1056-0.0024-0.02340.1240.00860.028227.0728-3.333760.5088
312.0930.8513-8.59555.08054.300110.91140.36540.28030.2757-0.2836-0.1237-0.0299-0.5695-0.3806-0.24170.10770.0748-0.01630.12070.02680.038816.0729-7.580772.1795
411.65992.4606-6.13033.0199-3.4785.61240.03860.1453-0.26160.006-0.0616-0.0645-0.1827-0.15030.02310.05820.04290.04830.119-0.00620.0663.8399-9.646681.4468
513.67091.4516-9.15890.4553-0.02459.12330.0905-0.3777-0.08160.0029-0.0556-0.0364-0.08130.1866-0.03490.0013-0.00360.00130.09970.01660.0085-8.6474-11.892890.1334
616.26622.3443-2.751.8885-3.80817.9731-0.1735-0.1985-0.44470.0807-0.0425-0.131-0.20280.05560.2160.0174-0.01450.00630.07660.03360.054-22.9618-15.145999.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 62
2X-RAY DIFFRACTION2A63 - 77
3X-RAY DIFFRACTION3A78 - 88
4X-RAY DIFFRACTION4A89 - 98
5X-RAY DIFFRACTION5A99 - 109
6X-RAY DIFFRACTION6A110 - 121

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