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- PDB-8ujl: Crystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex -

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Basic information

Entry
Database: PDB / ID: 8ujl
TitleCrystal structure of human CTDNEP1-NEP1R1 protein phosphatase complex
ComponentsCTD nuclear envelope phosphatase 1,Nuclear envelope phosphatase-regulatory subunit 1
KeywordsHYDROLASE / phosphatase / nuclear envelope
Function / homology
Function and homology information


Nem1-Spo7 phosphatase complex / Depolymerization of the Nuclear Lamina / nuclear envelope organization / positive regulation of triglyceride biosynthetic process / mitotic nuclear membrane disassembly / gamete generation / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / mesoderm development / phosphoprotein phosphatase activity ...Nem1-Spo7 phosphatase complex / Depolymerization of the Nuclear Lamina / nuclear envelope organization / positive regulation of triglyceride biosynthetic process / mitotic nuclear membrane disassembly / gamete generation / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / mesoderm development / phosphoprotein phosphatase activity / protein localization to nucleus / canonical Wnt signaling pathway / protein dephosphorylation / lipid droplet / lipid metabolic process / nuclear envelope / positive regulation of canonical Wnt signaling pathway / nuclear membrane / endoplasmic reticulum membrane / cytoplasm / cytosol
Similarity search - Function
Nuclear envelope phosphatase-regulatory subunit 1 / Transmembrane protein 188 / Dullard phosphatase domain, eukaryotic / : / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Nuclear envelope phosphatase-regulatory subunit 1 / CTD nuclear envelope phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsGao, S. / Airola, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology.
Authors: Gao, S. / Carrasquillo Rodriguez, J.W. / Bahmanyar, S. / Airola, M.V.
History
DepositionOct 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: 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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTD nuclear envelope phosphatase 1,Nuclear envelope phosphatase-regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)31,6971
Polymers31,6971
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.151, 98.849, 103.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein CTD nuclear envelope phosphatase 1,Nuclear envelope phosphatase-regulatory subunit 1 / Transmembrane protein 188


Mass: 31697.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope phosphatase-regulatory subunit 1,Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope ...Details: Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope phosphatase-regulatory subunit 1,Fusion of human CTD nuclear envelope phosphatase 1 and human nuclear envelope phosphatase-regulatory subunit 1
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDNEP1, CNEP1R1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95476, UniProt: H3BUT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 6% PEG 3350, 0.2 M lithium citrate, 0.4% CHAPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2023 / Details: KB bimorph mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.908→29.08 Å / Num. obs: 23447 / % possible obs: 99.74 % / Redundancy: 2 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05073 / Rpim(I) all: 0.05073 / Rrim(I) all: 0.07175 / Net I/σ(I): 7.92
Reflection shellResolution: 1.908→1.976 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7953 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 2260 / CC1/2: 0.412 / CC star: 0.764 / Rpim(I) all: 0.7953 / Rrim(I) all: 1.125 / % possible all: 98.01

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→29.08 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2119 1109 4.73 %
Rwork0.1908 22337 -
obs0.1917 23446 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.79 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 0 179 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051789
X-RAY DIFFRACTIONf_angle_d0.56262426
X-RAY DIFFRACTIONf_chiral_restr0.0426278
X-RAY DIFFRACTIONf_plane_restr0.0045309
X-RAY DIFFRACTIONf_dihedral_angle_d4.6068239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.990.33211590.31172674X-RAY DIFFRACTION98.3
1.99-2.10.27851390.26492757X-RAY DIFFRACTION100
2.1-2.230.2751280.22872791X-RAY DIFFRACTION100
2.23-2.40.20721290.19362768X-RAY DIFFRACTION99.97
2.4-2.650.20361700.17492759X-RAY DIFFRACTION100
2.65-3.030.22041480.17812792X-RAY DIFFRACTION100
3.03-3.810.18211330.16742826X-RAY DIFFRACTION99.97
3.81-29.080.18871030.18422970X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -30.1150173489 Å / Origin y: -13.3384256528 Å / Origin z: -5.92299529952 Å
111213212223313233
T0.212243473525 Å2-0.00213260303297 Å2-0.0252226983073 Å2-0.149489525272 Å20.000257323762686 Å2--0.194064106352 Å2
L1.7632513504 °20.238262496034 °2-0.216219019194 °2-1.42232752022 °2-0.0347933644403 °2--2.22838713734 °2
S-0.0532772357126 Å °0.0366301830906 Å °0.0468373654582 Å °0.0697633086256 Å °0.00654316978426 Å °0.022787905089 Å °0.0429794950276 Å °-0.0517221812048 Å °0.0354788949305 Å °
Refinement TLS groupSelection details: all

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