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- PDB-6i7h: Crystal structure of dimeric FICD mutant K256S -

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Basic information

Entry
Database: PDB / ID: 6i7h
TitleCrystal structure of dimeric FICD mutant K256S
ComponentsAdenosine monophosphate-protein transferase FICD
KeywordsTRANSFERASE / Fic / AMPylation / UPR / BiP
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding / response to endoplasmic reticulum stress / protein-folding chaperone binding / endoplasmic reticulum membrane / protein homodimerization activity / ATP binding / identical protein binding
Similarity search - Function
Fido domain-containing protein / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPerera, L.A. / Yan, Y. / Read, R.J. / Ron, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K50127X/1 United Kingdom
Wellcome Trust200848/Z/16/Z United Kingdom
Wellcome Trust082961/Z/07/Z United Kingdom
Wellcome Trust100140 United Kingdom
CitationJournal: Embo J. / Year: 2019
Title: An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP.
Authors: Perera, L.A. / Rato, C. / Yan, Y. / Neidhardt, L. / McLaughlin, S.H. / Read, R.J. / Preissler, S. / Ron, D.
History
DepositionNov 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: 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: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4312
Polymers39,4071
Non-polymers241
Water3,783210
1
A: Adenosine monophosphate-protein transferase FICD
hetero molecules

A: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8634
Polymers78,8142
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area1840 Å2
ΔGint-22 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.815, 76.508, 131.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Adenosine monophosphate-protein transferase FICD / AMPylator FICD / De-AMPylase FICD / FIC domain-containing protein / Huntingtin yeast partner E / ...AMPylator FICD / De-AMPylase FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin-interacting protein 13 / HIP-13 / Huntingtin-interacting protein E


Mass: 39407.020 Da / Num. of mol.: 1 / Mutation: K256S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7 Express lysY/Iq
References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5; 0.05 M Magnesium Chloride; 40% Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.25→65.99 Å / Num. obs: 21825 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.079 / Rrim(I) all: 0.136 / Net I/σ(I): 6.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1978 / CC1/2: 0.547 / Rpim(I) all: 0.295 / Rrim(I) all: 0.488 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u0u

4u0u


Resolution: 2.25→65.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.142 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25863 1098 5 %RANDOM
Rwork0.20763 ---
obs0.21009 20678 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.468 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2---0.16 Å20 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 2.25→65.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 1 210 2851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132696
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172492
X-RAY DIFFRACTIONr_angle_refined_deg1.181.6463659
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5695759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9995330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96121.867150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7415462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.071520
X-RAY DIFFRACTIONr_chiral_restr0.0520.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
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_it1.8614.5621323
X-RAY DIFFRACTIONr_mcbond_other1.8614.561322
X-RAY DIFFRACTIONr_mcangle_it3.0686.8331652
X-RAY DIFFRACTIONr_mcangle_other3.0676.8371653
X-RAY DIFFRACTIONr_scbond_it2.0184.6641373
X-RAY DIFFRACTIONr_scbond_other2.0184.6671374
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4366.9112007
X-RAY DIFFRACTIONr_long_range_B_refined5.76154.2223175
X-RAY DIFFRACTIONr_long_range_B_other5.60353.9243100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 87 -
Rwork0.275 1506 -
obs--99.81 %

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