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- PDB-6i7g: Crystal structure of dimeric wild type FICD complexed with ATP -

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Basic information

Entry
Database: PDB / ID: 6i7g
TitleCrystal structure of dimeric wild type FICD complexed with ATP
ComponentsAdenosine monophosphate-protein transferase FICD
KeywordsTRANSFERASE / Fic / AMPylation / UPR / BiP
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / protein adenylylation / AMPylase activity / protein adenylyltransferase / regulation of IRE1-mediated unfolded protein response / negative regulation of GTPase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / response to unfolded protein / Hsp70 protein binding ...protein deadenylylation / protein adenylylhydrolase activity / protein adenylylation / AMPylase activity / protein adenylyltransferase / regulation of IRE1-mediated unfolded protein response / negative regulation of GTPase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / response to unfolded protein / Hsp70 protein binding / response to endoplasmic reticulum stress / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP binding / identical protein binding
Similarity search - Function
Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. ...Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine monophosphate-protein transferase FICD
B: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6908
Polymers78,8982
Non-polymers1,7916
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dimer by SEC-MALS, gel filtration, Dimer by GF
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-8 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.671, 107.652, 132.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 105 - 432 / Label seq-ID: 3 - 330

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#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: 39449.121 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.55 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5; 20% PEG 300; 5% PEG8K; 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→83.58 Å / Num. obs: 31293 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.104 / Rrim(I) all: 0.195 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4091 / CC1/2: 0.72 / Rpim(I) all: 0.456 / Rrim(I) all: 0.851 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u0u

4u0u


Resolution: 2.7→83.58 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.882 / SU B: 22.439 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.38 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31868 1497 4.8 %RANDOM
Rwork0.28291 ---
obs0.28458 29763 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.904 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å20 Å2
2--6.56 Å20 Å2
3----4.22 Å2
Refinement stepCycle: 1 / Resolution: 2.7→83.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5362 0 114 140 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135592
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175175
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.6557577
X-RAY DIFFRACTIONr_angle_other_deg1.0271.58111973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5985667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22721.639305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77515949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2251542
X-RAY DIFFRACTIONr_chiral_restr0.0340.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
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_it0.9616.0242674
X-RAY DIFFRACTIONr_mcbond_other0.9616.0232673
X-RAY DIFFRACTIONr_mcangle_it1.7459.0323339
X-RAY DIFFRACTIONr_mcangle_other1.7449.0333340
X-RAY DIFFRACTIONr_scbond_it0.6846.0072918
X-RAY DIFFRACTIONr_scbond_other0.6846.0072918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3078.9794239
X-RAY DIFFRACTIONr_long_range_B_refined5.05569.8756216
X-RAY DIFFRACTIONr_long_range_B_other5.02369.9786187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10475 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 114 -
Rwork0.438 2162 -
obs--99.91 %

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