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- PDB-6i7l: Crystal structure of monomeric FICD mutant L258D complexed with M... -

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Basic information

Entry
Database: PDB / ID: 6i7l
TitleCrystal structure of monomeric FICD mutant L258D complexed with MgAMP-PNP
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 / 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 / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / 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. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat ...Fido domain-containing protein / Fido-like domain / Fic-like fold / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)39,9823
Polymers39,4511
Non-polymers5312
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric by gel filtration, equilibrium centrifugation, Monomeric by fluorescent detection system sedimentation velocity analytical ultracentrifugation (FDS-SV-AUC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-16 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.358, 186.358, 77.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

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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: 39451.051 Da / Num. of mol.: 1 / Mutation: L258D
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 4.95 Å3/Da / Density % sol: 75.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Sodium Chloride; 10% Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.31→93.18 Å / Num. obs: 34573 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.054 / Rrim(I) all: 0.089 / Net I/σ(I): 10.3
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3351 / CC1/2: 0.523 / Rpim(I) all: 0.465 / Rrim(I) all: 0.771 / % possible all: 99.1

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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: 2.32→93.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.373 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25095 1660 4.8 %RANDOM
Rwork0.21453 ---
obs0.21635 32586 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.459 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.36 Å20 Å2
2--0.71 Å20 Å2
3----2.31 Å2
Refinement stepCycle: 1 / Resolution: 2.32→93.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 32 184 2909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132819
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172611
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.6543820
X-RAY DIFFRACTIONr_angle_other_deg1.1241.5736045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.215339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36721.456158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051523
X-RAY DIFFRACTIONr_chiral_restr0.0460.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it2.1185.981350
X-RAY DIFFRACTIONr_mcbond_other2.1045.9771349
X-RAY DIFFRACTIONr_mcangle_it3.5288.9671691
X-RAY DIFFRACTIONr_mcangle_other3.5288.9721692
X-RAY DIFFRACTIONr_scbond_it2.4156.261469
X-RAY DIFFRACTIONr_scbond_other2.4156.2591467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1919.262130
X-RAY DIFFRACTIONr_long_range_B_refined6.78970.5313247
X-RAY DIFFRACTIONr_long_range_B_other6.70370.323177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 95 -
Rwork0.338 2388 -
obs--99.56 %

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