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- PDB-7b80: DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2) -

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Basic information

Entry
Database: PDB / ID: 7b80
TitleDeAMPylation complex of monomeric FICD and AMPylated BiP (state 2)
Components
  • Endoplasmic reticulum chaperone BiP
  • Protein adenylyltransferase FICD
KeywordsHYDROLASE / FICD / Fic / HYPE / BiP / Grp78 / AMPylation / deAMPylation / deAMPylase / ER stress / Complex / adenylation / adenylylation / Hsp70 / chaperone / transferase
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / negative regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / post-translational protein targeting to membrane, translocation / negative regulation of GTPase activity ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / negative regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / post-translational protein targeting to membrane, translocation / negative regulation of GTPase activity / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly / Hsp70 protein binding / response to endoplasmic reticulum stress / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / protein-folding chaperone binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
Fido domain-containing protein / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / Endoplasmic reticulum targeting sequence. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. ...Fido domain-containing protein / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / Endoplasmic reticulum targeting sequence. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Endoplasmic reticulum chaperone BiP / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsPerera, L.A. / Ron, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200848/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD.
Authors: Perera, L.A. / Preissler, S. / Zaccai, N.R. / Prevost, S. / Devos, J.M. / Haertlein, M. / Ron, D.
History
DepositionDec 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Endoplasmic reticulum chaperone BiP
A: Protein adenylyltransferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,40013
Polymers96,9272
Non-polymers1,47311
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-32 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.000, 103.890, 104.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Endoplasmic reticulum chaperone BiP / 78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock ...78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock protein 70 family protein 5 / HSP70 family protein 5 / Heat shock protein family A member 5 / Immunoglobulin heavy chain-binding protein


Mass: 57543.043 Da / Num. of mol.: 1 / Mutation: T229A, V461F
Source method: isolated from a genetically manipulated source
Details: Covalent modification of T518 with AMP moiety / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli M15 (bacteria)
References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase
#2: Protein Protein adenylyltransferase 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: 39383.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2.7.7.n1 / Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 7 types, 601 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8.0 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.87→52.4 Å / Num. obs: 86247 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.9
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.793 / Mean I/σ(I) obs: 1 / Num. unique obs: 6270 / CC1/2: 0.536 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4P, 6I7L

5o4p

6i7l


Resolution: 1.87→52.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.688 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 4190 4.9 %RANDOM
Rwork0.2008 ---
obs0.2021 81979 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.79 Å2 / Biso mean: 37.354 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-0 Å2
2---1.09 Å20 Å2
3---2.68 Å2
Refinement stepCycle: final / Resolution: 1.87→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 84 590 7440
Biso mean--50.61 42.72 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176855
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.6519636
X-RAY DIFFRACTIONr_angle_other_deg1.1511.58115826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73422.83371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.621151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6971546
X-RAY DIFFRACTIONr_chiral_restr0.0480.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
LS refinement shellResolution: 1.87→1.919 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 333 -
Rwork0.353 5931 -
all-6264 -
obs--99.97 %
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)
11.9322-0.53510.07250.9258-0.05070.5638-0.00230.04310.29940.0318-0.0210.0192-0.1281-0.050.02330.04940.0042-0.01030.00890.00720.0665-33.53911.524-8.303
21.55410.0186-0.50020.8013-0.0950.66630.00490.06690.006-0.08540.0194-0.10010.0580.0576-0.02430.02970.0133-0.01460.0347-0.020.04639.139-11.498-7.875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B27 - 549
2X-RAY DIFFRACTION1B601
3X-RAY DIFFRACTION2A103 - 442
4X-RAY DIFFRACTION2A501 - 504

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