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- PDB-6eof: Crystal structure of AMPylated GRP78 in ADP state -

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Basic information

Entry
Database: PDB / ID: 6eof
TitleCrystal structure of AMPylated GRP78 in ADP state
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / GRP78 / BIP / AMPylation / ADP
Function / homology
Function and homology information


negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process ...negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsYan, Y. / Preissler, S. / Read, R.J. / Ron, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust082961/Z/07/Z United Kingdom
Wellcome Trust200848/Z/16/Z United Kingdom
British Heart FoundationPG/12/41/29679 United Kingdom
CitationJournal: Elife / Year: 2017
Title: AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation.
Authors: Preissler, S. / Rohland, L. / Yan, Y. / Chen, R. / Read, R.J. / Ron, D.
History
DepositionOct 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2784
Polymers57,4081
Non-polymers8703
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein sample was shown as monomeric by gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-29 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.047, 75.610, 97.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 78 kDa glucose-regulated protein


Mass: 57407.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: I79_019946 / Production host: Escherichia coli (E. coli) / References: UniProt: G3I8R9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 9% PEG1000, 0.1M Na2HPO4-Citrate, ph4.4, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.59→97.5 Å / Num. obs: 69830 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.145 / Net I/σ(I): 8.8
Reflection shellResolution: 1.59→1.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3451 / CC1/2: 0.836 / Rrim(I) all: 0.988 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4P

5o4p


Resolution: 1.59→59.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.993 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22479 3383 4.8 %RANDOM
Rwork0.20625 ---
obs0.20717 66447 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.094 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å2-0 Å2
2---0.38 Å20 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 1.59→59.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 36 172 4150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194047
X-RAY DIFFRACTIONr_bond_other_d0.0010.023802
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.985491
X-RAY DIFFRACTIONr_angle_other_deg0.88938823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13825.294170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05215695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5881521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
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_it0.6792.0932084
X-RAY DIFFRACTIONr_mcbond_other0.6792.0922083
X-RAY DIFFRACTIONr_mcangle_it1.1573.1382605
X-RAY DIFFRACTIONr_mcangle_other1.1573.1382606
X-RAY DIFFRACTIONr_scbond_it0.9542.2421963
X-RAY DIFFRACTIONr_scbond_other0.9492.2381957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4683.2982878
X-RAY DIFFRACTIONr_long_range_B_refined2.78924.8984173
X-RAY DIFFRACTIONr_long_range_B_other2.76724.7644151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.586→1.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 247 -
Rwork0.261 4876 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: -33.9188 Å / Origin y: -1.1719 Å / Origin z: -11.453 Å
111213212223313233
T0.0068 Å2-0.0013 Å20.0026 Å2-0.0052 Å2-0.0028 Å2--0.0076 Å2
L1.0404 °2-0.2469 °2-0.2255 °2-0.9984 °2-0.0405 °2--0.9318 °2
S0.0116 Å °0.0127 Å °0.0664 Å °0.0131 Å °-0.0203 Å °-0.0269 Å °-0.0512 Å °-0.0411 Å °0.0087 Å °

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