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- PDB-6dfm: Crystal structure of human GRP78 in complex with 8-aminoadenosine -

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Basic information

Entry
Database: PDB / ID: 6dfm
TitleCrystal structure of human GRP78 in complex with 8-aminoadenosine
ComponentsEndoplasmic reticulum chaperone BiP
KeywordsCHAPERONE / Endoplasmic reticulum / Unfolded protein response / Nucleoside analog
Function / homology
Function and homology information


regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / maintenance of protein localization in endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / cerebellar Purkinje cell layer development ...regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / maintenance of protein localization in endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / PERK regulates gene expression / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / ERAD pathway / ER overload response / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / endoplasmic reticulum-Golgi intermediate compartment / Regulation of HSF1-mediated heat shock response / cellular response to glucose starvation / negative regulation of protein-containing complex assembly / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / substantia nigra development / cellular response to interleukin-4 / response to endoplasmic reticulum stress / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / melanosome / unfolded protein binding / ribosome binding / Platelet degranulation / midbody / protein-folding chaperone binding / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / focal adhesion / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / 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 / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3BH / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsFerrie, R.P. / Chen, Y. / Antoshchenko, T. / Cooney, O.M. / Huang, Y. / Park, H.W.
CitationJournal: To be Published
Title: Crystal structure of human GRP78 in complex with 8-aminoadenosine
Authors: Ferrie, R.P. / Chen, Y. / Antoshchenko, T. / Cooney, O.M. / Huang, Y. / Park, H.W.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum chaperone BiP
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8764
Polymers84,3112
Non-polymers5652
Water7,927440
1
A: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4382
Polymers42,1561
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4382
Polymers42,1561
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.662, 74.775, 89.485
Angle α, β, γ (deg.)90.000, 99.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 42155.715 Da / Num. of mol.: 2 / Fragment: UNP residues 26-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli)
References: UniProt: P11021, non-chaperonin molecular chaperone ATPase
#2: Chemical ChemComp-3BH / (2R,3R,4S,5R)-2-(6,8-diaminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol / 8-aminoadenosine


Mass: 282.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N6O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.18 Å3/Da / Density % sol: 43.54 % / Description: Plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Triclinic crystals of apo GRP78 were observed in 0.1 M Tris-HCl, 25% PEG3350, 0.1 M sodium/potassium tartrate. Initial crystals were then microseeded in 25% PEG3350, 0.1 M Tris-HCl, 0.2 M ...Details: Triclinic crystals of apo GRP78 were observed in 0.1 M Tris-HCl, 25% PEG3350, 0.1 M sodium/potassium tartrate. Initial crystals were then microseeded in 25% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride. These new apo monoclinic crystals were soaked with 5 mM 8-aminoadenosine for one week.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03327 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03327 Å / Relative weight: 1
ReflectionResolution: 2.14→88.263 Å / Num. obs: 39667 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.08 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Rsym value: 0.1 / Net I/av σ(I): 6.6 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.14-2.266.50.6391.255500.2680.6940.63995.4
2.26-2.470.4681.654690.1910.5050.468100
2.4-2.566.70.3312.351900.1380.3590.33199.9
2.56-2.776.80.2133.547960.0880.2310.21399.9
2.77-3.0370.145.344170.0570.1510.1499.9
3.03-3.396.70.0917.940190.0380.0990.09199.9
3.39-3.916.80.06710.535580.0280.0730.06799.9
3.91-4.796.70.05512.329910.0230.0590.05599.8
4.79-6.776.70.05611.923690.0240.0610.056100
6.77-44.2546.30.04213.713080.0180.0460.04299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.757
Highest resolutionLowest resolution
Rotation44.26 Å4 Å

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Processing

Software
NameVersionClassification
XDSINTEL64_Linux_x86_64data reduction
SCALA3.3.21data scaling
MOLREPphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→31.17 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.275 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1922 4.85 %RANDOM
Rwork0.187 ---
obs0.189 39640 98.9 %-
Displacement parametersBiso max: 130.18 Å2 / Biso mean: 40.5 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1--15.2358 Å20 Å24.9818 Å2
2--4.6603 Å20 Å2
3---10.5755 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.14→31.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 40 440 6410
Biso mean--40.74 40.55 -
Num. residues----764
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2180SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes178HARMONIC2
X-RAY DIFFRACTIONt_gen_planes866HARMONIC5
X-RAY DIFFRACTIONt_it6064HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion808SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7561SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6064HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8186HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion17.9
LS refinement shellResolution: 2.14→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 140 5.47 %
Rwork0.23 2421 -
all0.232 2561 -
obs--86.97 %

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