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- PDB-6cz1: Crystal structure of ATPase domain of Human GRP78 bound to Ver155008 -

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Basic information

Entry
Database: PDB / ID: 6cz1
TitleCrystal structure of ATPase domain of Human GRP78 bound to Ver155008
ComponentsEndoplasmic reticulum chaperone BiP
KeywordsCHAPERONE / GRP78 / ATPase domain / Ver155008
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 / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / 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 / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / 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 / 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 interleukin-4 / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / ERAD pathway / protein folding chaperone / endoplasmic reticulum unfolded protein response / heat shock protein binding / substantia nigra development / 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 / unfolded protein binding / melanosome / Platelet degranulation / ribosome binding / midbody / protein-folding chaperone binding / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / 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 / cytoplasm / cytosol
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-3FD / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsAntoshchenko, T. / Chen, Y. / Hughes, S. / Park, H.
CitationJournal: To be Published
Title: Crystallographic selection of adenosine analogs that fit the mold of the active site of human GRP78 and beyond
Authors: Antoshchenko, T. / Chen, Y. / Park, H.
History
DepositionApr 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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: Endoplasmic reticulum chaperone BiP
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4736
Polymers84,3112
Non-polymers1,1614
Water8,593477
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A: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7363
Polymers42,1561
Non-polymers5812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7363
Polymers42,1561
Non-polymers5812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.280, 74.920, 86.200
Angle α, β, γ (deg.)90.000, 98.520, 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P11021, non-chaperonin molecular chaperone ATPase
#2: Chemical ChemComp-3FD / 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile


Mass: 556.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23Cl2N7O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24-26% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 31, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.68→85.263 Å / Num. obs: 79224 / % possible obs: 99.5 % / Redundancy: 5 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.073 / Rsym value: 0.065 / Net I/av σ(I): 9.9 / Net I/σ(I): 17.5
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 5822 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALA3.3.21data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EVZ

5evz


Resolution: 1.68→24.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3972 5.01 %RANDOM
Rwork0.187 ---
obs0.189 79224 100 %-
Displacement parametersBiso max: 113.66 Å2 / Biso mean: 27.27 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.0727 Å20 Å21.5484 Å2
2--1.2809 Å20 Å2
3----1.3536 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.68→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 78 477 6467
Biso mean--21.76 31.16 -
Num. residues----762
LS refinement shellResolution: 1.68→1.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 282 4.84 %
Rwork0.216 5540 -
all0.216 5822 -
obs--100 %
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)
10.42220.20590.01990.62580.08650.50890.00180.0104-0.015-0.01530.0335-0.0114-0.00440.0518-0.0353-0.0415-0.0049-0.0027-0.0323-0.0156-0.01191.07210.636539.2469
20.58120.0551-0.0350.56290.46492.11350.0520.0515-0.00090.04890.02090.0042-0.1283-0.2456-0.0729-0.04760.01110.0099-0.0310.0162-0.0787-18.75658.5273-4.1941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A26 - 407
2X-RAY DIFFRACTION2{ B|* }B27 - 407

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