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- PDB-5ey4: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -

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Basic information

Entry
Database: PDB / ID: 5ey4
TitleCrystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 2'-deoxy-ATP
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / ATPase domain / nucleotide-binding / endoplasmic reticulum
Function / homology
Function and homology information


regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / negative regulation of IRE1-mediated unfolded protein response / PERK regulates gene expression / cerebellar Purkinje cell layer development / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / protein serine/threonine kinase inhibitor activity / Modulation of host responses by IFN-stimulated genes / ER overload response / IRE1-mediated unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of PERK-mediated unfolded protein response / non-chaperonin molecular chaperone ATPase / : / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / ERAD pathway / heat shock protein binding / substantia nigra development / protein folding chaperone / 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 / negative regulation of transforming growth factor beta receptor signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome / Platelet degranulation / protein-folding chaperone binding / ribosome binding / protein refolding / midbody / 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 / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular exosome / ATP binding / nucleus / membrane / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsHughes, S.J. / Antoshchenko, T. / Song, J.H. / Pizarro, J. / Park, H.W.
CitationJournal: Plos One / Year: 2016
Title: Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs.
Authors: Hughes, S.J. / Antoshchenko, T. / Chen, Y. / Lu, H. / Pizarro, J.C. / Park, H.W.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,6954
Polymers88,7122
Non-polymers9822
Water9,188510
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8472
Polymers44,3561
Non-polymers4911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8472
Polymers44,3561
Non-polymers4911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.456, 74.781, 85.747
Angle α, β, γ (deg.)90.000, 98.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 78 kDa glucose-regulated protein / GRP-78 / Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78 / Heat shock 70 kDa protein 5 / ...GRP-78 / Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78 / Heat shock 70 kDa protein 5 / Immunoglobulin heavy chain-binding protein / BiP


Mass: 44356.090 Da / Num. of mol.: 2 / Fragment: ATPase domain (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 BL21(DE3) (bacteria) / References: UniProt: P11021
#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
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: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2015
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.86→34.22 Å / Num. obs: 59159 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Χ2: 2.711 / Net I/av σ(I): 42.118 / Net I/σ(I): 19.2 / Num. measured all: 268759
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.893.70.21629110.9490.1260.2511.5298.5
1.89-1.9340.19329450.9610.1070.2221.631100
1.93-1.964.50.16729560.9760.0870.1891.735100
1.96-24.70.15329420.980.0780.1721.981100
2-2.054.70.13729660.9830.0690.1542.005100
2.05-2.094.70.11929550.9880.060.1342.193100
2.09-2.154.70.11129390.9880.0560.1252.369100
2.15-2.214.70.10229490.9910.0510.1142.517100
2.21-2.274.70.09329550.9920.0470.1042.597100
2.27-2.344.70.08529650.9930.0430.0962.683100
2.34-2.434.70.08229550.9930.0410.0922.898100
2.43-2.524.70.07629650.9940.0380.0852.897100
2.52-2.644.70.0729410.9940.0350.0793.095100
2.64-2.784.70.06329720.9960.0320.0713.171100
2.78-2.954.60.05829720.9960.0290.0663.351100
2.95-3.184.50.05429660.9960.0280.0613.49899.9
3.18-3.54.50.05229660.9960.0270.0593.779100
3.5-4.014.50.0529970.9960.0260.0563.82999.8
4.01-5.054.40.04529990.9970.0230.0513.49599.9
5.05-504.40.03829430.9970.0190.0432.56896.3

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Processing

Software
NameVersionClassification
DENZO5.7.0032data reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EXW

5exw


Resolution: 1.86→34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2164 / WRfactor Rwork: 0.1761 / FOM work R set: 0.8755 / SU B: 5.735 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1521 / SU Rfree: 0.1365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 2980 5 %RANDOM
Rwork0.1726 ---
obs0.1746 56062 99.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 108.86 Å2 / Biso mean: 26.782 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0.69 Å2
2---0.44 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.86→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 60 510 6469
Biso mean--42.72 30.74 -
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196078
X-RAY DIFFRACTIONr_bond_other_d0.0010.025902
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9778214
X-RAY DIFFRACTIONr_angle_other_deg0.714313599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1655760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34124.964278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6191538
X-RAY DIFFRACTIONr_chiral_restr0.0720.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021322
X-RAY DIFFRACTIONr_mcbond_it0.8841.2913043
X-RAY DIFFRACTIONr_mcbond_other0.8821.2913042
X-RAY DIFFRACTIONr_mcangle_it1.371.933802
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 212 -
Rwork0.201 3983 -
all-4195 -
obs--95.89 %
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)
11.5251-0.15640.09012.05420.11651.290.0160.1082-0.0493-0.0966-0.0314-0.13410.01890.13470.01530.01820.00390.01710.04280.00410.021125.23582.2269-8.1222
20.89780.3055-0.01422.14790.01881.4991-0.0087-0.0144-0.0053-0.01060.0342-0.10180.00310.1386-0.02550.00380.0034-0.00740.0182-0.00490.039912.5441-9.6402-37.2451
31.00320.38110.75355.47260.29462.52230.1065-0.109-0.17760.4203-0.0569-0.43720.1480.1793-0.04960.0932-0.0328-0.02460.09290.02640.083430.9046.92711.7796
41.54780.67770.19096.2512-0.15212.0241-0.08240.2510.1989-0.49620.07940.1474-0.21930.01690.0030.0857-0.0094-0.03350.08380.02030.05141.0979-13.8894-54.566
51.7911-0.1702-0.23231.0927-0.2892.65670.0007-0.0379-0.0742-0.02640.03160.2055-0.0134-0.4032-0.03230.0471-0.0052-0.00220.0814-0.00750.06195.19131.9176-2.5617
63.5692-0.43220.21211.1077-0.19661.2872-0.0085-0.4143-0.24210.13740.13450.21960.059-0.2456-0.12590.0853-0.00050.0160.11370.04050.125-4.0541-12.0136-24.6412
73.7191-1.39712.72451.9302-1.38374.5863-0.0687-0.2684-0.06660.17750.1251-0.17250.1253-0.0498-0.05640.1422-0.0198-0.00320.10760.02460.089217.2185-13.522619.876
83.3455-2.07642.29453.4355-2.65366.62440.13330.2860.0371-0.5383-0.01030.01880.172-0.0088-0.1230.1824-0.0075-0.01450.11710.00910.1334-18.06154.7843-45.2661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 63
2X-RAY DIFFRACTION1A142 - 214
3X-RAY DIFFRACTION2B26 - 63
4X-RAY DIFFRACTION2B142 - 214
5X-RAY DIFFRACTION3A64 - 141
6X-RAY DIFFRACTION4B64 - 141
7X-RAY DIFFRACTION5A215 - 253
8X-RAY DIFFRACTION5A332 - 407
9X-RAY DIFFRACTION6B215 - 253
10X-RAY DIFFRACTION6B332 - 407
11X-RAY DIFFRACTION7A254 - 331
12X-RAY DIFFRACTION8B254 - 331

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