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- PDB-6asy: BiP-ATP2 -

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Basic information

Entry
Database: PDB / ID: 6asy
TitleBiP-ATP2
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / Hsp70s
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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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 ...Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / 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 / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLiu, Q. / Yang, J. / Zong, Y. / Columbus, L. / Zhou, L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098592 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM109193 United States
American Heart Association17GRNT33660506 United States
Virginia Commonwealth UniversityBlick Scholar Award United States
CitationJournal: Nat Commun / Year: 2017
Title: Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s.
Authors: Yang, J. / Zong, Y. / Su, J. / Li, H. / Zhu, H. / Columbus, L. / Zhou, L. / Liu, Q.
History
DepositionAug 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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: 78 kDa glucose-regulated protein
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,94530
Polymers134,4762
Non-polymers3,46928
Water21,7801209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-159 kcal/mol
Surface area53750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.829, 75.752, 78.791
Angle α, β, γ (deg.)62.05, 62.23, 73.42
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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: 67237.977 Da / Num. of mol.: 2 / Fragment: residues 25-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Plasmid: pET28 / Details (production host): Kan resistant
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 (DE3) / References: UniProt: P11021

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Non-polymers , 5 types, 1237 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1209 / 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: 2.62 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 18-22% PEG 1000, 0.1 M phosphate citrate (pH 4.2-7.0), and 0.2 M Li2SO4
PH range: 4.2 - 7.0 / Temp details: incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 113887 / % possible obs: 97.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→39.087 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 18.72
RfactorNum. reflection% reflection
Rfree0.1892 5717 5.02 %
Rwork0.1585 --
obs0.16 113887 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9418 0 200 1209 10827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099921
X-RAY DIFFRACTIONf_angle_d1.20213434
X-RAY DIFFRACTIONf_dihedral_angle_d13.9213784
X-RAY DIFFRACTIONf_chiral_restr0.0521518
X-RAY DIFFRACTIONf_plane_restr0.0051744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8492-1.87020.24951670.21613287X-RAY DIFFRACTION90
1.8702-1.89220.25341990.21463596X-RAY DIFFRACTION96
1.8922-1.91520.22841870.19973553X-RAY DIFFRACTION97
1.9152-1.93950.21311760.17933610X-RAY DIFFRACTION97
1.9395-1.9650.22191910.16963539X-RAY DIFFRACTION97
1.965-1.99190.20512050.17063609X-RAY DIFFRACTION97
1.9919-2.02040.23941670.1683576X-RAY DIFFRACTION97
2.0204-2.05050.21372010.17173554X-RAY DIFFRACTION96
2.0505-2.08260.20962030.16063539X-RAY DIFFRACTION98
2.0826-2.11670.19651970.15733619X-RAY DIFFRACTION97
2.1167-2.15320.20012260.16843595X-RAY DIFFRACTION97
2.1532-2.19240.22132010.16233531X-RAY DIFFRACTION98
2.1924-2.23450.19771970.16093607X-RAY DIFFRACTION97
2.2345-2.28010.19411720.16183649X-RAY DIFFRACTION97
2.2801-2.32970.21052000.16013584X-RAY DIFFRACTION98
2.3297-2.38390.181820.16213627X-RAY DIFFRACTION98
2.3839-2.44350.22551860.16783644X-RAY DIFFRACTION98
2.4435-2.50960.20691610.16673597X-RAY DIFFRACTION98
2.5096-2.58340.2031970.16553627X-RAY DIFFRACTION98
2.5834-2.66680.21382000.17023649X-RAY DIFFRACTION98
2.6668-2.7620.20021730.17063646X-RAY DIFFRACTION98
2.762-2.87260.19072100.16643599X-RAY DIFFRACTION99
2.8726-3.00330.18741960.16363633X-RAY DIFFRACTION99
3.0033-3.16160.22791850.16673703X-RAY DIFFRACTION99
3.1616-3.35950.17891710.16093640X-RAY DIFFRACTION99
3.3595-3.61880.17521870.14673700X-RAY DIFFRACTION99
3.6188-3.98260.15032040.13723663X-RAY DIFFRACTION99
3.9826-4.55820.15532030.12573613X-RAY DIFFRACTION99
4.5582-5.73990.15691890.1423713X-RAY DIFFRACTION99
5.7399-39.09610.16681840.16183668X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.1206 Å / Origin y: 12.5049 Å / Origin z: 4.8823 Å
111213212223313233
T0.0956 Å20.0076 Å20.0001 Å2-0.0925 Å20.0005 Å2--0.0958 Å2
L0.0835 °20.056 °2-0.0132 °2-0.0657 °2-0.0068 °2--0.0449 °2
S-0.0058 Å °-0.0089 Å °-0.0012 Å °-0.0089 Å °0.0024 Å °-0.0024 Å °0.0076 Å °0.0057 Å °0 Å °
Refinement TLS groupSelection details: all

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