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- PDB-5e86: isolated SBD of BiP with loop34 modification -

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Basic information

Entry
Database: PDB / ID: 5.0E+86
Titleisolated SBD of BiP with loop34 modification
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / molecular chaperones / Hsp70 / BiP / Protein Folding / endoplasmic reticulum / allosteric coupling
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 / ER overload response / negative regulation of PERK-mediated unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment / non-chaperonin molecular chaperone ATPase / : / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / substantia nigra development / protein folding chaperone / response to endoplasmic reticulum stress / cellular response to interleukin-4 / 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 / ribosome binding / protein-folding chaperone binding / midbody / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / 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 / 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 / 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, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.681 Å
AuthorsLiu, Q. / Yang, J. / Nune, M. / Zong, Y. / Zhou, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM098592, 1RO1GM109193 United States
CitationJournal: Structure / Year: 2015
Title: Close and Allosteric Opening of the Polypeptide-Binding Site in a Human Hsp70 Chaperone BiP.
Authors: Yang, J. / Nune, M. / Zong, Y. / Zhou, L. / Liu, Q.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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


Theoretical massNumber of molelcules
Total (without water)26,0291
Polymers26,0291
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.536, 82.593, 150.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-705-

HOH

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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: 26029.449 Da / Num. of mol.: 1 / Fragment: unp residues 418-637 / Mutation: loop34 modification
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11021
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.5 M ammonium sulfate, 0.1 M acetate acid, pH 5.0, and 66.7 mM sodium malonate, pH 7.0
PH range: 5

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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: 2.68→41.3 Å / Num. all: 6391 / Num. obs: 6391 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 38.6
Reflection shellResolution: 2.68→2.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 9.6 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.681→41.297 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 297 4.65 %Random selection
Rwork0.216 ---
obs0.2184 6391 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.681→41.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 0 16 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031811
X-RAY DIFFRACTIONf_angle_d0.7092446
X-RAY DIFFRACTIONf_dihedral_angle_d13.745698
X-RAY DIFFRACTIONf_chiral_restr0.044286
X-RAY DIFFRACTIONf_plane_restr0.003318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6805-3.37690.30141410.25332985X-RAY DIFFRACTION100
3.3769-41.30140.23891560.20073109X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.2961 Å / Origin y: 43.5966 Å / Origin z: 56.7999 Å
111213212223313233
T0.2543 Å2-0.0787 Å2-0.0396 Å2-0.2347 Å20.02 Å2--0.2434 Å2
L0.8311 °2-0.4534 °2-0.2147 °2-0.4325 °20.5644 °2--1.0299 °2
S-0.0268 Å °-0.0153 Å °-0.0111 Å °-0.1606 Å °-0.0347 Å °0.1534 Å °-0.1556 Å °0.0748 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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