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- PDB-5e84: ATP-bound state of BiP -

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Basic information

Entry
Database: PDB / ID: 5.0E+84
TitleATP-bound state of BiP
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 / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes ...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 / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / negative 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 / endoplasmic reticulum-Golgi intermediate compartment / chaperone cofactor-dependent protein refolding / 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 / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / substantia nigra development / response to endoplasmic reticulum stress / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _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 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
C: 78 kDa glucose-regulated protein
D: 78 kDa glucose-regulated protein
E: 78 kDa glucose-regulated protein
F: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,33648
Polymers403,2486
Non-polymers5,08842
Water57632
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0809
Polymers67,2081
Non-polymers8728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0809
Polymers67,2081
Non-polymers8728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0327
Polymers67,2081
Non-polymers8246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0809
Polymers67,2081
Non-polymers8728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0327
Polymers67,2081
Non-polymers8246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0327
Polymers67,2081
Non-polymers8246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)222.468, 222.468, 209.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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: 67207.953 Da / Num. of mol.: 6 / Mutation: T229A, loop34
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

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Non-polymers , 5 types, 74 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.72 Å3/Da / Density % sol: 66.97 % / Description: hexagonal plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8%-12% PEG 3000, 0.1 M acetate acid, pH 4.5, and 0.2 M zinc acetate
PH range: 4.5

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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
RadiationMonochromator: focusing monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.99→40.76 Å / Num. all: 111753 / Num. obs: 111753 / % possible obs: 97.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 25.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 4.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JNE

4jne


Resolution: 2.99→40.76 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.855 / SU B: 19.146 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28701 5907 5 %RANDOM
Rwork0.24268 ---
obs0.24489 111753 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.682 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-1.28 Å2-0 Å2
2---1.28 Å2-0 Å2
3---4.17 Å2
Refinement stepCycle: 1 / Resolution: 2.99→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28206 0 246 32 28484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01928782
X-RAY DIFFRACTIONr_bond_other_d0.0010.0227863
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.98338896
X-RAY DIFFRACTIONr_angle_other_deg0.805364385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72853630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00425.5541309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.276155299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.45615162
X-RAY DIFFRACTIONr_chiral_restr0.0980.24443
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02132470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025970
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9947.59914538
X-RAY DIFFRACTIONr_mcbond_other4.9937.59914537
X-RAY DIFFRACTIONr_mcangle_it7.92611.3918162
X-RAY DIFFRACTIONr_mcangle_other7.92611.3918163
X-RAY DIFFRACTIONr_scbond_it5.0317.86114242
X-RAY DIFFRACTIONr_scbond_other5.0167.85814219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.05211.61820698
X-RAY DIFFRACTIONr_long_range_B_refined11.60257.45630900
X-RAY DIFFRACTIONr_long_range_B_other11.60257.45630901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.992→3.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 429 -
Rwork0.293 8039 -
obs--95.69 %

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