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- PDB-6h9u: Crystal structure of the BiP NBD and MANF SAP complex -

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Basic information

Entry
Database: PDB / ID: 6h9u
TitleCrystal structure of the BiP NBD and MANF SAP complex
Components
  • Endoplasmic reticulum chaperone BiP
  • Mesencephalic astrocyte-derived neurotrophic factor
KeywordsCHAPERONE / MANF / BiP / NDI / HSP70 / ARMET
Function / homology
Function and homology information


vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure / regulation of response to endoplasmic reticulum stress / sulfatide binding / negative regulation of IRE1-mediated unfolded protein response / sarcoplasmic reticulum lumen / Platelet degranulation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly ...vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure / regulation of response to endoplasmic reticulum stress / sulfatide binding / negative regulation of IRE1-mediated unfolded protein response / sarcoplasmic reticulum lumen / Platelet degranulation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly / growth factor activity / ATP-dependent protein folding chaperone / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / cytosol
Similarity search - Function
ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / SAP domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Defensin A-like - #30 ...ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / SAP domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Endoplasmic reticulum chaperone BiP / Mesencephalic astrocyte-derived neurotrophic factor
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYan, Y. / Ron, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust200848/Z/16/Z United Kingdom
Wellcome Trust100140 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: MANF antagonizes nucleotide exchange by the endoplasmic reticulum chaperone BiP.
Authors: Yan, Y. / Rato, C. / Rohland, L. / Preissler, S. / Ron, D.
History
DepositionAug 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum chaperone BiP
B: Mesencephalic astrocyte-derived neurotrophic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9264
Polymers47,7692
Non-polymers1572
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Two components ran through gel filtration column separately, both of which were shown as monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-12 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.310, 66.750, 44.300
Angle α, β, γ (deg.)90.00, 106.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-687-

HOH

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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: 42557.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli M15 (bacteria)
References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase
#2: Protein/peptide Mesencephalic astrocyte-derived neurotrophic factor / Arginine-rich protein / Protein ARMET


Mass: 5212.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Manf, Armet / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CXI5
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.92 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→42.47 Å / Num. obs: 59404 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.05 / Rrim(I) all: 0.074 / Net I/σ(I): 11.3
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.86 / Num. unique obs: 4405 / CC1/2: 0.52 / Rpim(I) all: 0.781 / Rrim(I) all: 1.165 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LDN

3ldn


Resolution: 1.57→42.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.049 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20411 2861 4.8 %RANDOM
Rwork0.18447 ---
obs0.18542 56543 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.53 Å2
2---1.2 Å2-0 Å2
3---0.67 Å2
Refinement stepCycle: 1 / Resolution: 1.57→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 10 350 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193289
X-RAY DIFFRACTIONr_bond_other_d0.0020.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9674438
X-RAY DIFFRACTIONr_angle_other_deg0.86637207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18124.832149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77415588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.461521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
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_it0.9772.41674
X-RAY DIFFRACTIONr_mcbond_other0.9772.3981673
X-RAY DIFFRACTIONr_mcangle_it1.6083.5932089
X-RAY DIFFRACTIONr_mcangle_other1.6073.5942090
X-RAY DIFFRACTIONr_scbond_it1.4382.6251615
X-RAY DIFFRACTIONr_scbond_other1.4392.6261612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3623.8472348
X-RAY DIFFRACTIONr_long_range_B_refined4.30729.4963727
X-RAY DIFFRACTIONr_long_range_B_other4.09228.8383617
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 172 -
Rwork0.301 4224 -
obs--99.82 %

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