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- PDB-6ha7: Crystal structure of the BiP NBD and MANF complex -

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Basic information

Entry
Database: PDB / ID: 6ha7
TitleCrystal structure of the BiP NBD and MANF complex
Components
  • Endoplasmic reticulum chaperone BiP
  • Mesencephalic astrocyte-derived neurotrophic factor
KeywordsCHAPERONE / MANF / BiP / NBD / NDI / ARMET / HSP70
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 / dopaminergic neuron differentiation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / response to unfolded protein ...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 / dopaminergic neuron differentiation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / growth factor activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular space / ATP binding / cytosol
Similarity search - Function
ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / SAP domain superfamily / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like ...ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / 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 / Alpha Beta
Similarity search - Domain/homology
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: 2.49 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 7, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,8636
Polymers121,7394
Non-polymers1242
Water23413
1
A: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7062
Polymers42,6441
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Mesencephalic astrocyte-derived neurotrophic factor


Theoretical massNumber of molelcules
Total (without water)18,2251
Polymers18,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7062
Polymers42,6441
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mesencephalic astrocyte-derived neurotrophic factor


Theoretical massNumber of molelcules
Total (without water)18,2251
Polymers18,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.420, 60.960, 96.110
Angle α, β, γ (deg.)81.13, 88.33, 74.33
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA27 - 4051 - 379
21SERSERLEULEUBC27 - 4051 - 379
12ARGARGALAALACB23 - 1752 - 154
22ARGARGALAALADD23 - 1752 - 154

NCS ensembles :
ID
1
2

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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: 42644.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli (E. coli)
References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase
#2: Protein Mesencephalic astrocyte-derived neurotrophic factor / Arginine-rich protein / Protein ARMET


Mass: 18225.166 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 7% PEG6000, 0.1 M Tris-HCl pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.49→36.52 Å / Num. obs: 43348 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.072 / Net I/σ(I): 13.3
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3227 / CC1/2: 0.617 / Rpim(I) all: 0.707 / Rrim(I) all: 0.999 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H9U, 2W51

6h9u

2w51


Resolution: 2.49→36.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 30.646 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.574 / ESU R Free: 0.291 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25608 2085 4.8 %RANDOM
Rwork0.22636 ---
obs0.22782 41261 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-1.18 Å2-0.53 Å2
2---2.37 Å2-0.55 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.49→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8214 0 8 13 8235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0148352
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177715
X-RAY DIFFRACTIONr_angle_refined_deg0.7941.6611271
X-RAY DIFFRACTIONr_angle_other_deg0.6861.64718073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8323.365416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.654151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9411547
X-RAY DIFFRACTIONr_chiral_restr0.0330.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021448
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_it0.7565.2074258
X-RAY DIFFRACTIONr_mcbond_other0.7565.2074257
X-RAY DIFFRACTIONr_mcangle_it1.3267.8095312
X-RAY DIFFRACTIONr_mcangle_other1.3267.8095313
X-RAY DIFFRACTIONr_scbond_it0.6655.2694094
X-RAY DIFFRACTIONr_scbond_other0.6655.2694094
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1757.875960
X-RAY DIFFRACTIONr_long_range_B_refined2.06159.8198682
X-RAY DIFFRACTIONr_long_range_B_other2.06159.8248683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A115160.06
12B115160.06
21C42950.08
22D42950.08
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 135 -
Rwork0.33 3070 -
obs--98.04 %
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)
11.3161-0.6575-0.60982.74040.89632.0371-0.00440.0837-0.14940.07540.0140.21690.2384-0.1631-0.00960.0366-0.0289-0.01170.10570.04830.0637-19.4489-6.60262.1582
24.04511.4324-1.0820.5691-0.52970.7794-0.0557-0.1657-0.0093-0.0485-0.0527-0.06450.080.14130.10830.01440.00010.03470.13240.03720.2077-1.606929.631216.9017
31.13830.6671-0.30622.0333-0.40112.69680.09150.09090.12480.2442-0.0442-0.1237-0.00290.1665-0.04730.03040.0011-0.01520.0614-0.01690.0732-33.215313.053155.869
41.10130.7380.51032.54452.63883.1037-0.02080.10040.0102-0.0879-0.13110.3532-0.084-0.32050.15190.1751-0.0235-0.00840.1560.06420.2644-60.3921-20.524356.1041
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 406
2X-RAY DIFFRACTION2C23 - 179
3X-RAY DIFFRACTION3B27 - 407
4X-RAY DIFFRACTION4D22 - 176

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