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- PDB-6zmd: Crystal structure of HYPE covalently tethered to BiP bound to AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 6zmd
TitleCrystal structure of HYPE covalently tethered to BiP bound to AMP-PNP
Components
  • Endoplasmic reticulum chaperone BiP
  • Protein adenylyltransferase FICD
KeywordsTRANSFERASE / AMPylation / Endoplasmic reticulum / Fic enzyme / chaperone / post-translational modification
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / 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 / AMPylase activity ...protein deadenylylation / protein adenylylhydrolase activity / 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 / AMPylase activity / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / protein adenylyltransferase / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes / protein adenylylation / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / PERK regulates gene expression / protein folding in endoplasmic reticulum / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / misfolded protein binding / post-translational protein targeting to membrane, translocation / ERAD pathway / negative regulation of GTPase activity / ER overload response / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / 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 / Hsp70 protein binding / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fido domain-containing protein / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / 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. ...Fido domain-containing protein / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Chem-QMK / Endoplasmic reticulum chaperone BiP / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsFauser, J. / Gulen, B. / Pett, C. / Hedberg, C. / Itzen, A. / Pogenberg, V.
Funding support Germany, Sweden, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 B05 Germany
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2021
Title: Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD.
Authors: Fauser, J. / Gulen, B. / Pogenberg, V. / Pett, C. / Pourjafar-Dehkordi, D. / Krisp, C. / Hopfner, D. / Konig, G. / Schluter, H. / Feige, M.J. / Zacharias, M. / Hedberg, C. / Itzen, A.
History
DepositionJul 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / database_2 ...citation / database_2 / pdbx_contact_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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum chaperone BiP
B: Protein adenylyltransferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3318
Polymers97,2192
Non-polymers1,1116
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-44 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.466, 83.466, 169.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#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: 57827.379 Da / Num. of mol.: 1 / Mutation: T229A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Production host: Escherichia coli (E. coli)
References: UniProt: P11021, non-chaperonin molecular chaperone ATPase
#2: Protein Protein adenylyltransferase FICD / AMPylator FICD / De-AMPylase FICD / FIC domain-containing protein / Huntingtin yeast partner E / ...AMPylator FICD / De-AMPylase FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin-interacting protein 13 / HIP-13 / Huntingtin-interacting protein E


Mass: 39392.117 Da / Num. of mol.: 1 / Mutation: T168A, T183A, E234G, L258D, E404C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 5 types, 80 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-QMK / ~{N}-[2-[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1,2,3-triazol-4-yl]ethyl]ethanamide


Mass: 366.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N4O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2 and 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.64→83.47 Å / Num. obs: 34024 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 59.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.1
Reflection shellResolution: 2.64→2.77 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4518 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U04, 5O4P

4u04

5o4p


Resolution: 2.64→41.73 Å / SU ML: 0.3476 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 1647 4.85 %
Rwork0.1924 32301 -
obs0.1944 33948 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.52 Å2
Refinement stepCycle: LAST / Resolution: 2.64→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 66 74 6858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156901
X-RAY DIFFRACTIONf_angle_d0.39049342
X-RAY DIFFRACTIONf_chiral_restr0.04021065
X-RAY DIFFRACTIONf_plane_restr0.00291210
X-RAY DIFFRACTIONf_dihedral_angle_d10.70754192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.720.33461570.28292667X-RAY DIFFRACTION99.93
2.72-2.810.2791200.2622690X-RAY DIFFRACTION99.93
2.81-2.910.30151340.26922706X-RAY DIFFRACTION99.79
2.91-3.020.33061300.26242677X-RAY DIFFRACTION99.79
3.02-3.160.30541120.24142686X-RAY DIFFRACTION99.96
3.16-3.330.24491500.22912690X-RAY DIFFRACTION99.93
3.33-3.530.24711320.2182686X-RAY DIFFRACTION99.96
3.53-3.810.22791310.19262718X-RAY DIFFRACTION99.96
3.81-4.190.22251780.17342658X-RAY DIFFRACTION100
4.19-4.80.19421370.15992686X-RAY DIFFRACTION99.96
4.8-6.040.2211450.1812705X-RAY DIFFRACTION99.86
6.04-41.730.21111210.15062732X-RAY DIFFRACTION99.65
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)
12.3775342564-0.2385635689810.5333249431554.525325670721.337428262554.488240428590.1404291471960.432054855561-0.115063791465-0.7978175328060.101100805387-0.1358858681630.1703325190040.443455390229-0.2365878995330.53727402816-0.0451254287746-0.08058392827820.475546652515-0.008507462253050.36632544935421.885190313932.3263077708-3.89429429826
22.59055150766-0.004779337080461.179489857254.045225917682.155275412996.038057348680.2370117524520.598955472395-0.382303997136-0.9823310964390.0216705027206-0.1044162874210.6382859801090.649097150191-0.3017147270570.8476473124720.0265448586804-0.05529432578460.495850457134-0.05912563508040.40182074162624.921628210623.785153849-10.1480244136
34.26883170902-0.514467980527-0.26965792512.82407253573-0.1368773521924.674453205380.02815291858250.0553159164024-0.122148585995-0.279410929010.1997464804050.2605767666710.4358391165120.0422890609923-0.2305773621490.331872917262-0.0311338095083-0.09725930630.2313225540180.02855492686190.35342501688619.006111226625.123977806310.6852492499
41.32467977634-0.8723768992171.181116328822.25294117228-0.1245848438823.455800683730.266745822640.34162347415-0.250830445021-1.006147689140.0314819055670.5218310022770.288640214153-0.130694965659-0.2760117181070.727025761544-0.110139870018-0.322205422420.5293920347050.03816322538970.6466623308254.7585091850229.8321354722-9.5993605797
52.18081048343-0.6189002138560.3706449274522.3267715822-0.7626805635863.30885082210.00196850418358-0.155018591161-0.309565063566-0.2965706709030.3932296550960.9026661755870.166722795083-0.730350198838-0.3220726313750.423847678708-0.100665659988-0.2371952499810.5467851214450.1539238263710.822309237529-1.7272510710427.12009475496.04689925234
61.71777963704-0.8606226006130.1916704413281.64851551294-1.483603831172.00734563031-0.0551648361785-0.282272743896-0.0765959618088-0.2769445533110.1968667327370.1571805269540.27151937628-0.0505930458861-0.1084344417950.4821813653830.0256247092057-0.09808344315160.358249949782-0.0005470426921660.41207291268519.763261182320.670801085515.5128540793
72.76988959976-2.30584380435-0.2320918320627.344054725420.09983136475721.83951177615-0.155438133170.208609696692-0.6729946965170.01597344705220.2775182087670.04579648723321.286370837490.149093061169-0.09428873281791.136900186770.0256032193643-0.132011108650.469226239542-0.0236740511180.65358211187122.4690301974-2.208046321989.5043471977
81.660451917991.07223720004-1.104087420486.22634892865-4.057190593864.795978060140.4522253443580.16943160003-0.255408614701-0.46019887174-0.587226506114-0.4599413305770.6929496694870.8992045216430.05361648445030.9774685406070.176830687040.02015497256150.792631562946-0.131803466250.79265644348735.50712727138.689974617611.4658906225
90.3382075909990.07779456444460.07251135707533.19059707721.868338874521.177429340230.0227432253423-0.036703063879-0.07695011860390.759037236649-0.01264028878360.2820915885080.454248301257-0.181157883003-0.01610464713820.5888895267540.0128664011419-0.0068244733210.505737826670.003320199837360.361457200621.7544937670.80906455384638.367906919
102.005805569430.684616128675-0.01449550825724.661108255911.881207587483.297910011390.24196646015-0.3561930049010.0937793771111.144598422290.26865912498-1.230344927720.4240067659760.394938644212-0.4641721064690.8402531333630.0830194802796-0.3418196553880.466358548555-0.09344281496530.77042811276231.9203765856-28.916479643431.189611668
113.64038370279-0.53561528290.007236656629357.575191088473.435492001953.524551800160.311503627248-0.05071759574230.06380553252121.427306467510.0345220076916-0.4556028507430.5661592707330.0220169199745-0.254264011140.861357803797-0.0219166873283-0.2117304503120.360630124592-0.03546703772890.51131164174525.5338178343-17.349406417135.9999672601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 229 )
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 317 )
5X-RAY DIFFRACTION5chain 'A' and (resid 318 through 392 )
6X-RAY DIFFRACTION6chain 'A' and (resid 393 through 431 )
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 515 )
8X-RAY DIFFRACTION8chain 'A' and (resid 516 through 548 )
9X-RAY DIFFRACTION9chain 'B' and (resid 102 through 234 )
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 347 )
11X-RAY DIFFRACTION11chain 'B' and (resid 348 through 433 )

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