[English] 日本語
Yorodumi
- PDB-7b80: DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b80
TitleDeAMPylation complex of monomeric FICD and AMPylated BiP (state 2)
Components
  • Endoplasmic reticulum chaperone BiP
  • Protein adenylyltransferase FICD
KeywordsHYDROLASE / FICD / Fic / HYPE / BiP / Grp78 / AMPylation / deAMPylation / deAMPylase / ER stress / Complex / adenylation / adenylylation / Hsp70 / chaperone / transferase
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / negative regulation of IRE1-mediated unfolded protein response / negative regulation of GTPase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / post-translational protein targeting to membrane, translocation ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / negative regulation of IRE1-mediated unfolded protein response / negative regulation of GTPase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly / Hsp70 protein binding / response to endoplasmic reticulum stress / ATP-dependent protein folding chaperone / melanosome / protein-folding chaperone binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
Fido domain-containing protein / Fido-like domain / Fic-like fold / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Endoplasmic reticulum targeting sequence. / Heat shock hsp70 proteins family signature 2. ...Fido domain-containing protein / Fido-like domain / Fic-like fold / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Fido-like domain superfamily / Fic/DOC family / Fido domain / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / Tetratricopeptide repeat domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Nucleotidyltransferase; domain 5 / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Endoplasmic reticulum chaperone BiP / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsPerera, L.A. / Ron, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200848/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD.
Authors: Perera, L.A. / Preissler, S. / Zaccai, N.R. / Prevost, S. / Devos, J.M. / Haertlein, M. / Ron, D.
History
DepositionDec 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,40013
Polymers96,9272
Non-polymers1,47311
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-32 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.000, 103.890, 104.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules BA

#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: 57543.043 Da / Num. of mol.: 1 / Mutation: T229A, V461F
Source method: isolated from a genetically manipulated source
Details: Covalent modification of T518 with AMP moiety / 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 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: 39383.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2.7.7.n1 / Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

-
Non-polymers , 7 types, 601 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8.0 25% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.87→52.4 Å / Num. obs: 86247 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.9
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.793 / Mean I/σ(I) obs: 1 / Num. unique obs: 6270 / CC1/2: 0.536 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4P, 6I7L

5o4p

6i7l


Resolution: 1.87→52.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.688 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 4190 4.9 %RANDOM
Rwork0.2008 ---
obs0.2021 81979 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.79 Å2 / Biso mean: 37.354 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-0 Å2
2---1.09 Å20 Å2
3---2.68 Å2
Refinement stepCycle: final / Resolution: 1.87→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 84 590 7440
Biso mean--50.61 42.72 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176855
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.6519636
X-RAY DIFFRACTIONr_angle_other_deg1.1511.58115826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73422.83371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.621151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6971546
X-RAY DIFFRACTIONr_chiral_restr0.0480.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
LS refinement shellResolution: 1.87→1.919 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 333 -
Rwork0.353 5931 -
all-6264 -
obs--99.97 %
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)
11.9322-0.53510.07250.9258-0.05070.5638-0.00230.04310.29940.0318-0.0210.0192-0.1281-0.050.02330.04940.0042-0.01030.00890.00720.0665-33.53911.524-8.303
21.55410.0186-0.50020.8013-0.0950.66630.00490.06690.006-0.08540.0194-0.10010.0580.0576-0.02430.02970.0133-0.01460.0347-0.020.04639.139-11.498-7.875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B27 - 549
2X-RAY DIFFRACTION1B601
3X-RAY DIFFRACTION2A103 - 442
4X-RAY DIFFRACTION2A501 - 504

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more