[English] 日本語
Yorodumi
- PDB-4u0z: Eukaryotic Fic Domain containing protein with bound APCPP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u0z
TitleEukaryotic Fic Domain containing protein with bound APCPP
ComponentsAdenosine monophosphate-protein transferase FICD
KeywordsTRANSFERASE / TPR / FIC / APCPP / adenylation
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 GTPase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / response to unfolded protein / Hsp70 protein binding ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / negative regulation of GTPase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / response to unfolded protein / Hsp70 protein binding / response to endoplasmic reticulum stress / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP binding / identical protein binding
Similarity search - Function
Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. ...Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCole, A.R. / Bunney, T.D. / Katan, M.
CitationJournal: Structure / Year: 2014
Title: Crystal structure of the human, FIC-domain containing protein HYPE and implications for its functions.
Authors: Bunney, T.D. / Cole, A.R. / Broncel, M. / Esposito, D. / Tate, E.W. / Katan, M.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: 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_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_label_asym_id / _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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine monophosphate-protein transferase FICD
B: Adenosine monophosphate-protein transferase FICD
C: Adenosine monophosphate-protein transferase FICD
D: Adenosine monophosphate-protein transferase FICD
E: Adenosine monophosphate-protein transferase FICD
F: Adenosine monophosphate-protein transferase FICD
G: Adenosine monophosphate-protein transferase FICD
H: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,62224
Polymers316,3868
Non-polymers4,23616
Water14,700816
1
G: Adenosine monophosphate-protein transferase FICD
hetero molecules

A: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
MethodPISA
2
A: Adenosine monophosphate-protein transferase FICD
hetero molecules

G: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area30120 Å2
MethodPISA
3
B: Adenosine monophosphate-protein transferase FICD
H: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area30370 Å2
MethodPISA
4
E: Adenosine monophosphate-protein transferase FICD
hetero molecules

C: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
5
C: Adenosine monophosphate-protein transferase FICD
hetero molecules

E: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3700 Å2
ΔGint-32 kcal/mol
Surface area30840 Å2
MethodPISA
6
F: Adenosine monophosphate-protein transferase FICD
hetero molecules

D: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
7
D: Adenosine monophosphate-protein transferase FICD
hetero molecules

F: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 83.754, 130.023
Angle α, β, γ (deg.)89.92, 89.57, 89.43
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Adenosine monophosphate-protein transferase FICD / AMPylator FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin- ...AMPylator FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin-interacting protein 13 / HIP-13 / Huntingtin-interacting protein E


Mass: 39548.273 Da / Num. of mol.: 8 / Fragment: UNP residues 102-445
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
#2: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.95→43.34 Å / Num. obs: 65073 / % possible obs: 94.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 55.82 Å2 / Net I/σ(I): 4.4
Reflection shellResolution: 2.95→3.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cuc

3cuc


Resolution: 2.95→43.34 Å / Cor.coef. Fo:Fc: 0.8842 / Cor.coef. Fo:Fc free: 0.8616 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 3307 5.08 %RANDOM
Rwork0.2059 ---
obs0.2082 65073 95.02 %-
Displacement parametersBiso mean: 61.13 Å2
Baniso -1Baniso -2Baniso -3
1-10.1178 Å22.6388 Å21.8468 Å2
2---26.9335 Å2-3.9114 Å2
3---16.8157 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.95→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20256 0 1072 816 22144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120963HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1128555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7118SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes469HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3173HARMONIC5
X-RAY DIFFRACTIONt_it20963HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion21.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2843SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24240SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2793 112 4.67 %
Rwork0.2316 2285 -
all0.2338 2397 -
obs--95.02 %

+
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