[English] 日本語
Yorodumi
- PDB-4z4k: Crystal structure of GFP-TAX1BP1 UBZ1+2 domain fusion protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z4k
TitleCrystal structure of GFP-TAX1BP1 UBZ1+2 domain fusion protein
ComponentsGreen fluorescent protein,Tax1-binding protein 1
KeywordsFlurorescent Protein / Metal Binding Protein / GFP / TAX1BP1 / UBZ / Zinc-finger
Function / homology
Function and homology information


protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / autophagosome / bioluminescence ...protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / autophagosome / bioluminescence / generation of precursor metabolites and energy / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding / cytoplasmic vesicle / protein-macromolecule adaptor activity / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Green Fluorescent Protein / Green fluorescent protein ...Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein / Tax1-binding protein 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRohaim, A. / Kawasaki, M. / Wakatsuki, S.
CitationJournal: Febs J. / Year: 2016
Title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.
Authors: Suzuki, N. / Rohaim, A. / Kato, R. / Dikic, I. / Wakatsuki, S. / Kawasaki, M.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _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 / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein,Tax1-binding protein 1
B: Green fluorescent protein,Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7646
Polymers66,5032
Non-polymers2624
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-5 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.885, 83.334, 128.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTHRTHRAA3 - 636 - 66
21LYSLYSTHRTHRBB3 - 636 - 66
12VALVALPHEPHEAA68 - 28969 - 290
22VALVALPHEPHEBB68 - 28969 - 290

NCS ensembles :
ID
1
2

-
Components

#1: Protein Green fluorescent protein,Tax1-binding protein 1 / TRAF6-binding protein


Mass: 33251.355 Da / Num. of mol.: 2 / Fragment: UBZ1 and UBZ2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, TAX1BP1, T6BP, PRO0105 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: Q86VP1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14819 / % possible obs: 99.64 % / Redundancy: 6.6 % / Net I/σ(I): 4.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA

1ema


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 37.403 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27968 774 5 %RANDOM
Rwork0.20596 ---
obs0.20966 14819 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.733 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2---0.46 Å20 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 4 58 4642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194706
X-RAY DIFFRACTIONr_bond_other_d00.024318
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9526356
X-RAY DIFFRACTIONr_angle_other_deg3.60639994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59425.124242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12915793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3371514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215337
X-RAY DIFFRACTIONr_gen_planes_other0.010.021109
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_it1.8472.8732246
X-RAY DIFFRACTIONr_mcbond_other1.8462.8712245
X-RAY DIFFRACTIONr_mcangle_it3.1474.32797
X-RAY DIFFRACTIONr_mcangle_other3.1464.3032798
X-RAY DIFFRACTIONr_scbond_it1.8673.0852460
X-RAY DIFFRACTIONr_scbond_other1.8673.0872461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2314.5423560
X-RAY DIFFRACTIONr_long_range_B_refined5.34522.7695072
X-RAY DIFFRACTIONr_long_range_B_other5.33922.7815071
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)
11A28870.13
12B28870.13
21A115240.16
22B115240.16
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.455 43 -
Rwork0.304 1080 -
obs--99.01 %
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)
10.86030.10810.34971.3686-0.04170.69890.04440.08910.01210.0322-0.05240.0421-0.04730.02240.00790.08560.0133-0.00180.0589-0.00870.0916-28.5886-2.8568-2.2059
21.30440.43470.34941.06370.59021.39670.26-0.17820.20980.4378-0.26160.00250.1291-0.17810.00160.3324-0.10970.03080.0686-0.01360.0402-19.952612.865525.1785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 289
2X-RAY DIFFRACTION2B3 - 289

+
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