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- PDB-3vht: Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in comp... -

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Basic information

Entry
Database: PDB / ID: 3vht
TitleCrystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin
Components
  • Green fluorescent protein
  • Green fluorescent protein,ATPase WRNIP1
  • Ubiquitin
KeywordsFLUORESCENT PROTEIN/PROTEIN BINDING / GREEN FLUORESCENT PROTEIN / FUSION PROTEIN / ZINC FINGER / UBIQUITIN-BINDING DOMAIN / FLUORESCENT PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription ...Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / Formation of a pool of free 40S subunits / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / SRP-dependent cotranslational protein targeting to membrane / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Dual incision in TC-NER / Oncogene Induced Senescence / PINK1-PRKN Mediated Mitophagy / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Inactivation of CSF3 (G-CSF) signaling / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / translation at postsynapse / Autodegradation of the E3 ubiquitin ligase COP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / Regulation of TNFR1 signaling / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs
Similarity search - Function
WRNIP1, ubiquitin-binding domain / Werner helicase-interacting protein 1 ubiquitin-binding domain / MgsA AAA+ ATPase C-terminal / AAA C-terminal domain / : / MgsA AAA+ ATPase C terminal / AAA C-terminal domain / Rad18-like CCHC zinc finger / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Classic Zinc Finger ...WRNIP1, ubiquitin-binding domain / Werner helicase-interacting protein 1 ubiquitin-binding domain / MgsA AAA+ ATPase C-terminal / AAA C-terminal domain / : / MgsA AAA+ ATPase C terminal / AAA C-terminal domain / Rad18-like CCHC zinc finger / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Classic Zinc Finger / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Green Fluorescent Protein / Green fluorescent protein / Double Stranded RNA Binding Domain / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Green fluorescent protein / Ubiquitin-ribosomal protein eS31 fusion protein / ATPase WRNIP1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSuzuki, N. / Wakatsuki, S. / Kawasaki, M.
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
DepositionSep 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein,ATPase WRNIP1
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4924
Polymers65,4273
Non-polymers651
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-7 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.950, 143.692, 106.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Green fluorescent protein


Mass: 26306.564 Da / Num. of mol.: 1 / Fragment: GFP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212*PLUS
#2: Protein Green fluorescent protein,ATPase WRNIP1 / Werner helicase-interacting protein 1


Mass: 30543.525 Da / Num. of mol.: 1 / Fragment: GFP,Wrnip1 UBZ domain (UNP RESIDUES 9-46)
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN, LINKER (GLY-SER) AND HUMAN WRNIP1 UBZ
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, WRNIP1, WHIP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96S55, UniProt: P42212*PLUS, EC: 3.6.1.3
#3: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62983
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details(1) THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN NOT CURRENTLY EXIST IN UNIPROT. THIS ...(1) THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN NOT CURRENTLY EXIST IN UNIPROT. THIS SEQUENCE IS FOUND IN GENBANK WITH ACCESSION CODE: ABI82055. (2) IN THE CHAIN A, RESIDUES -2, -1, 0, 231, 232 ARE EXPRESSION TAGS. (3) THE CHAIN B IS FUSION PROTEIN OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN (RESIDUES 1-230), LINKER (GLY-SER) AND HUMAN WRNIP1 (RESIDUES 9-46). RESIDUES -2, -1, 0 ARE EXPRESSION TAGS.

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M DL-Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→75.63 Å / Num. obs: 26943 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 21.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1328 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AI5

3ai5


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.892 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23768 1347 5 %RANDOM
Rwork0.19114 ---
obs0.1935 25484 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.581 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---1.24 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 1 133 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224597
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9666202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19525.204221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83415804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7781517
X-RAY DIFFRACTIONr_chiral_restr0.1140.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027737
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9121.52792
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78524507
X-RAY DIFFRACTIONr_scbond_it2.90131805
X-RAY DIFFRACTIONr_scangle_it4.7224.51695
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 83 -
Rwork0.263 1809 -
obs--96.73 %
Refinement TLS params.Method: refined / Origin x: -14.8285 Å / Origin y: -56.4302 Å / Origin z: -10.6721 Å
111213212223313233
T0.0483 Å20.0127 Å2-0.0297 Å2-0.045 Å20.0084 Å2--0.0328 Å2
L0.6759 °20.2402 °2-0.0375 °2-1.0357 °20.5445 °2--0.9658 °2
S-0.0052 Å °0.0982 Å °0.086 Å °-0.0756 Å °-0.0649 Å °0.0931 Å °-0.0623 Å °0.0438 Å °0.0701 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 231
2X-RAY DIFFRACTION1B2 - 229
3X-RAY DIFFRACTION1B237 - 270
4X-RAY DIFFRACTION1C1 - 76

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