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- PDB-7azx: Crystal structure of the MIZ1-BTB-domain in complex with a HUWE1-... -

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Basic information

Entry
Database: PDB / ID: 7azx
TitleCrystal structure of the MIZ1-BTB-domain in complex with a HUWE1-derived peptide
Components
  • E3 ubiquitin-protein ligase HUWE1
  • Zinc finger and BTB domain-containing protein 17 isoform X1
KeywordsTRANSCRIPTION / BTB-domain / HUWE1 / transcription factor / dimer
Function / homology
Function and homology information


ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding ...ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / ubiquitin-protein transferase activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding
Similarity search - Function
C2H2-type zinc finger / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac ...C2H2-type zinc finger / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1 / Zinc finger and BTB domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOrth, B. / Sander, B. / Diederichs, K. / Lorenz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Structure / Year: 2021
Title: Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1.
Authors: Orth, B. / Sander, B. / Moglich, A. / Diederichs, K. / Eilers, M. / Lorenz, S.
History
DepositionNov 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 17, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 21, 2022Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _entity.pdbx_description ..._citation.page_last / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_src_syn.organism_common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.4Jan 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: Zinc finger and BTB domain-containing protein 17 isoform X1
B: Zinc finger and BTB domain-containing protein 17 isoform X1
C: E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)29,7273
Polymers29,7273
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-42 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.110, 69.110, 97.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Zinc finger and BTB domain-containing protein 17 isoform X1 / Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60


Mass: 13281.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB17, MIZ1, ZNF151, ZNF60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13105
#2: Protein/peptide E3 ubiquitin-protein ligase HUWE1


Mass: 3164.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: H0Y659
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 4000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.25→37.72 Å / Num. obs: 9023 / % possible obs: 68 % / Redundancy: 34.2 % / CC1/2: 0.999 / Rpim(I) all: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2.25→2.4 Å / Redundancy: 27 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 450 / CC1/2: 0.622 / Rpim(I) all: 0.684 / % possible all: 18.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M52

3m52


Resolution: 2.25→34.56 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.92 / Stereochemistry target values: ML
Details: Collected data were analyzed by the staraniso server and very weak reflections were removed. Therefore the completeness is only 68% during refinement.
RfactorNum. reflection% reflection
Rfree0.2785 450 4.99 %
Rwork0.2284 8569 -
obs0.231 9011 68.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.08 Å2 / Biso mean: 52.3112 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: final / Resolution: 2.25→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 0 16 1951
Biso mean---35.5 -
Num. residues----253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.248-2.3280.3574120.2943218
2.5706-3.23840.35811720.2672320877
3.2384-37.7160.24882300.21034326100
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)
12.9932-0.2697-1.00371.3842-0.03522.59940.04540.1486-0.11330.0035-0.13690.39570.0031-0.260.02550.2172-0.0217-0.00640.12140.01890.0416-31.859418.9075-11.4634
23.82010.1226-0.49621.10170.46573.2518-0.0477-0.2686-0.30960.048-0.0873-0.20580.25670.76740.11790.28450.09480.05010.26210.08510.1465-10.793515.2867-15.5875
39.1254-2.591-5.51482.25471.00393.6748-0.3912-1.9482-0.36210.26880.3812-0.01750.03650.86580.01410.4668-0.04140.02870.45330.03110.1566-23.767717.09911.8069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -3 through 115)A-3 - 115
2X-RAY DIFFRACTION2(chain 'B' and resid -3 through 111)B-3 - 111
3X-RAY DIFFRACTION3(chain 'C' and resid 3874 through 3893)C3874 - 3893

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