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- PDB-7ppp: Crystal structure of ZAD-domain of ZNF_276 protein from rabbit. -

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Basic information

Entry
Database: PDB / ID: 7ppp
TitleCrystal structure of ZAD-domain of ZNF_276 protein from rabbit.
ComponentsZinc finger protein 276
KeywordsTRANSCRIPTION / Zinc-finger associated domain / ZAD / protein interaction / dimerization / M1BP / 9797 / zinc binding / treble-cleft-like
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / zinc ion binding / nucleus
Similarity search - Function
ZAD domain profile. / Zinc finger, AD-type / Zinc-finger associated domain (zf-AD) / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein 276
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsBoyko, K.M. / Bonchuk, A.N. / Nikolaeva, A.Y. / Georgiev, P.G. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10099 Russian Federation
CitationJournal: Structure / Year: 2022
Title: Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity.
Authors: Bonchuk, A.N. / Boyko, K.M. / Nikolaeva, A.Y. / Burtseva, A.D. / Popov, V.O. / Georgiev, P.G.
History
DepositionSep 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 9, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / entity_src_gen / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_conn / struct_ncs_dom_lim / struct_ncs_ens / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr_ncs.pdbx_number / _refine_ls_restr_ncs.pdbx_type / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_restr_ncs.weight_position / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_ncs_dom_lim.pdbx_component_id / _struct_ncs_dom_lim.pdbx_refine_code / _struct_ncs_ens.details
Description: Polymer geometry / Details: Ramachandran plot improved. / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.3Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein 276
B: Zinc finger protein 276
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4444
Polymers20,3132
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-65 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.940, 82.940, 134.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 3 - 86 / Label seq-ID: 6 - 89

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Zinc finger protein 276


Mass: 10156.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ZNF276 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5F9DAT3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M bicine pH 8.5, PEG 20000 5%, dextrane sulfate 5%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313, 1.282
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.873131
21.2821
ReflectionResolution: 2.9→49.1 Å / Num. obs: 6460 / % possible obs: 98.8 % / Redundancy: 11.043 % / Biso Wilson estimate: 108.322 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.054 / Χ2: 0.883 / Net I/σ(I): 25.91 / Num. measured all: 71337
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-311.5861.3631.8770566106090.7441.4299.8
3-3.511.6640.5035.4124704212221180.9460.52499.8
3.5-3.811.3610.13517.3789307917860.9940.14199.4
3.8-411.1290.07228.3744854074030.9980.07699
4-4.511.0610.04938.4180977407320.9990.05198.9
4.5-511.0320.03750.2351304724650.9990.03898.5
5-610.4270.03352.07573556355010.03497.7
6-109.30.02759.7356366246060.9990.02897.1
10-49.18.1880.02470.1515642111910.9980.02690.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.1 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.877 / SU B: 39.303 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R: 0.62 / ESU R Free: 0.419
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3399 609 9.429 %RANDOM
Rwork0.2896 5850 --
all0.295 ---
obs-6459 98.777 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 99.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.526 Å20.263 Å20 Å2
2--0.526 Å2-0 Å2
3----1.706 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 2 0 979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131007
X-RAY DIFFRACTIONr_bond_other_d0.0040.014858
X-RAY DIFFRACTIONr_angle_refined_deg2.9221.6421363
X-RAY DIFFRACTIONr_angle_other_deg1.4671.5831937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5035130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91120.18953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.43215127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.116158
X-RAY DIFFRACTIONr_chiral_restr0.1230.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021178
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02258
X-RAY DIFFRACTIONr_nbd_refined0.1610.2183
X-RAY DIFFRACTIONr_symmetry_nbd_other0.120.2752
X-RAY DIFFRACTIONr_nbtor_refined0.1370.2418
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2493
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0740.23
X-RAY DIFFRACTIONr_nbd_other0.1650.223
X-RAY DIFFRACTIONr_mcbond_it7.7618.024532
X-RAY DIFFRACTIONr_mcbond_other7.7668.019531
X-RAY DIFFRACTIONr_mcangle_it11.59612.021658
X-RAY DIFFRACTIONr_mcangle_other11.58812.026659
X-RAY DIFFRACTIONr_scbond_it9.428.021475
X-RAY DIFFRACTIONr_scbond_other9.4138.023476
X-RAY DIFFRACTIONr_scangle_it11.89711.945705
X-RAY DIFFRACTIONr_scangle_other11.8911.945705
X-RAY DIFFRACTIONr_lrange_it13.49292.902961
X-RAY DIFFRACTIONr_lrange_other13.48192.875961
X-RAY DIFFRACTIONr_ncsr_local_group_10.2020.051319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.20160.05004
12BX-RAY DIFFRACTIONLocal ncs0.20160.05004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.515540.397414X-RAY DIFFRACTION99.7868
2.975-3.0570.431460.351405X-RAY DIFFRACTION99.7788
3.057-3.1450.433340.3407X-RAY DIFFRACTION100
3.145-3.2420.429430.306390X-RAY DIFFRACTION100
3.242-3.3480.379410.279375X-RAY DIFFRACTION99.7602
3.348-3.4650.387340.281366X-RAY DIFFRACTION99.5025
3.465-3.5960.339340.265362X-RAY DIFFRACTION99.7481
3.596-3.7420.357270.265342X-RAY DIFFRACTION99.4609
3.742-3.9080.351290.232334X-RAY DIFFRACTION99.4521
3.908-4.0980.199400.207317X-RAY DIFFRACTION98.892
4.098-4.3190.239240.197300X-RAY DIFFRACTION98.4802
4.319-4.580.305310.243285X-RAY DIFFRACTION98.1366
4.58-4.8950.471230.248279X-RAY DIFFRACTION99.0164
4.895-5.2850.361310.274249X-RAY DIFFRACTION97.9021
5.285-5.7860.292230.306238X-RAY DIFFRACTION98.4906
5.786-6.4640.425220.368215X-RAY DIFFRACTION97.9339
6.464-7.4540.332220.38194X-RAY DIFFRACTION97.2973
7.454-9.1040.346290.301153X-RAY DIFFRACTION94.7917
9.104-12.7730.226140.233135X-RAY DIFFRACTION95.5128
12.773-49.10.61180.46890X-RAY DIFFRACTION87.5
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)
14.8428-2.97720.49482.3387-1.20923.1404-0.1722-0.4599-0.72610.10060.13070.60620.00170.41570.04150.0845-0.06420.00530.26760.11190.277213.598842.81397.448
24.6553-0.9888-2.1331.601-1.22153.0966-0.05660.2999-1.5943-0.5687-0.31360.68750.77110.02820.37010.26460.0437-0.09350.2762-0.19050.74136.620634.7796-4.0069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 87
2X-RAY DIFFRACTION2ALLB3 - 87

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