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- PDB-7mrj: Crystal structure of a novel ubiquitin-like TINCR -

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Basic information

Entry
Database: PDB / ID: 7mrj
TitleCrystal structure of a novel ubiquitin-like TINCR
ComponentsUbiquitin domain-containing protein TINCR
KeywordsUNKNOWN FUNCTION / novel ubiquitin-like protein
Function / homologyUbiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / ACETATE ION / Ubiquitin domain-containing protein TINCR
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsForouhar, F. / Morgado-Palacin, L. / Brown, J.A. / Martinez, T. / Pedrero, J.M.G. / Reglero, C. / Chaudhry, I. / Vaughan, J. / Rodriguez-Perales, S. / Allonca, E. ...Forouhar, F. / Morgado-Palacin, L. / Brown, J.A. / Martinez, T. / Pedrero, J.M.G. / Reglero, C. / Chaudhry, I. / Vaughan, J. / Rodriguez-Perales, S. / Allonca, E. / Granda-Diaz, R. / Quinn, S.A. / Fernandez, A.F. / Fraga, M.F. / Kim, A.L. / Santos-Juanes, J. / Owens, D.M. / Rodrigo, J.P. / Saghatelian, A. / Ferrando, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA210065 United States
CitationJournal: Nat Commun / Year: 2023
Title: The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma.
Authors: Morgado-Palacin, L. / Brown, J.A. / Martinez, T.F. / Garcia-Pedrero, J.M. / Forouhar, F. / Quinn, S.A. / Reglero, C. / Vaughan, J. / Heydary, Y.H. / Donaldson, C. / Rodriguez-Perales, S. / ...Authors: Morgado-Palacin, L. / Brown, J.A. / Martinez, T.F. / Garcia-Pedrero, J.M. / Forouhar, F. / Quinn, S.A. / Reglero, C. / Vaughan, J. / Heydary, Y.H. / Donaldson, C. / Rodriguez-Perales, S. / Allonca, E. / Granda-Diaz, R. / Fernandez, A.F. / Fraga, M.F. / Kim, A.L. / Santos-Juanes, J. / Owens, D.M. / Rodrigo, J.P. / Saghatelian, A. / Ferrando, A.A.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 2.0Jun 22, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 25, 2023Group: 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: Ubiquitin domain-containing protein TINCR
B: Ubiquitin domain-containing protein TINCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2765
Polymers24,0892
Non-polymers1873
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-15 kcal/mol
Surface area9670 Å2
Unit cell
Length a, b, c (Å)67.676, 67.676, 89.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ubiquitin domain-containing protein TINCR


Mass: 12044.681 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TINCR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0GVN0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5
Details: 0.1 M Magnesium sulfate heptahydrate, 0.1 M Sodium Acetate, and 20% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.12→53.99 Å / Num. obs: 12340 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15
Reflection shellResolution: 2.12→2.21 Å / Rmerge(I) obs: 0.66 / Num. unique obs: 1186 / CC1/2: 0.83 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWI

4hwi


Resolution: 2.12→53.99 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 1224 9.92 %
Rwork0.1882 11116 -
obs0.1928 12340 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.04 Å2 / Biso mean: 55.2554 Å2 / Biso min: 25.75 Å2
Refinement stepCycle: final / Resolution: 2.12→53.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 11 87 1402
Biso mean--77.41 55.22 -
Num. residues----160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.12-2.210.33661390.257911861325
2.21-2.310.29711440.239312121356
2.31-2.430.27791260.23612111337
2.43-2.580.33681330.265612101343
2.58-2.780.30331270.243712151342
2.78-3.060.2521550.188912121367
3.06-3.50.21281210.186412541375
3.5-4.410.21181350.158412561391
4.41-53.990.19741440.163313601504
Refinement TLS params.Method: refined / Origin x: -37.3715 Å / Origin y: -6.4594 Å / Origin z: -9.1476 Å
111213212223313233
T0.284 Å2-0.026 Å2-0.0233 Å2-0.3418 Å20.027 Å2--0.3225 Å2
L0.474 °2-0.4852 °2-0.1598 °2-0.5681 °2-0.2048 °2--1.2829 °2
S-0.0565 Å °0.0369 Å °-0.1628 Å °-0.0035 Å °0.0603 Å °0.0517 Å °0.0836 Å °-0.2439 Å °0.0071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 86
2X-RAY DIFFRACTION1allB12 - 86
3X-RAY DIFFRACTION1allA101 - 103
4X-RAY DIFFRACTION1allS1 - 89

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