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- PDB-6qaj: Structure of the tripartite motif of KAP1/TRIM28 -

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Basic information

Entry
Database: PDB / ID: 6qaj
TitleStructure of the tripartite motif of KAP1/TRIM28
ComponentsEndolysin,Transcription intermediary factor 1-beta
KeywordsNUCLEAR PROTEIN / Transcriptional repressor / epigenetic silencing / histone H3 lysine 9 methylation (H3K9me3) / endogenous retrovirus / retrotransposon / transposable element / tripartite motif (TRIM) / SUMO / ubiquitin / E3 ligase
Function / homology
Function and homology information


convergent extension involved in axis elongation / : / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting / chromo shadow domain binding ...convergent extension involved in axis elongation / : / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / viral release from host cell by cytolysis / positive regulation of DNA repair / peptidoglycan catabolic process / SUMOylation of transcription cofactors / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / HCMV Early Events / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / chromatin organization / host cell cytoplasm / transcription coactivator activity / protein kinase activity / defense response to bacterium / DNA repair / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / bromo domain / Bromodomain / Bromodomain-like superfamily / Lysozyme-like domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Endolysin / Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.901 Å
AuthorsStoll, G.A. / Oda, S. / Yu, M. / Modis, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Wellcome Trust205833/Z/16/Z United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing.
Authors: Stoll, G.A. / Oda, S.I. / Chong, Z.S. / Yu, M. / McLaughlin, S.H. / Modis, Y.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: Endolysin,Transcription intermediary factor 1-beta
B: Endolysin,Transcription intermediary factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,46710
Polymers122,9442
Non-polymers5238
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-109 kcal/mol
Surface area51580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.774, 169.332, 374.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid -109 and (name N or name...
21(chain B and (resid -109 through -106 or resid -102...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYR(chain A and ((resid -109 and (name N or name...AA-10922
12ASNASNZNZN(chain A and ((resid -109 and (name N or name...AA - F-111 - 50320
13ASNASNZNZN(chain A and ((resid -109 and (name N or name...AA - F-111 - 50320
14ASNASNZNZN(chain A and ((resid -109 and (name N or name...AA - F-111 - 50320
15ASNASNZNZN(chain A and ((resid -109 and (name N or name...AA - F-111 - 50320
21TYRTYRGLYGLY(chain B and (resid -109 through -106 or resid -102...BB-109 - -10622 - 25
22GLUGLUGLUGLU(chain B and (resid -109 through -106 or resid -102...BB-102 - -9629 - 35
23LYSLYSLYSLYS(chain B and (resid -109 through -106 or resid -102...BB-8843
24ASNASNZNZN(chain B and (resid -109 through -106 or resid -102...BB - I-111 - 50320
25ASNASNZNZN(chain B and (resid -109 through -106 or resid -102...BB - I-111 - 50320
26ASNASNZNZN(chain B and (resid -109 through -106 or resid -102...BB - I-111 - 50320
27ASNASNZNZN(chain B and (resid -109 through -106 or resid -102...BB - I-111 - 50320

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Components

#1: Protein Endolysin,Transcription intermediary factor 1-beta / Lysis protein / Lysozyme / Muramidase / TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-associated ...Lysis protein / Lysozyme / Muramidase / TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-associated protein 1 / KAP-1 / KRAB-interacting protein 1 / KRIP-1 / Nuclear corepressor KAP-1 / RING finger protein 96 / RING-type E3 ubiquitin transferase TIF1-beta / Tripartite motif-containing protein 28


Mass: 61471.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: TRIM28, KAP1, RNF96, TIF1B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00720, UniProt: Q13263, lysozyme, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 4.03 Å3/Da / Density % sol: 69.5 % / Description: Plate-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% (w/v) PEG 3350, 75 mM MgCl2, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.28189 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28189 Å / Relative weight: 1
ReflectionResolution: 2.63→187 Å / Num. obs: 33980 / % possible obs: 32.4 % / Redundancy: 8.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.029 / Net I/σ(I): 13.4
Reflection shellResolution: 2.63→3.17 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.832 / Num. unique obs: 5596 / CC1/2: 0.82 / Rpim(I) all: 0.363 / % possible all: 3.9

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.8 / FOM acentric: 0.82 / FOM centric: 0.73 / Reflection: 17869 / Reflection acentric: 15332 / Reflection centric: 2537
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.5-1870.860.90.7526282007621
4.7-7.50.820.830.7574356508927
3.8-4.70.830.840.7547704242528
3.3-3.80.70.720.6117471534213
2.8-3.30.650.660.621203990213
2.6-2.80.70.640.78865135

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
PHENIX1.14-3260phasing
RESOLVE2.15phasing
PDB_EXTRACT3.24data extraction
XDSJan 26, 2018 BUILT=20180409data reduction
autoPROC1.0.5data scaling
RefinementMethod to determine structure: SAD
Starting model: 1LYD, 2YVR

1lyd

2yvr


Resolution: 2.901→62.798 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.89
RfactorNum. reflection% reflection
Rfree0.291 1633 4.86 %
Rwork0.2611 --
obs0.2625 33635 41.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 465.81 Å2 / Biso mean: 111.34 Å2 / Biso min: 33.83 Å2
Refinement stepCycle: final / Resolution: 2.901→62.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 8 0 6963
Biso mean--167.04 --
Num. residues----880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3068X-RAY DIFFRACTION14.661TORSIONAL
12B3068X-RAY DIFFRACTION14.661TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9012-2.98660.4823130.50543073205
2.9866-3.0830.4466350.45624224577
3.083-3.19320.4505380.416262666410
3.1932-3.3210.472390.455187891713
3.321-3.47220.4253520.436784089213
3.4722-3.65520.3709710.35911497156824
3.6552-3.88420.41810.30971532161330
3.8842-4.18410.34121540.27762700285448
4.1841-4.6050.31812440.25594271451566
4.605-5.27110.27892760.25816088636494
5.2711-6.63980.32263200.303264476767100
6.6398-62.81230.22783100.21426394670499
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)
18.07360.6335-2.18210.7128-0.5518.0447-0.8276-0.4246-1.5507-0.1720.55930.00870.5621-0.72760.35380.90070.18970.0380.68490.00961.296417.565220.9367134.6937
22.24520.1032-0.87180.2641-0.78872.39780.0213-0.9967-1.19940.1558-0.8-0.7091.3727-1.20310.69331.5307-0.9250.30612.1971-0.04592.09291.191718.5069140.8318
30.66710.24460.06441.574-0.66113.0877-0.1399-0.2024-0.71810.70620.274-0.21290.90850.2092-0.17561.52230.413-0.10470.73340.04371.08829.746420.3763141.3558
43.49433.13611.60874.5215-1.34955.8794-0.09370.4381-0.5233-0.19480.07310.98890.7785-0.8432-0.05150.67690.14570.03790.8158-0.11360.677411.157535.1196119.2004
55.91780.8314-1.23826.35094.07525.5927-0.4162.4855-0.3296-1.13220.0904-0.280.6118-0.31580.38831.585-0.2348-0.02461.508-0.17750.659917.660735.7557103.0408
69.0820.44138.66312.0552-3.28242.05570.10811.20120.2377-1.1410.57010.7659-0.5464-1.0096-0.58831.14760.1457-0.20991.30650.04620.728120.10151.361897.3592
70.49720.4104-0.20430.2604-1.27075.92840.02290.0673-0.0548-0.0783-0.4254-0.1469-0.28062.35090.50070.87020.1206-0.0090.70670.05390.435232.009942.9715177.4593
89.22923.68630.73379.41472.32015.7322-0.0049-1.1702-0.56540.5390.01430.28411.478-1.04620.0510.1878-0.42010.17080.98810.05790.206927.572624.6113255.125
9-0.4619-0.01460.48480.2409-1.53932.68170.2138-0.6242-0.1467-0.31930.217-0.0665-1.2484-0.712-0.28322.08550.4223-0.20460.6112-0.37630.771825.376350.8534205.8901
102.6719-1.2582-0.35722.7763-0.79732.69480.29210.4837-0.0823-1.4104-0.114-0.48231.0001-0.4952-0.20432.0866-0.67230.28711.0159-0.12451.031237.261110.5288224.1199
111.9979-1.2061-0.01484.02950.86090.2465-0.75691.0171-0.1527-0.9562-0.340.85360.0334-0.30480.63752.8631-1.3883-0.13991.3016-0.70421.427619.24592.6394219.8277
122.99150.39160.55532.75190.36173.4387-0.35320.5949-0.8538-0.4310.1398-0.06631.2597-0.54660.17671.405-0.40120.14520.86860.0030.600534.935715.8533245.0019
137.1384-5.4766-3.75929.45331.54642.3462-0.7501-1.303-0.64750.9110.32030.13121.30460.45050.39481.83-0.15250.01221.20580.1210.774731.600716.646269.6187
14-0.4115-0.23190.60.2268-1.31598.5465-0.0575-0.33250.0450.13150.0790.0954-0.5243-1.6968-0.02170.9368-0.02070.02151.17490.13360.57524.030138.984205.5556
15-0.049-0.28890.8555-0.1302-0.54474.5315-0.13150.3101-0.25061.4159-0.05710.5178-0.89381.00290.33460.9236-0.0454-0.51560.49380.25640.33627.44352.2615151.7728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -111 through -68 )A-111 - -68
2X-RAY DIFFRACTION2chain 'A' and (resid -67 through -48 )A-67 - -48
3X-RAY DIFFRACTION3chain 'A' and (resid -47 through 63 )A-47 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 129 )A64 - 129
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 215 )A130 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 244 )A216 - 244
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 349 )A245 - 349
8X-RAY DIFFRACTION8chain 'A' and (resid 350 through 369 )A350 - 369
9X-RAY DIFFRACTION9chain 'A' and (resid 370 through 405 )A370 - 405
10X-RAY DIFFRACTION10chain 'B' and (resid -111 through -1 )B-111 - -1
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 35 )B0 - 35
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 136 )B36 - 136
13X-RAY DIFFRACTION13chain 'B' and (resid 137 through 220 )B137 - 220
14X-RAY DIFFRACTION14chain 'B' and (resid 221 through 353 )B221 - 353
15X-RAY DIFFRACTION15chain 'B' and (resid 354 through 405 )B354 - 405

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