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- PDB-7z36: Crystal structure of the KAP1 tripartite motif in complex with th... -

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Basic information

Entry
Database: PDB / ID: 7z36
TitleCrystal structure of the KAP1 tripartite motif in complex with the ZNF93 KRAB domain
Components
  • Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of Transcription intermediary factor 1-beta
  • SMARCAD1 CUE1 domain
  • Zinc finger protein 93
KeywordsTRANSCRIPTION / Transcription factor / TRIM family / KRAB domain / CRISPRi
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 ...: / 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 / viral release from host cell by cytolysis / positive regulation of DNA repair / embryo implantation / peptidoglycan catabolic process / SUMOylation of transcription cofactors / promoter-specific chromatin binding / RING-type E3 ubiquitin transferase / euchromatin / positive regulation of protein import into nucleus / HCMV Early Events / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / protein kinase activity / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / 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 / Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C2H2 type / zinc finger / Endolysin T4 type / Zinc finger C2H2 type domain profile. / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Zinc finger C2H2 superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger C2H2 type domain signature. / Ring finger / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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 / Zinc finger protein 93 / Transcription intermediary factor 1-beta / Isoform 2 of Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStoll, G.A. / Modis, Y.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S021604/1 United Kingdom
Wellcome Trust205833/Z/16/Z United Kingdom
Wellcome Trust205833/Z/16/Z United Kingdom
CitationJournal: Embo J. / Year: 2022
Title: Structure and functional mapping of the KRAB-KAP1 repressor complex.
Authors: Stoll, G.A. / Pandiloski, N. / Douse, C.H. / Modis, Y.
History
DepositionMar 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of Transcription intermediary factor 1-beta
B: Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of Transcription intermediary factor 1-beta
C: SMARCAD1 CUE1 domain
D: Zinc finger protein 93
S: SMARCAD1 CUE1 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,60713
Polymers134,0845
Non-polymers5238
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.283, 68.583, 149.111
Angle α, β, γ (deg.)90.000, 114.050, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 19 through 42 or (resid 43...
d_2ens_1(chain "B" and ((resid 19 through 20 and (name N...
d_1ens_2(chain "C" and (resid 2 or (resid 3 through 5...
d_2ens_2(chain "S" and resid 2 through 47)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUVALA1 - 430
d_21ens_1GLULEUB4 - 208
d_22ens_1THRMETB212 - 234
d_23ens_1TYRVALB245 - 446
d_11ens_2SERMETC1 - 46
d_21ens_2SERMETM2 - 47

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.479392694904, 0.772842768189, -0.415808489249), (0.74983083396, 0.114518122707, -0.651643552883), (-0.456000399688, -0.624179185194, -0.634400488851)50.6230074663, 15.2642387383, 88.0558916689
2given(-0.556907058089, 0.624662874851, -0.547403709737), (0.760632652759, 0.118853278584, -0.638209891593), (-0.33360530003, -0.771796729037, -0.541329209298)65.4084101532, 17.6048693625, 72.7933603801

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Components

#1: Protein Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of 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: 54755.484 Da / Num. of mol.: 2 / Mutation: KAP1 B-box 1 domain (residues 141-202) deleted
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag followed by TEV protease cleavage site; KAP1 B-box 1 domain (residues 141-202) deleted.,N-terminal hexahistidine tag followed by TEV protease cleavage site; KAP1 ...Details: N-terminal hexahistidine tag followed by TEV protease cleavage site; KAP1 B-box 1 domain (residues 141-202) deleted.,N-terminal hexahistidine tag followed by TEV protease cleavage site; KAP1 B-box 1 domain (residues 141-202) deleted.,N-terminal hexahistidine tag followed by TEV protease cleavage site; KAP1 B-box 1 domain (residues 141-202) deleted.
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM28, KAP1, RNF96, TIF1B / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P00720, UniProt: Q13263, UniProt: Q13263-2, lysozyme, RING-type E3 ubiquitin transferase
#2: Protein SMARCAD1 CUE1 domain


Mass: 8189.081 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag and TEV protease cleavage site
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Protein Zinc finger protein 93 / / Zinc finger protein 505 / Zinc finger protein HTF34


Mass: 8194.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF93, ZNF505 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P35789
#4: Chemical
ChemComp-ZN / ZINC ION


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

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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: 3.32 Å3/Da / Density % sol: 62.93 % / Description: Shards
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 11% (w/v) PEG 5000 MME 5% Tacsimate 0.1 M HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→63.79 Å / Num. obs: 42537 / % possible obs: 97.26 % / Redundancy: 2.8 % / Biso Wilson estimate: 60.12 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.07466 / Rpim(I) all: 0.05181 / Net I/σ(I): 20.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5035 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 4206 / CC1/2: 0.702 / Rpim(I) all: 0.3428 / % possible all: 97.29

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Processing

Software
NameVersionClassification
xia23.4.devdata reduction
PHENIX1.20.1_4487refinement
DIALS3.dev.431-gf865f6176data scaling
Coot0.8.9.2model building
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QAJ

6qaj


Resolution: 2.8→63.79 Å / SU ML: 0.3953 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2224 5.23 %Test (R-free) flag value: 0
Rwork0.2267 40265 --
obs0.2291 42489 97.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.52 Å2
Refinement stepCycle: LAST / Resolution: 2.8→63.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7889 0 8 0 7897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01288011
X-RAY DIFFRACTIONf_angle_d1.551210833
X-RAY DIFFRACTIONf_chiral_restr0.06081247
X-RAY DIFFRACTIONf_plane_restr0.01971402
X-RAY DIFFRACTIONf_dihedral_angle_d5.46241091
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS4.53401114096
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.831852055894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.39451450.36642481X-RAY DIFFRACTION97.33
2.86-2.930.38211150.3292500X-RAY DIFFRACTION97.21
2.93-30.32431380.28722520X-RAY DIFFRACTION97.51
3-3.080.311360.27672494X-RAY DIFFRACTION97.34
3.08-3.170.29951260.26922524X-RAY DIFFRACTION97.39
3.17-3.270.30921520.27672504X-RAY DIFFRACTION97.25
3.27-3.390.35171340.27772487X-RAY DIFFRACTION97.29
3.39-3.530.33141300.2692472X-RAY DIFFRACTION96.26
3.53-3.690.281490.22542461X-RAY DIFFRACTION96.03
3.69-3.880.24811500.21092493X-RAY DIFFRACTION96.81
3.88-4.130.28291430.20832523X-RAY DIFFRACTION98.27
4.13-4.440.25251580.19012531X-RAY DIFFRACTION98.5
4.44-4.890.23571370.18092566X-RAY DIFFRACTION98.36
4.89-5.60.28351450.20362576X-RAY DIFFRACTION98.52
5.6-7.050.26221320.24572558X-RAY DIFFRACTION97.75
7.05-630.21451340.192575X-RAY DIFFRACTION94.79
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)
10.01537240294270.0239472563863-0.009649555759760.0200379690929-0.02650374309860.024792003959-0.009015903241860.06657003290020.041346300210.10783466572-0.01237038898020.0685411647208-0.02681733392650.0351282823627-4.09087329211E-90.1963959716390.0113907076610.01517248426310.08826909867430.0154095765160.166505175618-12.541398568-14.145513188626.3956389635
20.004216253898380.001397425041150.002636005451518.84740900576E-6-0.00345434586894-0.00278181510401-0.0356232511972-0.01843789749520.0003741759173070.00357111976218-0.01739395744380.040719250418-0.0186857625101-0.01084379113472.82682833878E-90.339030760340.00953403077017-0.01982701471890.4497123423740.08222046004350.515097365519-36.4103420179-0.1692355473822.14880628103
30.001980332363970.103969905158-0.00647989811267-0.0417607416684-0.09537168293140.0157464487874-0.04423677944530.0126866062541-0.006172587288310.02425829080440.0096375236232-0.01628581973880.01141138414510.01481464276018.15893601071E-90.1976604126980.0489307648501-0.03400169521940.217733686844-0.04151996936620.1329915686130.83561178763.3214793822550.7783189283
49.11841535082E-50.0148469135797-0.004091279641480.0270228069834-0.02638794451340.02744382468240.004510829656970.07704016885410.0110667925496-0.09069300246290.114535834954-0.008458045531170.188702315952-0.123491257767-6.87244449825E-100.145785737315-0.04909900959510.01137262132330.1729587767650.05463267656680.16395688237941.7022443141-14.939150256889.8605908762
5-0.02297465851110.1600951721460.0743137601966-0.103960261555-0.115696986223-0.02713972777240.08252423370280.01542684771710.0613354547886-0.04749680555320.0811483775534-0.148903312938-0.0449540863890.0173572203174-1.37901668854E-8-0.04972402363340.137407456676-0.3297457435640.21749546875-0.0560132294475-0.37218645951228.62584715294.1425411158854.3514058716
6-0.0001826009993470.000564751216034-0.00191837062416-0.0003825420843440.001419681693123.74848402682E-5-0.008762448800460.003519263355190.003866577465950.00277457576269-0.0120057719584-0.0022962672036-3.68231839143E-50.005608030600721.12448634953E-70.234415312394-0.01864539790250.04925813371880.26655019801-0.0631840022930.20698986417767.18635790015.2170934207782.9092070487
70.000834982648585-0.0005373075094890.0002266869684090.000265969515085-0.0002311388505660.000159744325151-0.0029086132902-5.10436502239E-50.0002417772691770.00106257745827-0.002610361563650.0004942644277290.005049319471560.00152069700466-4.20418356276E-60.3618530462822.40076876043E-50.04454687686060.341829755151-0.002989243302970.35630414651463.7799818225-8.1199015788679.292047279
80.0003034252190730.000117758290736-0.000538831033523-5.81187307457E-5-0.0001593307482010.0002813311888780.00464160516878-0.001967890699850.00190703327363-0.003644011600530.0037467228779-0.00471433709543-0.01126591842640.004922950691021.15169186563E-60.361074706979-0.02155464194520.03462205692080.395994925010.006132285859470.38177375176668.97084928541.259917775374.5366135012
90.0002809673047377.85293590651E-5-0.0002684080399110.001563541491270.0009705890135440.0003988890694410.006645340436260.0050177221631-0.0093188589087-6.75614072129E-50.008218919282037.91938622137E-50.003803917150146.70613163625E-5-5.99535177882E-60.197911101746-0.00743135505680.009343804994010.198002851679-0.006321088532590.1796698148960.001181368-0.45784669568472.071149672
100.000264239824236-0.001516945767630.000915463992757-0.000457583388080.000655041793866-0.000151815151082-0.0001709670144660.0003634515087220.0034581906050.00491190421427-0.002404581989440.002065869973290.000644656181405-0.001794419336971.8182463305E-60.7648687909090.038897124484-0.00566253590.833529834814-0.001563296711610.7882272422724.74841989432.3986365993454.2837748517
110.000362348778052-0.0008338646901732.45871894936E-5-0.0007927037119760.0005495059678143.32710436572E-50.00331286919271-0.00104487049949-0.00089864868188-0.001282052538450.004254022405950.001068698786050.00109638421108-0.00301587178004-4.07776566126E-70.619653211535-0.00420579360794-0.03284504858510.645399546451-0.01124201068460.60099454381417.71635442544.3088433198545.2155925393
12-0.0002245436917330.000405704740399-0.0004873323789790.000487424589281-0.0007398974215514.67692267337E-5-0.0071192018104-0.00985969276128-0.001388808709610.01061128702670.0007277830770750.008906293174260.0010928180493-0.0007637361616052.91471056134E-80.5510673872780.00402113629929-0.02115755994250.5427675228470.05230335490780.546725828259-15.277551098915.5511427255.16650054492
13-0.000107980219188-0.0003833218913320.0003006716311880.0002854347880240.000182341261229-0.0001255538492050.001127751193730.002475879603860.00316713937807-0.00348205538715-0.00611345982619-0.00352909459473-0.004540077427090.007523759023643.43363870102E-70.6002065547420.0220225152643-0.01750517119670.5817956407990.01510089152410.61138097903-10.464804074620.043209253610.5898014677
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 194 )AA19 - 1941 - 176
22chain 'A' and (resid 195 through 313 )AA195 - 313177 - 265
33chain 'A' and (resid 314 through 481 )AA314 - 481266 - 433
44chain 'B' and (resid 16 through 267 )BB16 - 2671 - 235
55chain 'B' and (resid 268 through 478 )BB268 - 478236 - 446
66chain 'C' and (resid 2 through 18 )CC2 - 181 - 17
77chain 'C' and (resid 19 through 23 )CC19 - 2318 - 22
88chain 'C' and (resid 24 through 36 )CC24 - 3623 - 35
99chain 'C' and (resid 37 through 47 )CC37 - 4736 - 46
1010chain 'D' and (resid 4 through 22 )DD4 - 221 - 19
1111chain 'D' and (resid 23 through 45 )DD23 - 4520 - 42
1212chain 'S' and (resid 1 through 23 )SM1 - 231 - 23
1313chain 'S' and (resid 24 through 47 )SM24 - 4724 - 47

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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