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- PDB-8pk5: INTS13-INTS14 complex with ZNF609 -

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Basic information

Entry
Database: PDB / ID: 8pk5
TitleINTS13-INTS14 complex with ZNF609
Components
  • Integrator complex subunit 13
  • Integrator complex subunit 14,Zinc finger protein 609
KeywordsRNA BINDING PROTEIN / Protein Complex / RNA BINDING / STRUCTURAL PROTEIN
Function / homology
Function and homology information


regulation of myoblast proliferation / regulation of fertilization / snRNA 3'-end processing / snRNA processing / INTAC complex / protein localization to nuclear envelope / positive regulation of neuron migration / regulation of transcription elongation by RNA polymerase II / flagellated sperm motility / integrator complex ...regulation of myoblast proliferation / regulation of fertilization / snRNA 3'-end processing / snRNA processing / INTAC complex / protein localization to nuclear envelope / positive regulation of neuron migration / regulation of transcription elongation by RNA polymerase II / flagellated sperm motility / integrator complex / RNA polymerase II transcription initiation surveillance / centrosome localization / muscle organ development / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle / mitotic spindle organization / promoter-specific chromatin binding / DNA-binding transcription factor binding / nuclear body / cell division / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger protein 608/609 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / von Willebrand factor type A domain / von Willebrand factor, type A ...Zinc finger protein 608/609 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / von Willebrand factor type A domain / von Willebrand factor, type A / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein 609 / Integrator complex subunit 14 / Integrator complex subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSabath, K. / Jonas, S.
Funding support Switzerland, European Union, 6items
OrganizationGrant numberCountry
Swiss National Science Foundation141735 Switzerland
Swiss National Science Foundation182880 Switzerland
Swiss National Science Foundation205601 Switzerland
Other governmentMB22.00064
European Molecular Biology Organization (EMBO)4918European Union
Other governmentPhD scholarship Kevin Sabath
CitationJournal: Mol.Cell / Year: 2024
Title: Basis of gene-specific transcription regulation by the Integrator complex.
Authors: Sabath, K. / Nabih, A. / Arnold, C. / Moussa, R. / Domjan, D. / Zaugg, J.B. / Jonas, S.
History
DepositionJun 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrator complex subunit 13
B: Integrator complex subunit 14,Zinc finger protein 609
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2243
Polymers141,1992
Non-polymers241
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.065, 115.629, 147.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Integrator complex subunit 13 / Cell cycle regulator Mat89Bb homolog / Germ cell tumor 1 / Protein asunder homolog / Sarcoma antigen NY-SAR-95


Mass: 81586.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS13, ASUN, C12orf11, GCT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVM9
#2: Protein Integrator complex subunit 14,Zinc finger protein 609 / von Willebrand factor A domain-containing protein 9


Mass: 59612.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence of INTS14 is C-terminally extended by a short SGS linker followed by the binding site of ZNF609 (25-41),Sequence of INTS14 is C-terminally extended by a short SGS linker followed by ...Details: Sequence of INTS14 is C-terminally extended by a short SGS linker followed by the binding site of ZNF609 (25-41),Sequence of INTS14 is C-terminally extended by a short SGS linker followed by the binding site of ZNF609 (25-41)
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS14, C15orf44, VWA9, ZNF609, KIAA0295 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SY0, UniProt: O15014
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 5.81 Å3/Da / Density % sol: 78.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes-NaOH pH 6.5 0.9 M Na-Malonate 0.25 % (v/v) Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.94 Å / Num. obs: 112597 / % possible obs: 99.92 % / Redundancy: 13.6 % / Biso Wilson estimate: 70.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.57
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 11101 / CC1/2: 0.145

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SN1

6sn1


Resolution: 2.5→47.94 Å / SU ML: 0.4681 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2143 5579 4.96 %
Rwork0.1901 106982 -
obs0.1913 112561 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.66 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7967 0 1 49 8017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848132
X-RAY DIFFRACTIONf_angle_d0.999511051
X-RAY DIFFRACTIONf_chiral_restr0.05151281
X-RAY DIFFRACTIONf_plane_restr0.00621429
X-RAY DIFFRACTIONf_dihedral_angle_d17.25634963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.42911910.43073456X-RAY DIFFRACTION98.92
2.53-2.560.41021860.41653555X-RAY DIFFRACTION99.97
2.56-2.590.39081940.40263508X-RAY DIFFRACTION99.84
2.59-2.620.37541890.38653519X-RAY DIFFRACTION99.95
2.62-2.650.36881860.3643489X-RAY DIFFRACTION99.86
2.65-2.690.361980.36133579X-RAY DIFFRACTION99.97
2.69-2.730.36621930.34863468X-RAY DIFFRACTION99.86
2.73-2.770.3382010.32893522X-RAY DIFFRACTION99.87
2.77-2.810.36151880.31073526X-RAY DIFFRACTION99.95
2.81-2.860.32041890.30833533X-RAY DIFFRACTION99.97
2.86-2.910.30012020.2983514X-RAY DIFFRACTION99.97
2.91-2.960.28781850.28783556X-RAY DIFFRACTION100
2.96-3.020.30751790.2853548X-RAY DIFFRACTION99.97
3.02-3.080.33661770.2773568X-RAY DIFFRACTION100
3.08-3.150.32911660.27753542X-RAY DIFFRACTION100
3.15-3.220.2911680.25283574X-RAY DIFFRACTION99.97
3.22-3.30.25911780.22373568X-RAY DIFFRACTION99.97
3.3-3.390.24411680.21483552X-RAY DIFFRACTION100
3.39-3.490.22711830.19683563X-RAY DIFFRACTION100
3.49-3.60.22041890.1883564X-RAY DIFFRACTION100
3.6-3.730.19931650.17743599X-RAY DIFFRACTION100
3.73-3.880.21371910.16533561X-RAY DIFFRACTION99.97
3.88-4.060.16741790.14993569X-RAY DIFFRACTION100
4.06-4.270.15261600.12973627X-RAY DIFFRACTION100
4.27-4.540.14691800.11543587X-RAY DIFFRACTION100
4.54-4.890.13361940.11933594X-RAY DIFFRACTION100
4.89-5.380.16822060.13673611X-RAY DIFFRACTION100
5.38-6.160.19691960.17263636X-RAY DIFFRACTION100
6.16-7.750.20571870.17723680X-RAY DIFFRACTION100
7.75-47.940.17312110.1623814X-RAY DIFFRACTION99.73
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)
11.90710566646-0.7762370912240.6845552455313.09317162186-0.3268168754152.219011386520.07409816892520.1733560818930.125382497642-0.82403070640.0544150351949-0.318733741432-0.5783106673830.147098800507-0.09501172383581.75817566033-0.1564468144380.3090427207770.629182087601-0.04806111180610.694998378333143.25936856930.945059189485.2657391799
24.60626067782-3.43599868247-0.7611687479276.166098352281.996931477262.38152758989-0.21741609068-0.360273408936-0.273881964572-0.8095333503280.191450456389-0.6989831053410.4671750078410.463165020066-0.05640799673541.00110219332-0.01836677845510.2974307581840.647154808837-0.02470355146250.699609512873151.94225823715.680053635112.24311549
33.205043786631.30927162772-1.658412854422.43665357983-0.8411970390861.84492687883-0.2830218163460.237782396312-0.109544044125-0.553863821150.2182122638880.281254003260.228968934856-0.3207734637730.1364201415720.4541488636880.0443612547013-0.06854918460420.504464491097-0.00284427214270.553803492902123.08708212915.6446297756130.585379565
45.6398635660.77763977959-0.1942968636776.12961306659-2.084704677238.42982905848-0.292829395043-0.580006332284-0.1111694787220.2469242814030.005209501443580.5471275684190.0230218157036-0.3316566809730.2528448457290.2463942592470.01432872845360.1059911254490.689662039218-0.02611499719080.854153889307102.9133568824.80710283777144.930223162
52.347657606722.966297739031.126490657535.379425187611.425483424171.11825059345-0.2975134611980.08022631834740.216116737305-0.7033167352340.253297604218-0.0256134392016-0.2036494554520.2435101068760.03806160659590.468044053719-0.01380779697490.01324721151310.610011863458-0.00357079003190.501013405398145.06474277246.8768989576136.01448566
63.929178320040.840496546909-1.010717397084.56781266686-0.3230068314527.25504625706-0.204009443845-0.0607190839771-0.0301586491547-0.3914681435610.114783495369-0.0623752857403-0.04056675504870.2163317458980.05174410560790.3253242889650.0286033444238-0.07915113539630.4145999267360.02649315247880.469790473587129.13110829620.9518317499129.244628109
71.34927769716-0.201580863784-0.3715666419565.038591969463.324795121264.203138865230.09532780561090.0206672078321-0.257877195262-0.2377664150770.0377025422677-0.1553970201980.4509627373530.0910607524537-0.1262359545211.84117296316-0.01008343303670.2488123624560.739177033071-0.01172540846060.709694635125145.924810766-1.1726232340883.4995476813
86.508922180340.4196744847110.5112289547899.555029533030.6755345037742.006564028150.4235738296830.802899685115-0.836077291563-0.7635524813960.630793217836-0.5603754975160.7936531277951.70698424037-1.206952080291.458055674540.1772040431250.3781346872071.27809567912-0.1554964740171.32492806917155.606816256-0.280960856848107.431330552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 255 )
2X-RAY DIFFRACTION2chain 'A' and (resid 256 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 487 )
4X-RAY DIFFRACTION4chain 'A' and (resid 488 through 564 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 262 )
6X-RAY DIFFRACTION6chain 'B' and (resid 263 through 394 )
7X-RAY DIFFRACTION7chain 'B' and (resid 395 through 513 )
8X-RAY DIFFRACTION8chain 'B' and (resid 525 through 537 )

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