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- PDB-8pk6: INTS13 complex with ZNF655 -

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Basic information

Entry
Database: PDB / ID: 8pk6
TitleINTS13 complex with ZNF655
Components
  • Integrator complex subunit 13
  • Zinc finger protein 655
KeywordsDNA BINDING PROTEIN / Protein Complex
Function / homology
Function and homology information


regulation of fertilization / snRNA processing / flagellated sperm motility / protein localization to nuclear envelope / integrator complex / regulation of transcription elongation by RNA polymerase II / Generic Transcription Pathway / centrosome localization / negative regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes ...regulation of fertilization / snRNA processing / flagellated sperm motility / protein localization to nuclear envelope / integrator complex / regulation of transcription elongation by RNA polymerase II / Generic Transcription Pathway / centrosome localization / negative regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle / mitotic spindle organization / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / intracellular membrane-bounded organelle / nucleolus / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / 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 655 / Integrator complex subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsSabath, K. / Jonas, S.
Funding support Switzerland, European Union, Germany, 6items
OrganizationGrant numberCountry
Swiss National Science Foundation141735 Switzerland
Swiss National Science Foundation182880 Switzerland
Swiss National Science Foundation205601 Switzerland
Other governmentMB22.00064 Switzerland
European Molecular Biology Organization (EMBO)4918European Union
Other governmentPh.D. fellowship Kevin Sabath Germany
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

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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: Zinc finger protein 655
C: Integrator complex subunit 13
D: Zinc finger protein 655
E: Integrator complex subunit 13
F: Zinc finger protein 655


Theoretical massNumber of molelcules
Total (without water)93,6476
Polymers93,6476
Non-polymers00
Water00
1
A: Integrator complex subunit 13
B: Zinc finger protein 655


Theoretical massNumber of molelcules
Total (without water)31,2162
Polymers31,2162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-14 kcal/mol
Surface area12230 Å2
2
C: Integrator complex subunit 13
D: Zinc finger protein 655


Theoretical massNumber of molelcules
Total (without water)31,2162
Polymers31,2162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-13 kcal/mol
Surface area13130 Å2
3
E: Integrator complex subunit 13
F: Zinc finger protein 655


Theoretical massNumber of molelcules
Total (without water)31,2162
Polymers31,2162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-16 kcal/mol
Surface area12780 Å2
Unit cell
Length a, b, c (Å)126.997, 188.103, 52.757
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

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
11LYSLYSSERSER(chain 'A' and ((resid 2 through 3 and (name N...AA2 - 78 - 13
12LYSLYSTYRTYR(chain 'A' and ((resid 2 through 3 and (name N...AA9 - 1915 - 25
13SERSERSERSER(chain 'A' and ((resid 2 through 3 and (name N...AA30 - 3936 - 45
14GLUGLUCYSCYS(chain 'A' and ((resid 2 through 3 and (name N...AA41 - 4347 - 49
178ILEILEILEILE(chain 'A' and ((resid 2 through 3 and (name N...AA4551
15ASPASPPROPRO(chain 'A' and ((resid 2 through 3 and (name N...AA48 - 5154 - 57
16LYSLYSTHRTHR(chain 'A' and ((resid 2 through 3 and (name N...AA53 - 7259 - 78
17ASPASPALAALA(chain 'A' and ((resid 2 through 3 and (name N...AA75 - 9581 - 101
18GLUGLUCYSCYS(chain 'A' and ((resid 2 through 3 and (name N...AA98 - 99104 - 105
19SERSERGLUGLU(chain 'A' and ((resid 2 through 3 and (name N...AA101 - 122107 - 128
110THRTHRLEULEU(chain 'A' and ((resid 2 through 3 and (name N...AA125 - 127131 - 133
111GLUGLUGLUGLU(chain 'A' and ((resid 2 through 3 and (name N...AA129135
112GLYGLYVALVAL(chain 'A' and ((resid 2 through 3 and (name N...AA135 - 152141 - 158
113METMETHISHIS(chain 'A' and ((resid 2 through 3 and (name N...AA154 - 164160 - 170
114ASNASNASNASN(chain 'A' and ((resid 2 through 3 and (name N...AA167173
115LEULEULEULEU(chain 'A' and ((resid 2 through 3 and (name N...AA169175
116ALAALAASNASN(chain 'A' and ((resid 2 through 3 and (name N...AA171 - 172177 - 178
117HISHISGLNGLN(chain 'A' and ((resid 2 through 3 and (name N...AA175 - 178181 - 184
118CYSCYSPROPRO(chain 'A' and ((resid 2 through 3 and (name N...AA182 - 191188 - 197
119VALVALASPASP(chain 'A' and ((resid 2 through 3 and (name N...AA198 - 200204 - 206
120SERSERSERSER(chain 'A' and ((resid 2 through 3 and (name N...AA202208
121LYSLYSLYSLYS(chain 'A' and ((resid 2 through 3 and (name N...AA204210
122LEULEUALAALA(chain 'A' and ((resid 2 through 3 and (name N...AA206 - 219212 - 225
123LEULEULYSLYS(chain 'A' and ((resid 2 through 3 and (name N...AA223 - 226229 - 232
124ASNASNGLNGLN(chain 'A' and ((resid 2 through 3 and (name N...AA228 - 232234 - 238
125HISHISHISHIS(chain 'A' and ((resid 2 through 3 and (name N...AA234240
226LYSLYSSERSER(chain 'C' and (resid 2 through 7 or resid 9...CC2 - 78 - 13
227LYSLYSTYRTYR(chain 'C' and (resid 2 through 7 or resid 9...CC9 - 1915 - 25
228SERSERSERSER(chain 'C' and (resid 2 through 7 or resid 9...CC30 - 3936 - 45
229GLUGLUCYSCYS(chain 'C' and (resid 2 through 7 or resid 9...CC41 - 4347 - 49
230ILEILEILEILE(chain 'C' and (resid 2 through 7 or resid 9...CC4551
231ASPASPPROPRO(chain 'C' and (resid 2 through 7 or resid 9...CC48 - 5154 - 57
232LYSLYSTHRTHR(chain 'C' and (resid 2 through 7 or resid 9...CC53 - 7259 - 78
233ASPASPALAALA(chain 'C' and (resid 2 through 7 or resid 9...CC75 - 9581 - 101
234GLUGLUCYSCYS(chain 'C' and (resid 2 through 7 or resid 9...CC98 - 99104 - 105
235SERSERGLUGLU(chain 'C' and (resid 2 through 7 or resid 9...CC101 - 122107 - 128
236THRTHRLEULEU(chain 'C' and (resid 2 through 7 or resid 9...CC125 - 127131 - 133
237GLUGLUGLUGLU(chain 'C' and (resid 2 through 7 or resid 9...CC129135
238GLYGLYVALVAL(chain 'C' and (resid 2 through 7 or resid 9...CC135 - 152141 - 158
239METMETHISHIS(chain 'C' and (resid 2 through 7 or resid 9...CC154 - 164160 - 170
240ASNASNASNASN(chain 'C' and (resid 2 through 7 or resid 9...CC167173
241LEULEULEULEU(chain 'C' and (resid 2 through 7 or resid 9...CC169175
242ALAALAASNASN(chain 'C' and (resid 2 through 7 or resid 9...CC171 - 172177 - 178
243HISHISGLNGLN(chain 'C' and (resid 2 through 7 or resid 9...CC175 - 178181 - 184
244CYSCYSPROPRO(chain 'C' and (resid 2 through 7 or resid 9...CC182 - 191188 - 197
245VALVALASPASP(chain 'C' and (resid 2 through 7 or resid 9...CC198 - 200204 - 206
246SERSERSERSER(chain 'C' and (resid 2 through 7 or resid 9...CC202208
247LYSLYSLYSLYS(chain 'C' and (resid 2 through 7 or resid 9...CC204210
248LEULEUALAALA(chain 'C' and (resid 2 through 7 or resid 9...CC206 - 219212 - 225
249LEULEULYSLYS(chain 'C' and (resid 2 through 7 or resid 9...CC223 - 226229 - 232
250ASNASNGLNGLN(chain 'C' and (resid 2 through 7 or resid 9...CC228 - 232234 - 238
251HISHISHISHIS(chain 'C' and (resid 2 through 7 or resid 9...CC234240
352LYSLYSSERSER(chain 'E' and (resid 2 through 7 or resid 9...EE2 - 78 - 13
353LYSLYSTYRTYR(chain 'E' and (resid 2 through 7 or resid 9...EE9 - 1915 - 25
354SERSERSERSER(chain 'E' and (resid 2 through 7 or resid 9...EE30 - 3936 - 45
355GLUGLUCYSCYS(chain 'E' and (resid 2 through 7 or resid 9...EE41 - 4347 - 49
356ILEILEILEILE(chain 'E' and (resid 2 through 7 or resid 9...EE4551
357ASPASPPROPRO(chain 'E' and (resid 2 through 7 or resid 9...EE48 - 5154 - 57
358LYSLYSTHRTHR(chain 'E' and (resid 2 through 7 or resid 9...EE53 - 7259 - 78
359ASPASPALAALA(chain 'E' and (resid 2 through 7 or resid 9...EE75 - 9581 - 101
360GLUGLUCYSCYS(chain 'E' and (resid 2 through 7 or resid 9...EE98 - 99104 - 105
361SERSERGLUGLU(chain 'E' and (resid 2 through 7 or resid 9...EE101 - 122107 - 128
362THRTHRLEULEU(chain 'E' and (resid 2 through 7 or resid 9...EE125 - 127131 - 133
363GLUGLUGLUGLU(chain 'E' and (resid 2 through 7 or resid 9...EE129135
364GLYGLYVALVAL(chain 'E' and (resid 2 through 7 or resid 9...EE135 - 152141 - 158
365METMETHISHIS(chain 'E' and (resid 2 through 7 or resid 9...EE154 - 164160 - 170
366ASNASNASNASN(chain 'E' and (resid 2 through 7 or resid 9...EE167173
367LEULEULEULEU(chain 'E' and (resid 2 through 7 or resid 9...EE169175
368ALAALAASNASN(chain 'E' and (resid 2 through 7 or resid 9...EE171 - 172177 - 178
369HISHISGLNGLN(chain 'E' and (resid 2 through 7 or resid 9...EE175 - 178181 - 184
370CYSCYSPROPRO(chain 'E' and (resid 2 through 7 or resid 9...EE182 - 191188 - 197
371VALVALASPASP(chain 'E' and (resid 2 through 7 or resid 9...EE198 - 200204 - 206
372SERSERSERSER(chain 'E' and (resid 2 through 7 or resid 9...EE202208
373LYSLYSLYSLYS(chain 'E' and (resid 2 through 7 or resid 9...EE204210
374LEULEUALAALA(chain 'E' and (resid 2 through 7 or resid 9...EE206 - 219212 - 225
375LEULEULYSLYS(chain 'E' and (resid 2 through 7 or resid 9...EE223 - 226229 - 232
376ASNASNGLNGLN(chain 'E' and (resid 2 through 7 or resid 9...EE228 - 232234 - 238
377HISHISHISHIS(chain 'E' and (resid 2 through 7 or resid 9...EE234240

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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: 27388.385 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS13, ASUN, C12orf11, GCT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NVM9
#2: Protein/peptide Zinc finger protein 655 / Vav-interacting Krueppel-like protein


Mass: 3827.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF655, VIK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N720

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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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.0, 100 mM MgCl2 and 8% (w/v) polyethylene glycol 6,000

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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: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.21→48.72 Å / Num. obs: 21358 / % possible obs: 99.54 % / Redundancy: 13.4 % / Biso Wilson estimate: 132.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.75
Reflection shellResolution: 3.22→3.33 Å / Num. unique obs: 2085 / CC1/2: 0.447

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→48.72 Å / SU ML: 0.6116 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 49.0108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3329 1095 5.14 %
Rwork0.2989 20189 -
obs0.3007 21284 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 192.71 Å2
Refinement stepCycle: LAST / Resolution: 3.21→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 0 0 5874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045980
X-RAY DIFFRACTIONf_angle_d0.78918104
X-RAY DIFFRACTIONf_chiral_restr0.0478945
X-RAY DIFFRACTIONf_plane_restr0.00591043
X-RAY DIFFRACTIONf_dihedral_angle_d17.08743634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.360.56071250.51852454X-RAY DIFFRACTION98.17
3.36-3.540.52571520.45342461X-RAY DIFFRACTION99.58
3.54-3.760.44081420.41732480X-RAY DIFFRACTION99.62
3.76-4.050.48271320.37772500X-RAY DIFFRACTION99.77
4.05-4.460.41781300.30442508X-RAY DIFFRACTION99.96
4.46-5.10.30061480.26752495X-RAY DIFFRACTION99.62
5.1-6.430.36061280.3432575X-RAY DIFFRACTION99.78
6.43-48.720.24851380.23452716X-RAY DIFFRACTION99.93
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)
16.252655640341.672434126531.523827475424.94955904588-0.3995131964214.03801167251-0.5352538846870.5066364521160.71736006217-0.0927441554874-0.09783676692010.401277977687-0.271769618866-0.0193262448399-0.2179546525880.908472999409-0.287130872020.04868863285540.8872230588620.2469714779750.8736113089755.8501107989526.97164800848.50835424988
23.17522620266-0.218040193738-1.445259514444.653614339880.7449372068123.24958418455-0.687461591166-0.489698422539-0.137731932877-0.9117589209880.641699615730.9332960329980.321959163851-0.181589021194-1.113710158730.545556553907-0.797483090571-0.2309917464571.258283279740.3085056342170.749931786934-7.1114056311713.034522078713.3032225557
34.368673355661.12640798278-1.718373584187.01317601779-2.32144164515.30384404828-0.0119286444697-0.0528059849888-0.6372971752750.862494105366-0.556910318196-0.7962849264440.6876993261980.6991211258150.1490505995312.312103366950.16293443815-0.3236844693961.105443432450.2304515922611.3160146431324.79263944862.3445799518321.0521178485
44.19809996051.21177103735-2.14443316523.73843791333-1.918277559271.754287193510.702194542101-1.27950198447-1.521509751510.456629401853-0.43960283696-3.007770537661.2910726420.3989954598390.1547225175561.05930535691-0.273473334341-0.5588359698291.80064306049-0.3124504448722.4047597085537.025522876717.22743180526.6602528317
51.11382453102-0.907282924606-0.2315339490912.815230119211.802017226495.32381096940.3496979794030.02663813472760.4004480067470.155936891932-0.7310836854431.108033771150.8273496807860.2866184063260.0009148503500211.91976124309-0.5882858814540.4412998459561.18027547187-0.01651355376571.8518626879525.769540128755.5141554438-5.83922212602
62.70732001020.00204454572641-0.3898631363522.8633919053-2.007156992181.46967733637-0.191375039479-0.890767998360.41417919890.0904456623118-0.985375189372-1.576250641760.3012837092970.481589415222-2.061933265640.304808534067-0.1649074039640.1210493268471.361528688690.3012241269251.6898956879334.168337456873.2025912599-9.37701249053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -1 through 236)
2X-RAY DIFFRACTION2(chain 'B' and resid 93 through 115)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 236)
4X-RAY DIFFRACTION4(chain 'D' and resid 95 through 115)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 236)
6X-RAY DIFFRACTION6(chain 'F' and resid 93 through 117)

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