PDB-8pk5: INTS13-INTS14 complex with ZNF609

ID or keywords:

Entry

Database: PDB / ID: 8pk5

Title

INTS13-INTS14 complex with ZNF609

Components

Integrator complex subunit 13
Integrator complex subunit 14,Zinc finger protein 609

Keywords

RNA 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 / flagellated sperm motility / protein localization to nuclear envelope / integrator complex / positive regulation of neuron migration / regulation of transcription elongation by RNA polymerase II / muscle organ development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Sabath, K. / Jonas, S.

Funding support

Switzerland, European Union, 6items

Organization	Grant number	Country
Swiss National Science Foundation	141735	Switzerland
Swiss National Science Foundation	182880	Switzerland
Swiss National Science Foundation	205601	Switzerland
Other government	MB22.00064
European Molecular Biology Organization (EMBO)	4918	European Union
Other government	PhD scholarship Kevin Sabath

Citation

Journal: 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

Deposition	Jun 25, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8pk5.cif.gz	504.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8pk5_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	8pk5_full_validation.pdf.gz	458 KB	Display
Data in XML	8pk5_validation.xml.gz	36.3 KB	Display
Data in CIF	8pk5_validation.cif.gz	50.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pk/8pk5 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pk5	HTTPS FTP

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Related structure data

Related structure data	8pk6C 6sn1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#87 - Mar 2007 Zinc Fingers similarity (3) #67 - Jul 2005 TATA-Binding Protein similarity (1) #166 - Oct 2013 Proteasome similarity (3) #134 - Feb 2011 Integrin similarity (2) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (4) #122 - Feb 2010 Enhanceosome similarity (3) #257 - May 2021 Fetal Hemoglobin similarity (3) #55 - Jul 2004 DNA Ligase similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#87 - Mar 2007
Zinc Fingers
similarity (3)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#166 - Oct 2013
Proteasome
similarity (3)
#134 - Feb 2011
Integrin
similarity (2)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (4)
#122 - Feb 2010
Enhanceosome
similarity (3)
#257 - May 2021
Fetal Hemoglobin
similarity (3)
#55 - Jul 2004
DNA Ligase
similarity (2)

Deposited unit

A: Integrator complex subunit 13

B: Integrator complex subunit 14,Zinc finger protein 609

hetero molecules

141 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

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 number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
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

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 5.81 Å³/Da / Density % sol: 78.84 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.94 Å / Num. obs: 112597 / % possible obs: 99.92 % / Redundancy: 13.6 % / B_iso Wilson estimate: 70.71 Å² / CC_1/2: 0.999 / Net I/σ(I): 16.57
Reflection shell	Resolution: 2.5→2.59 Å / Num. unique obs: 11101 / CC_1/2: 0.145

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
Coot		model building
XDS		data reduction
PHASER		phasing
XSCALE		data scaling

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2143	5579	4.96 %
R_work	0.1901	106982	-
obs	0.1913	112561	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 96.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→47.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7967	0	1	49	8017

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	8132
X-RAY DIFFRACTION	f_angle_d	0.9995	11051
X-RAY DIFFRACTION	f_chiral_restr	0.0515	1281
X-RAY DIFFRACTION	f_plane_restr	0.0062	1429
X-RAY DIFFRACTION	f_dihedral_angle_d	17.2563	4963

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.53	0.4291	191	0.4307	3456	X-RAY DIFFRACTION	98.92
2.53-2.56	0.4102	186	0.4165	3555	X-RAY DIFFRACTION	99.97
2.56-2.59	0.3908	194	0.4026	3508	X-RAY DIFFRACTION	99.84
2.59-2.62	0.3754	189	0.3865	3519	X-RAY DIFFRACTION	99.95
2.62-2.65	0.3688	186	0.364	3489	X-RAY DIFFRACTION	99.86
2.65-2.69	0.36	198	0.3613	3579	X-RAY DIFFRACTION	99.97
2.69-2.73	0.3662	193	0.3486	3468	X-RAY DIFFRACTION	99.86
2.73-2.77	0.338	201	0.3289	3522	X-RAY DIFFRACTION	99.87
2.77-2.81	0.3615	188	0.3107	3526	X-RAY DIFFRACTION	99.95
2.81-2.86	0.3204	189	0.3083	3533	X-RAY DIFFRACTION	99.97
2.86-2.91	0.3001	202	0.298	3514	X-RAY DIFFRACTION	99.97
2.91-2.96	0.2878	185	0.2878	3556	X-RAY DIFFRACTION	100
2.96-3.02	0.3075	179	0.285	3548	X-RAY DIFFRACTION	99.97
3.02-3.08	0.3366	177	0.277	3568	X-RAY DIFFRACTION	100
3.08-3.15	0.3291	166	0.2775	3542	X-RAY DIFFRACTION	100
3.15-3.22	0.291	168	0.2528	3574	X-RAY DIFFRACTION	99.97
3.22-3.3	0.2591	178	0.2237	3568	X-RAY DIFFRACTION	99.97
3.3-3.39	0.2441	168	0.2148	3552	X-RAY DIFFRACTION	100
3.39-3.49	0.2271	183	0.1968	3563	X-RAY DIFFRACTION	100
3.49-3.6	0.2204	189	0.188	3564	X-RAY DIFFRACTION	100
3.6-3.73	0.1993	165	0.1774	3599	X-RAY DIFFRACTION	100
3.73-3.88	0.2137	191	0.1653	3561	X-RAY DIFFRACTION	99.97
3.88-4.06	0.1674	179	0.1499	3569	X-RAY DIFFRACTION	100
4.06-4.27	0.1526	160	0.1297	3627	X-RAY DIFFRACTION	100
4.27-4.54	0.1469	180	0.1154	3587	X-RAY DIFFRACTION	100
4.54-4.89	0.1336	194	0.1193	3594	X-RAY DIFFRACTION	100
4.89-5.38	0.1682	206	0.1367	3611	X-RAY DIFFRACTION	100
5.38-6.16	0.1969	196	0.1726	3636	X-RAY DIFFRACTION	100
6.16-7.75	0.2057	187	0.1772	3680	X-RAY DIFFRACTION	100
7.75-47.94	0.1731	211	0.162	3814	X-RAY DIFFRACTION	99.73

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.90710566646	-0.776237091224	0.684555245531	3.09317162186	-0.326816875415	2.21901138652	0.0740981689252	0.173356081893	0.125382497642	-0.8240307064	0.0544150351949	-0.318733741432	-0.578310667383	0.147098800507	-0.0950117238358	1.75817566033	-0.156446814438	0.309042720777	0.629182087601	-0.0480611118061	0.694998378333	143.259368569	30.9450591894	85.2657391799
2	4.60626067782	-3.43599868247	-0.761168747927	6.16609835228	1.99693147726	2.38152758989	-0.21741609068	-0.360273408936	-0.273881964572	-0.809533350328	0.191450456389	-0.698983105341	0.467175007841	0.463165020066	-0.0564079967354	1.00110219332	-0.0183667784551	0.297430758184	0.647154808837	-0.0247035514625	0.699609512873	151.942258237	15.680053635	112.24311549
3	3.20504378663	1.30927162772	-1.65841285442	2.43665357983	-0.841197039086	1.84492687883	-0.283021816346	0.237782396312	-0.109544044125	-0.55386382115	0.218212263888	0.28125400326	0.228968934856	-0.320773463773	0.136420141572	0.454148863688	0.0443612547013	-0.0685491846042	0.504464491097	-0.0028442721427	0.553803492902	123.087082129	15.6446297756	130.585379565
4	5.639863566	0.77763977959	-0.194296863677	6.12961306659	-2.08470467723	8.42982905848	-0.292829395043	-0.580006332284	-0.111169478722	0.246924281403	0.00520950144358	0.547127568419	0.0230218157036	-0.331656680973	0.252844845729	0.246394259247	0.0143287284536	0.105991125449	0.689662039218	-0.0261149971908	0.854153889307	102.913356882	4.80710283777	144.930223162
5	2.34765760672	2.96629773903	1.12649065753	5.37942518761	1.42548342417	1.11825059345	-0.297513461198	0.0802263183474	0.216116737305	-0.703316735234	0.253297604218	-0.0256134392016	-0.203649455452	0.243510106876	0.0380616065959	0.468044053719	-0.0138077969749	0.0132472115131	0.610011863458	-0.0035707900319	0.501013405398	145.064742772	46.8768989576	136.01448566
6	3.92917832004	0.840496546909	-1.01071739708	4.56781266686	-0.323006831452	7.25504625706	-0.204009443845	-0.0607190839771	-0.0301586491547	-0.391468143561	0.114783495369	-0.0623752857403	-0.0405667550487	0.216331745898	0.0517441056079	0.325324288965	0.0286033444238	-0.0791511353963	0.414599926736	0.0264931524788	0.469790473587	129.131108296	20.9518317499	129.244628109
7	1.34927769716	-0.201580863784	-0.371566641956	5.03859196946	3.32479512126	4.20313886523	0.0953278056109	0.0206672078321	-0.257877195262	-0.237766415077	0.0377025422677	-0.155397020198	0.450962737353	0.0910607524537	-0.126235954521	1.84117296316	-0.0100834330367	0.248812362456	0.739177033071	-0.0117254084606	0.709694635125	145.924810766	-1.17262323408	83.4995476813
8	6.50892218034	0.419674484711	0.511228954789	9.55502953303	0.675534503774	2.00656402815	0.423573829683	0.802899685115	-0.836077291563	-0.763552481396	0.630793217836	-0.560375497516	0.793653127795	1.70698424037	-1.20695208029	1.45805567454	0.177204043125	0.378134687207	1.27809567912	-0.155496474017	1.32492806917	155.606816256	-0.280960856848	107.431330552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 255 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 256 through 372 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 373 through 487 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 488 through 564 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 262 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 263 through 394 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 395 through 513 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 525 through 537 )

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