PDB-8ati: Human CtBP2(31-364) in complex with RAI2 peptide(315-322)

ID or keywords:

Entry

Database: PDB / ID: 8ati

Title

Human CtBP2(31-364) in complex with RAI2 peptide(315-322)

Components

Isoform 2 of C-terminal-binding protein 2
Retinoic acid-induced protein 2

Keywords

TRANSCRIPTION / Complex / Tumorigenic / Tumorsuppressor

Function / homology

Function and homology information

animal organ development / embryo development ending in birth or egg hatching / Sensory processing of sound by inner hair cells of the cochlea / nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 Å

Authors

Mullapudi, E. / Goradia, N. / Wilmanns, M.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Human CtBP2(31-364) in complex with RAI2 peptide(315-322)
Authors: Goradia, N. / Mullapudi, E. / Wilmanns, M.

History

Deposition	Aug 23, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 23, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ati.cif.gz	710 KB	Display	PDBx/mmCIF format
PDB format	pdb8ati.ent.gz	454.5 KB	Display	PDB format
PDBx/mmJSON format	8ati.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ati_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8ati_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8ati_validation.xml.gz	51.4 KB	Display
Data in CIF	8ati_validation.cif.gz	70.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/at/8ati ftp://data.pdbj.org/pub/pdb/validation_reports/at/8ati	HTTPS FTP

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Related structure data

Related structure data	2omeS S: Starting model for refinement
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	#167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Isoform 2 of C-terminal-binding protein 2

B: Isoform 2 of C-terminal-binding protein 2

C: Isoform 2 of C-terminal-binding protein 2

D: Isoform 2 of C-terminal-binding protein 2

a: Retinoic acid-induced protein 2

b: Retinoic acid-induced protein 2

c: Retinoic acid-induced protein 2

hetero molecules

238 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Isoform 2 of C-terminal-binding protein 2

a: Retinoic acid-induced protein 2

hetero molecules

A: Isoform 2 of C-terminal-binding protein 2

a: Retinoic acid-induced protein 2

hetero molecules

defined by software
Evidence: electron microscopy
132 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Isoform 2 of C-terminal-binding protein 2

b: Retinoic acid-induced protein 2

hetero molecules

B: Isoform 2 of C-terminal-binding protein 2

b: Retinoic acid-induced protein 2

hetero molecules

defined by software
132 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Isoform 2 of C-terminal-binding protein 2

D: Isoform 2 of C-terminal-binding protein 2

c: Retinoic acid-induced protein 2

hetero molecules

defined by software
106 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.646, 126.646, 357.598
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 33 - 362 / Label seq-ID: 22 - 351

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Isoform 2 of C-terminal-binding protein 2 / CtBP2 Mass: 39230.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP2 / Plasmid: pETM14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P56545-2
#2: Protein	Retinoic acid-induced protein 2 Mass: 25972.781 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5P3
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 6000, 100 mM Tris pH 7.5

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Data collection

Diffraction	Mean temperature: 291 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976243 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976243 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 53115 / % possible obs: 99.9 % / Redundancy: 2 % / B_iso Wilson estimate: 55.96 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.03685 / R_rim(I) all: 0.05211 / Net I/σ(I): 12.87
Reflection shell	Resolution: 2.6→2.693 Å / R_merge(I) obs: 0.4276 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5227 / R_rim(I) all: 0.6048 / % possible all: 100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
SCALEPACK		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OME

2ome

Resolution: 2.6→49.869 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.892 / WR_factor R_free: 0.263 / WR_factor R_work: 0.212 / SU B: 28.027 / SU ML: 0.285 / Average fsc free: 0.9411 / Average fsc work: 0.9605 / Cross valid method: FREE R-VALUE / ESU R: 0.723 / ESU R Free: 0.346 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2833	2633	4.957 %
R_work	0.2283	50481	-
all	0.231	-	-
obs	-	53114	99.91 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 77.187 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.041 Å²	0.021 Å²	0 Å²
2-	-	0.041 Å²	-0 Å²
3-	-	-	-0.133 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→49.869 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10357	0	183	206	10746

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	10719
X-RAY DIFFRACTION	r_angle_refined_deg	1.779	1.648	14527
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.308	5	1323
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.976	5	99
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.53	10	1814
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.81	10	506
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	1668
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7960
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	4252
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	7237
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	383
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.226	0.2	276
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.21	0.2	49
X-RAY DIFFRACTION	r_mcbond_it	3.743	3.705	5316
X-RAY DIFFRACTION	r_mcangle_it	5.737	5.552	6631
X-RAY DIFFRACTION	r_scbond_it	4.651	3.905	5403
X-RAY DIFFRACTION	r_scangle_it	6.919	5.738	7896
X-RAY DIFFRACTION	r_lrange_it	9.85	57.991	15277
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	10134
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.086	0.05	10004
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.102	0.05	9560
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.092	0.05	9914
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.104	0.05	9507
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.106	0.05	9455

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07288	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07288	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08614	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08614	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10191	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10191	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.092	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.092	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.10369	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.10369	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10644	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10644	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.6-2.667	0.377	205	0.311	3627	0.315	3832	0.899	0.93	100	0.293
2.667-2.74	0.328	179	0.311	3582	0.312	3761	0.928	0.936	100	0.287
2.74-2.819	0.331	201	0.26	3454	0.264	3655	0.934	0.954	100	0.233
2.819-2.906	0.32	175	0.274	3349	0.277	3525	0.936	0.949	99.9716	0.242
2.906-3.001	0.323	181	0.251	3262	0.255	3445	0.93	0.956	99.9419	0.222
3.001-3.106	0.289	173	0.239	3154	0.241	3328	0.944	0.962	99.97	0.208
3.106-3.223	0.294	138	0.223	3092	0.226	3230	0.938	0.966	100	0.193
3.223-3.354	0.267	136	0.231	2981	0.233	3117	0.954	0.965	100	0.204
3.354-3.502	0.26	155	0.222	2831	0.224	2986	0.956	0.969	100	0.2
3.502-3.672	0.273	155	0.212	2700	0.215	2855	0.955	0.974	100	0.193
3.672-3.869	0.252	132	0.207	2607	0.209	2742	0.952	0.974	99.8906	0.19
3.869-4.103	0.265	138	0.214	2467	0.216	2606	0.955	0.972	99.9616	0.197
4.103-4.384	0.258	111	0.209	2350	0.211	2463	0.954	0.972	99.9188	0.2
4.384-4.732	0.243	89	0.188	2197	0.19	2287	0.964	0.977	99.9563	0.182
4.732-5.179	0.212	107	0.176	2017	0.177	2132	0.973	0.98	99.6248	0.168
5.179-5.782	0.268	87	0.215	1872	0.218	1960	0.953	0.973	99.949	0.203
5.782-6.662	0.364	87	0.268	1659	0.273	1746	0.925	0.958	100	0.254
6.662-8.123	0.298	75	0.236	1412	0.239	1492	0.947	0.962	99.6649	0.236
8.123-11.338	0.26	60	0.243	1149	0.244	1210	0.953	0.959	99.9174	0.256
11.338-49.869	0.386	49	0.285	719	0.291	774	0.9	0.943	99.2248	0.293

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	1.266	0.3322	0.5733	0.9699	0.6482	1.8798	-0.1701	-0.0741	0.296	0.0014	-0.0725	0.2124	-0.3172	-0.1845	0.2426	0.167	0.0282	-0.0717	0.0342	-0.0188	0.1069	7.7923	14.3683	-22.3232
2	1.3133	0.3705	-0.045	2.2608	0.1325	0.9633	-0.1002	-0.0073	0.0853	0.017	0.0854	-0.4189	-0.0523	0.2813	0.0148	0.0752	-0.0401	-0.0267	0.1012	0.0001	0.1002	41.0039	-4.4302	-23.0888
3	1.492	0.4876	0.559	2.1333	0.7066	0.7496	-0.1833	0.3634	-0.1824	-0.7749	0.5028	0.2447	-0.2121	-0.1457	-0.3195	0.5202	-0.2406	-0.0404	0.5215	0.3374	0.6416	40.5173	39.9973	-46.016
4	1.2551	-0.4182	-0.1073	1.3324	0.3589	0.735	-0.0475	0.154	0.0097	-0.143	-0.0221	0.5099	-0.1282	-0.5365	0.0696	0.6737	0.0805	-0.0686	0.7279	0.128	0.8568	8.571	57.0779	-43.9249
5	9.233	3.6282	2.0358	1.6403	-0.1903	5.6477	-0.0198	-0.1764	0.1685	-0.2265	0.0151	0.0767	0.6607	-0.1845	0.0047	0.4212	-0.0348	0.0297	0.2725	-0.086	0.2505	-3.2772	23.2413	2.4974
6	13.1905	-2.2009	13.5952	7.558	-2.4211	17.3491	-0.0994	0.1124	0.0581	-0.1945	-0.0999	-0.2371	0.3461	0.0442	0.1994	0.2528	-0.0486	0.0893	0.2258	0.0096	0.2887	62.8666	4.899	-38.7755
7	5.4821	3.9602	-0.1365	2.8623	-0.0994	0.0225	-0.0556	-0.1021	0.1689	-0.0821	-0.0589	0.1176	-0.0229	0.0149	0.1144	0.5756	0.0168	-0.1106	0.4417	0.0425	0.4883	56.3166	46.4247	-69.4568

Refinement TLS group

Selection: ALL

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