PDB-8ydd: Crystal structure of Nanog(R100A) in complex with Wdr5

ID or keywords:

Entry

Database: PDB / ID: 8ydd

Title

Crystal structure of Nanog(R100A) in complex with Wdr5

Components

Homeobox protein NANOG
WD repeat-containing protein 5

Keywords

NUCLEAR PROTEIN / transcription factor / protein-protein interaction

Function / homology

Function and homology information

negative regulation of endodermal cell fate specification / negative regulation of cell fate commitment / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / Formation of WDR5-containing histone-modifying complexes / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / mesodermal cell fate commitment / cellular response to erythropoietin / multidimensional cell growth / cell dedifferentiation / endodermal cell fate specification ...negative regulation of endodermal cell fate specification / negative regulation of cell fate commitment / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / Formation of WDR5-containing histone-modifying complexes / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / mesodermal cell fate commitment / cellular response to erythropoietin / multidimensional cell growth / cell dedifferentiation / endodermal cell fate specification / regulation of stem cell division / cellular response to rapamycin / HATs acetylate histones / gonad development / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / tissue regeneration / Neddylation / embryonic pattern specification / MLL3/4 complex / stem cell division / negative regulation of stem cell differentiation / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / stem cell population maintenance / transcription factor binding / regulation of cell division / regulation of embryonic development / MLL1 complex / somatic stem cell population maintenance / histone acetyltransferase complex / negative regulation of BMP signaling pathway / BMP signaling pathway / response to retinoic acid / : / positive regulation of gluconeogenesis / positive regulation of mitotic cell cycle / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / : / stem cell differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / mitotic spindle / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Wang, D. / Shi, X. / Zhao, L. / Wu, B. / Chen, Y.

Funding support

China, 4items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	31670748	China
National Natural Science Foundation of China (NSFC)	31970576	China
National Natural Science Foundation of China (NSFC)	32071195	China
National Natural Science Foundation of China (NSFC)	31900934	China

Citation

Journal: To Be Published
Title: Crystal structure of Nanog(R100A) in complex with Wdr5
Authors: Wang, D. / Shi, X. / Zhao, L. / Wu, B. / Chen, Y. / Li, Y.

History

Deposition	Feb 20, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ydd.cif.gz	408.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8ydd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yd/8ydd ftp://data.pdbj.org/pub/pdb/validation_reports/yd/8ydd	HTTPS FTP

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Related structure data

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	#112 - Apr 2009 Oct and Sox Transcription Factors similarity (6) #87 - Mar 2007 Zinc Fingers similarity (1) #166 - Oct 2013 Proteasome similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: WD repeat-containing protein 5

B: WD repeat-containing protein 5

C: WD repeat-containing protein 5

D: Homeobox protein NANOG

E: Homeobox protein NANOG

118 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	85.667, 87.604, 96.874
Angle α, β, γ (deg.)	90.00, 91.81, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein / WD repeat-containing protein BIG-3 Mass: 34390.992 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wdr5, Big, Big3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61965
#2: Protein	Homeobox protein NANOG / ES cell-associated protein 4 / Early embryo specific expression NK-type homeobox protein / Homeobox ...ES cell-associated protein 4 / Early embryo specific expression NK-type homeobox protein / Homeobox transcription factor Nanog Mass: 7443.760 Da / Num. of mol.: 2 / Mutation: R100A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nanog, Ecat4, Enk / Production host: Escherichia coli (E. coli) / References: UniProt: Q80Z64
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 3.09 Å³/Da / Density % sol: 60.18 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2017

Radiation

Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.5→50 Å / Num. obs: 49782 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.803 / Net I/σ(I): 2.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.5-2.54	6.9	0.65	2463	0.803	0.944	0.266	0.703	0.469	99.9
2.54-2.59	6.9	0.57	2482	0.853	0.96	0.233	0.616	0.473	100
2.59-2.64	6.8	0.58	2466	0.838	0.955	0.24	0.629	0.47	100
2.64-2.69	6.8	0.493	2472	0.874	0.966	0.204	0.534	0.486	100
2.69-2.75	6.6	0.448	2468	0.893	0.971	0.188	0.486	0.48	99.9
2.75-2.82	6.2	0.398	2467	0.902	0.974	0.174	0.435	0.477	100
2.82-2.89	6.6	0.378	2483	0.927	0.981	0.157	0.41	0.484	100
2.89-2.96	7.1	0.346	2503	0.946	0.986	0.139	0.373	0.476	99.9
2.96-3.05	7.1	0.298	2486	0.956	0.989	0.12	0.321	0.485	100
3.05-3.15	7	0.252	2461	0.966	0.991	0.102	0.273	0.485	100
3.15-3.26	7	0.216	2492	0.976	0.994	0.087	0.233	0.512	99.9
3.26-3.39	6.9	0.173	2474	0.982	0.995	0.07	0.187	0.527	100
3.39-3.55	6.7	0.15	2496	0.981	0.995	0.062	0.163	0.567	99.9
3.55-3.73	6.2	0.127	2509	0.986	0.996	0.055	0.138	0.575	99.8
3.73-3.97	7.2	0.121	2484	0.99	0.998	0.048	0.13	0.581	100
3.97-4.27	7.2	0.101	2484	0.992	0.998	0.04	0.109	0.606	99.9
4.27-4.7	7	0.09	2502	0.993	0.998	0.036	0.097	0.606	99.9
4.7-5.38	6.4	0.082	2515	0.994	0.999	0.034	0.089	0.518	99.8
5.38-6.78	6.9	0.097	2504	0.993	0.998	0.04	0.105	0.443	99.7
6.78-50	6.6	0.074	2571	0.996	0.999	0.031	0.081	0.569	99.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→37.57 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2214	1991	4.04 %
R_work	0.1736	-	-
obs	0.1755	49282	98.63 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→37.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7985	0	0	469	8454

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8206
X-RAY DIFFRACTION	f_angle_d	0.973	11125
X-RAY DIFFRACTION	f_dihedral_angle_d	7.229	1072
X-RAY DIFFRACTION	f_chiral_restr	0.058	1251
X-RAY DIFFRACTION	f_plane_restr	0.007	1381

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 (%)
2.5-2.56	0.275	146	0.2106	3148	X-RAY DIFFRACTION	94
2.56-2.63	0.2718	133	0.2115	3349	X-RAY DIFFRACTION	98
2.63-2.7	0.2811	142	0.2011	3348	X-RAY DIFFRACTION	98
2.7-2.79	0.2369	142	0.1957	3354	X-RAY DIFFRACTION	99
2.79-2.89	0.2668	138	0.2033	3372	X-RAY DIFFRACTION	99
2.89-3.01	0.2519	140	0.1955	3395	X-RAY DIFFRACTION	99
3.01-3.14	0.2445	140	0.1864	3408	X-RAY DIFFRACTION	99
3.14-3.31	0.2358	144	0.1783	3374	X-RAY DIFFRACTION	99
3.31-3.52	0.2397	143	0.1655	3406	X-RAY DIFFRACTION	100
3.52-3.79	0.169	144	0.1539	3395	X-RAY DIFFRACTION	99
3.79-4.17	0.1999	143	0.1487	3429	X-RAY DIFFRACTION	100
4.17-4.77	0.1843	147	0.1376	3421	X-RAY DIFFRACTION	100
4.77-6.01	0.1924	136	0.1619	3438	X-RAY DIFFRACTION	99
6.01-37.57	0.2072	153	0.1898	3454	X-RAY DIFFRACTION	98

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	1.3667	-0.3313	0.773	1.2004	0.0556	0.98	0.1813	-0.0498	-0.1961	0.2304	-0.0816	0.2526	0.1898	-0.0806	-0.0697	0.179	-0.03	-0.0013	0.1415	0.0177	0.2003	-25.726	5.207	-26.826
2	1.1684	0.0118	-0.2165	0.7479	-0.2008	1.3144	0.0214	0.1555	0.0154	-0.1041	0.0843	-0.1052	0.1079	0.0609	-0.1228	0.1793	0.0034	-0.0179	0.1495	-0.0193	0.1789	-32.254	11.375	-40.806
3	0.8545	0.7746	0.0931	1.298	0.3283	1.0647	-0.0156	0.1241	0.0479	-0.1514	0.0536	0.0711	-0.0626	-0.0523	0.0026	0.148	0.0077	-0.0025	0.1762	0.0408	0.2007	-31.515	26.385	-37.38
4	2.277	0.3158	-0.3305	0.5911	-0.2325	0.6112	0.3475	-0.2703	0.4011	0.3789	-0.2577	0.3308	-0.1057	0.107	0.0081	0.2379	-0.0399	0.0439	0.2071	0.0042	0.3063	-26.306	37.328	-30.374
5	0.3686	-0.2495	0.3153	2.3376	0.3085	1.2106	-0.1562	-0.0732	0.2996	0.1833	0.0829	-0.1414	-0.0621	-0.0436	0.0741	0.1888	-0.0019	-0.0086	0.1854	-0.0234	0.2391	-21.688	28.089	-22.48
6	0.2735	-0.1751	0.4627	1.3639	-0.119	0.9458	0.1011	0.2001	-0.0308	0.0991	-0.0679	-0.0069	-0.1928	-0.1878	0.0639	0.2183	0.0215	-0.044	0.1737	0.0158	0.0995	-21.448	17.508	-17.746
7	1.4057	-0.7776	-0.5795	2.3657	1.4107	2.16	-0.1378	-0.267	0.0143	0.4853	0.3827	-0.2684	0.3009	0.437	-0.1293	0.1984	-0.0069	-0.0483	0.1651	0.0037	0.2017	-16.272	16.919	-15.254
8	1.2993	0.4628	0.8647	1.625	0.093	0.5578	0.1025	-0.2528	-0.2188	0.3759	-0.0838	-0.0416	0.2062	0.045	-0.0539	0.2617	-0.0185	-0.0476	0.1259	0.0097	0.1918	-21.993	8.632	-21.812
9	1.2975	-0.1581	0.2867	1.3162	-0.7947	0.8583	0.0917	-0.1835	-0.0011	0.3533	-0.0502	0.0787	-0.0789	0.0054	-0.0603	0.2489	-0.0245	-0.0005	0.131	-0.0346	0.1487	-18.244	-11.257	-20.059
10	1.6538	-0.663	-0.0456	1.4131	-0.7542	0.5818	-0.0826	-0.2178	0.2854	0.0433	-0.0905	-0.1829	0.0636	0.0939	0.2117	0.2282	-0.0027	-0.0222	0.1748	0.0091	0.2195	-11.035	-7.543	-28.393
11	0.6014	0.3228	0.0224	1.5489	-0.1369	0.7943	0.0359	0.0326	-0.0721	-0.0982	-0.0574	-0.119	0.0261	0.1176	0.0017	0.1108	0.0069	0.0127	0.1475	-0.0144	0.1736	-8.302	-26.599	-35.641
12	1.5712	-0.0448	-0.3029	1.9394	-0.095	1.9405	-0.1801	-0.0001	-0.2848	0.1355	0.0435	0.0886	0.2769	0.1197	0.0987	0.1946	-0.0261	0.0319	0.1621	0.0242	0.1748	-18.005	-33.554	-19.862
13	0.9278	0.3689	-0.8351	1.9625	-0.2375	0.9656	0.0443	-0.1572	0.0067	0.218	-0.0193	0.1548	0.0226	-0.0372	0.0152	0.1755	0.0002	-0.0053	0.1288	-0.0235	0.1712	-18.97	-17.949	-15.483
14	1.224	-0.1182	-0.6496	0.6529	0.2606	0.8415	-0.1219	-0.3278	-0.2102	0.3539	0.0473	-0.1385	-0.0738	-0.0932	0.0365	0.2722	0.0185	0.0452	0.3431	-0.0181	0.0636	17.586	7.654	-8.08
15	1.5576	-0.091	-0.2576	1.1641	0.2117	2.7171	-0.0988	-0.1495	-0.1713	0.1449	0.0803	-0.0314	0.0743	0.1809	0.0689	0.1274	-0.0023	0.0257	0.1725	-0.0006	0.1748	26.837	0.103	-22.6
16	1.7494	-0.6814	-0.4729	0.8109	1.3445	3.0748	-0.1291	0.0838	0.1082	-0.2296	0.0286	0.4512	-0.6812	-0.3459	-0.0405	0.2816	-0.0008	0.0077	0.2125	-0.014	0.1508	15.103	7.879	-32.898
17	1.3108	-0.5771	-0.8979	1.791	0.6582	3.3238	0.0935	-0.1278	0.2151	-0.1286	-0.1172	0.1628	-0.7686	-0.4531	0.0038	0.3523	0.0637	0.0037	0.2761	-0.0424	0.197	12.748	15.245	-17.304
18	2.1753	0.6912	0.3639	2.8237	-0.0236	2.0516	-0.195	-0.0223	-0.0515	-0.3659	-0.2732	0.7429	-0.1824	-0.6402	0.2183	0.2427	-0.0009	-0.0251	0.1871	-0.0273	0.188	27.485	3.698	-50.136
19	1.8604	0.7116	-0.3861	1.667	0.8319	1.545	-0.0909	-0.4032	-0.0918	0.1498	-0.0767	0.2469	-0.3112	-0.066	0.1949	0.1579	-0.0106	-0.0564	0.2421	0.0217	0.1911	36.068	7.143	-44.304
20	1.4872	-0.1419	1.062	0.7885	-0.1459	1.5465	-0.241	0.0198	0.0941	0.0166	0.0763	-0.3735	-0.1861	0.6169	0.1764	0.1927	0.0027	0.0211	0.245	0.0259	0.2658	36.703	8.562	-53.685
21	0.5582	-0.2797	0.8493	2.2498	0.2881	1.5276	-0.4895	-0.1543	0.2195	0.0456	0.3799	0.0416	-0.2757	0.593	0.2082	0.2236	0.0057	-0.0956	0.2693	0.0253	0.337	28.376	19.927	-63.166
22	2.3173	0.6732	-0.685	2.5267	0.1622	0.2671	-0.0531	-0.2613	0.2052	-0.1995	0.0383	-0.3146	0.2121	0.1926	0.1343	0.1993	0.0093	0.0303	0.1526	-0.0167	0.2798	-9.356	40.644	-37.706
23	0.6924	1.1249	-0.7381	8.9066	-0.1147	1.0052	-0.3108	0.1725	0.0996	-0.9405	0.2759	0.4472	0.0025	-0.3599	0.1973	0.1299	0.0438	-0.0103	0.2656	-0.0374	0.2322	-15.168	35.29	-49.565
24	5.4768	1.2839	-1.8202	0.6634	-0.1497	0.8331	-0.5624	0.4484	-0.4374	0.2182	0.2517	-0.1215	0.9938	-0.3058	0.2489	0.3567	0.0156	0.0272	0.2713	-0.096	0.4052	-9.399	24.928	-52.141
25	0.9439	-0.2819	-0.3752	0.8419	0.4601	0.8567	0.0535	0.1796	-0.0795	0.0126	0.1204	-0.1386	-0.0138	0.1304	-0.0647	0.1817	0.014	0.0058	0.2092	-0.0028	0.1993	-4.673	33.471	-50.173
26	2.1614	-0.1211	2.1703	3.2961	-2.7518	4.4303	0.3713	0.0704	-0.3244	-0.1914	-0.0122	-0.5463	0.624	0.41	-0.7248	0.2255	0.0161	0.0358	0.2135	-0.0352	0.3115	-13.983	19.712	-37.288

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 31:83 )	A	31 - 83
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 84:126 )	A	84 - 126
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 127:199 )	A	127 - 199
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 200:216 )	A	200 - 216
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 217:263 )	A	217 - 263
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 264:282 )	A	264 - 282
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 283:303 )	A	283 - 303
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 304:334 )	A	304 - 334
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 31:53 )	B	31 - 53
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 54:83 )	B	54 - 83
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 84:210 )	B	84 - 210
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 211:263 )	B	211 - 263
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 264:334 )	B	264 - 334
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 30:64 )	C	30 - 64
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 65:199 )	C	65 - 199
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 200:233 )	C	200 - 233
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 234:334 )	C	234 - 334
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 102:117 )	D	102 - 117
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 118:136 )	D	118 - 136
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 137:149 )	D	137 - 149
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 150:155 )	D	150 - 155
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 96:104 )	E	96 - 104
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 105:117 )	E	105 - 117
24	X-RAY DIFFRACTION	24	( CHAIN E AND RESID 118:122 )	E	118 - 122
25	X-RAY DIFFRACTION	25	( CHAIN E AND RESID 123:148 )	E	123 - 148
26	X-RAY DIFFRACTION	26	( CHAIN E AND RESID 149:155 )	E	149 - 155

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