PDB-7bcy: X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herp...

ID or keywords:

Entry

Database: PDB / ID: 7bcy

Title

X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide

Components

ORF 73
WD repeat-containing protein 5

Keywords

TRANSFERASE / WD repeat-containing protein 5 LANA Histone Methyltransferase H3K4 /

TRANSCRIPTION

Function / homology

Function and homology information

MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex /

ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis /

histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...
Similarity search - Function

Biological species

Homo sapiens (human)

Human herpesvirus 8 type M

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

McVey, C.E. / Kaye, K.M.

Funding support

Portugal,

United States, 5items

Organization	Grant number	Country
Foundation for Science and Technology (FCT)	LISBOA-01-0145-FEDER-007344	Portugal
Foundation for Science and Technology (FCT)	IF/01023/2013/CP1173/CT0003	Portugal
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	CA082036	United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	DE025208	United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	DE024971	United States

Citation

Journal: Nucleic Acids Res. / Year: 2021
Title: MLL1 is regulated by KSHV LANA and is important for virus latency.
Authors: Tan, M. / Li, S. / Juillard, F. / Chitas, R. / Custodio, T.F. / Xue, H. / Szymula, A. / Sun, Q. / Liu, B. / Alvarez, A.L. / Chen, S. / Huang, J. / Simas, J.P. / McVey, C.E. / Kaye, K.M.

History

Deposition	Dec 21, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 15, 2021	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Dec 29, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7bcy.cif.gz	361.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7bcy.ent.gz	292 KB	Display	PDB format
PDBx/mmJSON format	7bcy.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/bc/7bcy ftp://data.pdbj.org/pub/pdb/validation_reports/bc/7bcy	HTTPS FTP

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Related structure data

Related structure data	7bedC 4eryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ear-1 4gm8-3 3psl-1 4gm8-4 3uvl-d 3smr-3 3eg6-d 6ofz-d 6ufx-d 2h6n-2 4ewr-d 7bcy-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: WD repeat-containing protein 5

B: WD repeat-containing protein 5

P: ORF 73

Q: ORF 73

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

1

A: WD repeat-containing protein 5

Q: ORF 73

defined by author&software
Evidence: gel filtration, WDR5-LANA peptide form a binary 1:1 complex
35.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: WD repeat-containing protein 5

P: ORF 73

defined by author&software
35.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.313, 53.171, 65.124
Angle α, β, γ (deg.)	72.579, 89.749, 73.156
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1

#1: Protein	WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein Mass: 34506.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET47b / Details (production host): T7 Kan / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P61964
#2: Protein/peptide	ORF 73 Mass: 1330.568 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: N-terminal acetylation and C-terminal amidation of LANA peptide Source: (synth.) Human herpesvirus 8 type M / References: UniProt: Q76SB0
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 692 / 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	Density Matthews: 1.94 Å³/Da / Density % sol: 36.7 % / Description: Rod-shaped
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350 PH range: 5.5 - 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Oxford cryostream / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2017 / Details: Vertical CRL / Horizontal Eliptical mirror
Radiation	Monochromator: Standard ESRF channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.4996→61.9364 Å / Num. obs: 78054 / % possible obs: 86.35 % / Redundancy: 3.1 % / B_iso Wilson estimate: 13.72 Å² / CC_1/2: 0.993 / R split: 0.069 / R_merge(I) obs: 0.068 / R_pim(I) all: 0.046 / R_rim(I) all: 0.082 / Χ²: 4.3 / Net I/av σ(I): 5.3 / Net I/σ(I): 7.8
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3941 / CC_1/2: 0.816 / R split: 0.381 / R_pim(I) all: 0.258 / R_rim(I) all: 0.461 / Χ²: 0.73 / % possible all: 87.4

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc7_4070	refinement
DIALS	1.10.0-gf2f43cdc6	data reduction
Aimless	0.7.1	data scaling
MOLREP	11.6.04	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ery

4ery

Resolution: 1.5→39 Å / SU ML: 0.1829 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.2669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2268	3891	4.99 %
R_work	0.1932	74131	-
obs	0.1949	78022	86.18 %

Solvent computation

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

Displacement parameters

B_iso mean: 17.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4713	0	0	692	5405

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0105	4860
X-RAY DIFFRACTION	f_angle_d	1.1561	6612
X-RAY DIFFRACTION	f_chiral_restr	0.0708	755
X-RAY DIFFRACTION	f_plane_restr	0.0089	825
X-RAY DIFFRACTION	f_dihedral_angle_d	7.5103	659

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 (%)
1.5-1.52	0.3065	131	0.2514	2704	X-RAY DIFFRACTION	87.12
1.52-1.54	0.3088	139	0.2406	2698	X-RAY DIFFRACTION	87.24
1.54-1.56	0.2517	167	0.2356	2588	X-RAY DIFFRACTION	86.17
1.56-1.58	0.3122	139	0.2292	2578	X-RAY DIFFRACTION	84.3
1.58-1.6	0.3154	123	0.222	2612	X-RAY DIFFRACTION	83.74
1.6-1.63	0.2545	136	0.2212	2480	X-RAY DIFFRACTION	80.94
1.63-1.65	0.2493	119	0.2012	2283	X-RAY DIFFRACTION	73.86
1.65-1.68	0.2539	142	0.1955	2557	X-RAY DIFFRACTION	84.87
1.68-1.71	0.2464	157	0.2019	2792	X-RAY DIFFRACTION	89.28
1.71-1.74	0.2399	139	0.2047	2698	X-RAY DIFFRACTION	89.5
1.74-1.77	0.2969	134	0.2113	2763	X-RAY DIFFRACTION	88.38
1.77-1.81	0.2934	133	0.2168	2680	X-RAY DIFFRACTION	87.41
1.81-1.85	0.256	146	0.2117	2683	X-RAY DIFFRACTION	87.15
1.85-1.89	0.2593	154	0.1968	2553	X-RAY DIFFRACTION	84.86
1.89-1.94	0.2356	129	0.1857	2479	X-RAY DIFFRACTION	80.62
1.94-1.99	0.2181	122	0.1778	2371	X-RAY DIFFRACTION	76.85
1.99-2.05	0.201	138	0.1822	2819	X-RAY DIFFRACTION	91.58
2.05-2.11	0.2477	147	0.1809	2804	X-RAY DIFFRACTION	90.88
2.11-2.19	0.217	149	0.1891	2754	X-RAY DIFFRACTION	90.27
2.19-2.28	0.2206	137	0.1859	2725	X-RAY DIFFRACTION	88.72
2.28-2.38	0.2291	137	0.1847	2679	X-RAY DIFFRACTION	87.1
2.38-2.51	0.2177	130	0.1855	2418	X-RAY DIFFRACTION	78.14
2.51-2.66	0.2303	132	0.1902	2708	X-RAY DIFFRACTION	88.03
2.66-2.87	0.2094	126	0.1881	2852	X-RAY DIFFRACTION	92.83
2.87-3.16	0.2161	156	0.1916	2766	X-RAY DIFFRACTION	90.44
3.16-3.61	0.1995	122	0.1768	2561	X-RAY DIFFRACTION	83.04
3.61-4.55	0.1844	155	0.173	2782	X-RAY DIFFRACTION	90.82
4.55-39	0.2224	152	0.2145	2744	X-RAY DIFFRACTION	89.38

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	0.553041459881	-0.0478517255462	-0.0632358047972	0.394456235485	0.0743705924452	0.450838301336	-0.0347672360758	0.0672005185106	-0.000602469377163	-0.120077319172	0.0344230939594	-0.0892333315328	-0.00313582717187	0.029575311259	0.000180031426624	0.118279632921	-0.0217360150152	0.0213066751619	0.120582508465	-0.00849370928116	0.10433571109	20.5697639929	-5.902035756	-20.0752975902
2	0.743101596622	0.173903149601	-0.0725326350225	0.634924091572	0.0829299305722	0.615099938959	-0.0489410604838	0.0107184223273	0.131163289214	-0.0614605063537	0.0401986926047	0.0155616651423	-0.0769435526497	-0.0579335775547	0.0025097152018	0.103358736357	0.0015900387239	-0.0109222792719	0.106250745076	0.0108634135171	0.11368651462	5.80172759079	3.33307797802	-15.7601409264
3	0.598542688543	-0.357238581661	0.0299724394249	0.689009725449	-0.297164019358	0.200723800235	0.0074438639077	-0.0696259976265	-0.147551755323	-0.0530385745821	0.0668434786096	0.14601867795	0.111366418564	-0.113429934111	-0.0304815789632	0.11009830255	-0.0107566734635	-0.00178134956166	0.144118320873	0.0135960165226	0.132368858104	-0.428161384201	-14.2917142907	-10.7914464644
4	0.429050811842	0.132691789376	-0.163790680977	0.632724514813	0.054150994022	0.495975245071	-0.00790870770877	-0.0449645389593	-0.111632831884	-0.0192439588824	0.0392494929247	-0.0357431023583	0.0830776007158	0.0311014622306	-0.0227700963989	0.141177910694	0.0131577439681	0.00900750421707	0.104618633768	0.0139371315277	0.142789127169	15.9634917915	-22.4468701181	-11.3436913366
5	1.05284291118	-0.0170272909937	0.145135400262	0.723255811414	-0.0502519432161	1.27761838389	-0.0464932702458	0.0383217549529	-0.100076145406	-0.0492459788591	0.0560388698326	-0.0421085683246	0.0470766689058	0.0997040626101	-0.0155167178546	0.150860678959	-0.0115276785555	0.022192571113	0.129062148447	-0.00617113539726	0.114843664296	22.1152502688	-16.0597619231	-17.8902257692
6	0.43219910864	0.191789733831	0.0577696114612	0.410156337259	0.155843137635	0.566028046767	-0.054440826925	-0.0169985553489	0.0813173434477	0.0374514524564	0.0267044057452	-0.0766214130443	-0.053987580784	0.0518522838665	0.00964984051671	0.110773349575	0.0201162164632	-0.0239105111819	0.101418074352	-0.00715098880825	0.123888784355	-0.735546573879	12.1675975178	19.8274901591
7	0.744553182675	-0.0199475394458	0.0524265291606	0.578694023024	0.0928846722158	0.344178428074	-0.0232130125905	-0.0197572530908	-0.0746493485689	0.0460540309326	0.0191039154358	0.0102852465629	0.0337266140972	-0.0207576292855	0.00867947978284	0.0908515098299	0.000554974161689	0.00646942740789	0.0793652369528	0.00240683154334	0.0821986416132	-15.6138198418	0.965267226619	15.7259303691
8	1.89168292544	0.00221424277795	-0.711882328005	1.29686082127	-0.200400432366	0.303361299107	-0.0614855452207	0.127105141325	0.177340078691	0.00341751635233	0.0482287460979	0.1352136768	-0.182868601119	-0.186698981316	0.0109363411069	0.111390689447	0.011641871472	-0.0078281642134	0.120874027985	0.0143905672514	0.138358861368	-21.5389192936	16.582225075	10.7362671727
9	0.589850807574	-0.0633003034562	0.302467184154	0.848964608799	-0.185175346019	0.691778335567	-0.0712473530106	0.0450740234074	0.109888044972	0.0580923992408	0.0446934747823	0.0235956963154	-0.0958757398335	0.033556162901	0.00816734880545	0.124317849209	-0.00635881208812	-0.00944103709411	0.0995701348778	0.0066843592716	0.123612998903	-7.96830701503	20.5931611337	12.7665263109
10	2.57787794383	0.162271824647	-0.821656251958	2.35414783872	0.0921039941843	1.21549455909	0.0297960568178	0.524824800998	-0.087144350618	-0.498121249149	0.0815208341555	0.0624728901483	0.0774266994405	-0.00576847830153	-0.0208043872683	0.207568547375	0.0122645001783	0.00983265670735	0.227125175191	-0.00936840066792	0.139610628437	-8.0550951042	5.40519434084	0.441000985978
11	1.99632953034	0.101789644522	0.835416388107	2.40670776556	0.179649147256	2.16492237592	-0.100586995561	-0.53323375396	-0.0264497706483	0.602184928845	-0.0481418675337	0.121418092664	0.0347033985305	-0.062976161412	-0.0100003775511	0.246566519297	0.000271655660085	0.00853111896912	0.246755172466	-0.011850179003	0.134526346895	15.2938263984	-5.86737562405	-0.878049124921

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 31 through 106 )	A	A	31 - 106	1 - 76
2	2	chain 'A' and (resid 107 through 167 )	A	A	107 - 167	77 - 137
3	3	chain 'A' and (resid 168 through 252 )	A	A	168 - 252	138 - 219
4	4	chain 'A' and (resid 253 through 303 )	A	A	253 - 303	220 - 270
5	5	chain 'A' and (resid 304 through 334 )	A	A	304 - 334	271 - 301
6	6	chain 'B' and (resid 30 through 64 )	B	B	30 - 64	1 - 35
7	7	chain 'B' and (resid 65 through 206 )	B	B	65 - 206	36 - 177
8	8	chain 'B' and (resid 207 through 233 )	B	B	207 - 233	178 - 202
9	9	chain 'B' and (resid 234 through 334 )	B	B	234 - 334	203 - 303
10	10	chain 'P' and (resid 23 through 29 )	P	D	23 - 29	2 - 8
11	11	chain 'Q' and (resid 23 through 29 )	Q	F	23 - 29	2 - 8

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