PDB-6t3x: Crystal structure of the truncated human cytomegalovirus pUL50-pU...

ID or keywords:

Entry

Database: PDB / ID: 6t3x

Title

Crystal structure of the truncated human cytomegalovirus pUL50-pUL53 complex

Components

Nuclear egress protein 2,Nuclear egress protein 1

Keywords

VIRAL PROTEIN / nuclear egress / fusion protein

Function / homology

Function and homology information

viral budding from nuclear membrane / host cell nuclear inner membrane / zinc ion binding / membrane
Similarity search - Function

Biological species

Human cytomegalovirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 Å

Authors

Muller, Y.A.

Funding support

Germany, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: High-resolution crystal structures of two prototypical beta- and gamma-herpesviral nuclear egress complexes unravel the determinants of subfamily specificity.
Authors: Muller, Y.A. / Hage, S. / Alkhashrom, S. / Hollriegl, T. / Weigert, S. / Dolles, S. / Hof, K. / Walzer, S.A. / Egerer-Sieber, C. / Conrad, M. / Holst, S. / Losing, J. / Sonntag, E. / Sticht, ...

History

Deposition	Oct 11, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6t3x.cif.gz	303.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6t3x.ent.gz	207.9 KB	Display	PDB format
PDBx/mmJSON format	6t3x.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6t3x_validation.pdf.gz	432.3 KB	Display	wwPDB validaton report
Full document	6t3x_full_validation.pdf.gz	437.5 KB	Display
Data in XML	6t3x_validation.xml.gz	18.8 KB	Display
Data in CIF	6t3x_validation.cif.gz	27 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t3/6t3x ftp://data.pdbj.org/pub/pdb/validation_reports/t3/6t3x	HTTPS FTP

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Related structure data

Related structure data	6t3zC 5d5nS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ki4-d 6f49-2 4nto-2 3ki2-d 4uow-6 2c8f-3 3ki6-d 1k7a-1 4nt2-d 1ij8-d 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: Nuclear egress protein 2,Nuclear egress protein 1

C: Nuclear egress protein 2,Nuclear egress protein 1

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

1

A: Nuclear egress protein 2,Nuclear egress protein 1

defined by author
Evidence: isothermal titration calorimetry
23.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Nuclear egress protein 2,Nuclear egress protein 1

defined by author
23.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	37.270, 82.570, 63.660
Angle α, β, γ (deg.)	90.000, 95.097, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Nuclear egress protein 2,Nuclear egress protein 1 Mass: 23920.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chain A contains the pUL50 part of the pUL50::pUL53 fusion protein,chain A contains the pUL50 part of the pUL50::pUL53 fusion protein Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: NEC2, UL50, NEC1, UL53 / Production host: Escherichia coli (E. coli) / References: UniProt: P16791, UniProt: P16794
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Nuclear egress protein 2,Nuclear egress protein 1

Mass: 23920.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chain A contains the pUL50 part of the pUL50::pUL53 fusion protein,chain A contains the pUL50 part of the pUL50::pUL53 fusion protein
Source: (gene. exp.)

Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: NEC2, UL50, NEC1, UL53 / Production host:

Escherichia coli (E. coli) / References: UniProt: P16791, UniProt: P16794

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.69 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of pUL50::pUL53 were ...Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of pUL50::pUL53 were obtained at 4 degree C with 20% PEG 4000, 10% propanol, 100 mM HEPES, pH 7.5 as a reservoir solution.

Crystal

Density Matthews: 2.04 Å³/Da / Density % sol: 39.69 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of pUL50::pUL53 were ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 28, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.48→41.29 Å / Num. obs: 63159 / % possible obs: 98.7 % / Redundancy: 4 % / B_iso Wilson estimate: 25.27 Å² / CC_1/2: 0.993 / R_rim(I) all: 0.09 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.48→1.52 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 4515 / CC_1/2: 0.592 / R_rim(I) all: 0.929 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
XSCALE		data scaling
MLPHARE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5d5n

5d5n

Resolution: 1.48→41.28 Å / SU ML: 0.1793 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4145

	R_factor	Num. reflection	% reflection
R_free	0.2249	5121	8.11 %
R_work	0.1918	-	-
obs	0.1944	63120	98.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 47.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.48→41.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3185	0	0	247	3432

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	3301
X-RAY DIFFRACTION	f_angle_d	0.7845	4469
X-RAY DIFFRACTION	f_chiral_restr	0.0655	520
X-RAY DIFFRACTION	f_plane_restr	0.0037	563
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4389	1260

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 (%)
1.48-1.5			0.3119	1950	X-RAY DIFFRACTION	92.02
1.5-1.51	0.2981	669	0.2849	1395	X-RAY DIFFRACTION	97.96
1.51-1.53			0.2647	2097	X-RAY DIFFRACTION	97.9
1.53-1.55			0.2687	2101	X-RAY DIFFRACTION	98.22
1.55-1.57			0.2677	2056	X-RAY DIFFRACTION	98.33
1.57-1.59	0.2902	599	0.2686	1484	X-RAY DIFFRACTION	97.89
1.59-1.62			0.2408	2111	X-RAY DIFFRACTION	98.14
1.62-1.64			0.2537	2081	X-RAY DIFFRACTION	98.49
1.64-1.67	0.2771	515	0.2396	1556	X-RAY DIFFRACTION	98.43
1.67-1.69	0.2558	34	0.2411	2081	X-RAY DIFFRACTION	98.37
1.69-1.72			0.245	2079	X-RAY DIFFRACTION	98.44
1.72-1.75	0.2656	374	0.2351	1722	X-RAY DIFFRACTION	98.73
1.75-1.79	0.2458	132	0.2359	1987	X-RAY DIFFRACTION	98.88
1.79-1.82			0.2297	2111	X-RAY DIFFRACTION	99.11
1.82-1.86	0.2389	459	0.2156	1677	X-RAY DIFFRACTION	98.98
1.86-1.91			0.2093	2067	X-RAY DIFFRACTION	99.04
1.91-1.95			0.2078	2133	X-RAY DIFFRACTION	99.07
1.95-2.01	0.2262	413	0.2046	1683	X-RAY DIFFRACTION	99.1
2.01-2.07			0.2023	2124	X-RAY DIFFRACTION	99.16
2.07-2.13	0.234	311	0.2037	1795	X-RAY DIFFRACTION	99.34
2.13-2.21			0.1982	2126	X-RAY DIFFRACTION	99.39
2.21-2.3	0.2182	285	0.1934	1833	X-RAY DIFFRACTION	99.25
2.3-2.4	0.2331	195	0.1897	1906	X-RAY DIFFRACTION	99.53
2.4-2.53	0.1821	57	0.1923	2120	X-RAY DIFFRACTION	99.63
2.53-2.69	0.2387	231	0.1948	1871	X-RAY DIFFRACTION	99.62
2.69-2.9	0.2617	196	0.2086	1933	X-RAY DIFFRACTION	99.3
2.9-3.19	0.2119	169	0.1972	1954	X-RAY DIFFRACTION	99.3
3.19-3.65	0.2199	131	0.17	2006	X-RAY DIFFRACTION	99.67
3.65-4.59	0.1919	172	0.1521	1972	X-RAY DIFFRACTION	99.26
4.59-41.28	0.2044	179	0.1787	1988	X-RAY DIFFRACTION	98.81

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	2.41132977704	-0.0665146351527	0.477980430592	3.08619325004	-0.701637477664	2.55837981969	0.0232727178791	0.152104180356	-0.241341010574	-0.47534224928	0.0329680815175	0.116213688413	0.255583775294	-0.0651468978357	-0.0231935544304	0.206967457227	0.00131217812239	-0.0111416200202	0.168463301744	-0.0179097463075	0.222349105387	7.244244714	14.006701944	27.456981467
2	2.43886860068	-1.62368895531	0.312227681248	3.44278951616	-0.831770424232	4.67013342291	-0.160985908051	-0.607178079724	-0.0450098846778	0.266665602608	0.221071591836	-0.271594860777	0.226147372773	0.222067148208	0.042388936703	0.27131117092	0.0730844070052	-0.0236333843081	0.275361653981	0.000399888328557	0.267718489562	15.4060780277	15.0959366322	42.3252242637
3	2.07558985792	1.49420982253	1.26970354278	4.35550219639	4.13354526708	4.25702059098	-0.201445712439	-0.591374164825	0.157854151719	0.730241950175	-0.291159011304	0.883267482259	-0.325306407841	-0.427963427446	0.428098082246	0.331994248184	0.0643388228926	0.0418393971684	0.256746298436	-0.0248996692077	0.297284584504	5.30372761076	24.2141642052	43.7255010704
4	4.54230921496	-2.9837252739	2.09492000391	3.7999642929	-1.48251192128	1.65375530614	-0.375254777063	0.0598167054047	0.849967077904	0.383817211145	-0.0204675476344	-0.706007511468	-0.33028544122	0.0760686826723	0.287957013748	0.227020590464	-0.00198883262801	-0.034049365669	0.224172423685	0.00941360947463	0.382901396704	10.2470380194	32.7792156177	33.4989085221
5	0.780473027442	-0.06396122369	0.331288995109	0.806190973674	-1.2392588593	1.9750152412	-0.928204927671	-1.48253485057	0.202927027724	1.51741166665	0.715158537101	1.42671114488	-0.262774668829	-1.24849064675	0.455494021264	0.617101984998	0.184923927467	0.157864082743	0.595522311164	0.0145273474399	0.568123760494	-8.26624992421	35.0483685494	34.6041268662
6	2.18197646741	-1.51259273263	-0.328850351799	2.16458255278	-0.827665630745	2.09849895856	0.240209491693	0.228083890963	-0.4803385672	-0.383479506481	-0.203075123047	0.625194969569	0.862961191467	-0.252836247802	-0.154879169045	0.392405649988	0.0141603575434	-0.0583145465322	0.293949442712	-0.0223198051812	0.38502386951	-3.95989519515	29.39063616	24.0927485203
7	8.89251297115	2.44977556495	5.11737390745	8.20975937266	1.27036419695	3.05438005045	0.0652743456536	0.648321337554	0.416327490441	-0.155509920712	0.134279251744	-0.654584818511	-0.289740416939	0.587422863334	-0.0964963585096	0.273783149443	0.000740274853565	0.0827484534671	0.348166877676	0.0184750698758	0.44404992937	8.30262642581	35.8549715873	26.5839365747
8	5.35267228697	0.299233327722	-0.0685995926726	5.27125163325	-0.748252131793	4.82401825271	0.167318179668	-0.495151000473	0.753226308231	0.344292467466	-0.133863044072	0.222122270015	-0.557258835094	-0.147364594908	-0.0118993730047	0.424669970282	0.107006740489	0.0312753877446	0.39835658458	-0.0899108325525	0.295889104902	-8.25297131517	31.4698456188	8.26519236593
9	4.85915966519	2.45023422628	-2.19862104982	3.58713039793	-2.25373043675	4.7859034538	0.0550622555639	-0.0511175287095	0.344118340095	-0.0557177020173	-0.00107929624521	0.0695871917708	0.0202399059024	0.142661926675	-0.0389918568028	0.390192854742	0.143942416217	0.0198246939461	0.316842318591	0.0174658615494	0.190133674659	-4.90183909973	25.3430268984	-0.361383720302
10	4.69503416601	-3.18167936487	-1.56092294824	7.11120210815	2.50600233084	3.76054788976	-0.0124262716766	0.456796206221	0.338882252559	-0.927693827407	0.151438719516	-0.0875236332527	-0.421207026199	-0.261213819098	-0.173824512641	0.470623977621	0.0539654160191	0.0452820201393	0.384709200898	0.119977421587	0.377950083041	-6.80397934708	29.9164721039	-9.16388127882
11	2.34525323363	1.19170367401	-1.08651857063	3.4678370716	-2.30910035269	3.95731115829	-0.108623984868	0.410967524956	-0.31603660452	-0.849111783332	-0.0173496371912	-0.174692060979	0.724156483645	0.00430813704623	0.0778484321848	0.518555910819	0.112255399313	0.0253653084336	0.378723028455	-0.0635594973822	0.249949928082	-4.19623675432	15.4709810261	-4.7900014253
12	8.56177931921	5.29983483178	6.6956945307	8.10774300261	7.12153971735	8.96162505554	-0.250351391013	1.14183080851	-0.220612268948	-2.20602564992	0.579213983211	1.93056319453	0.595244047858	-1.3698234916	-0.312660351472	0.94727370531	-0.13674015021	-0.259549407162	0.658426469046	0.0278481281359	0.668933666418	-20.0624165792	13.2183495976	2.40674613564
13	7.08997844809	-2.01145015179	-0.0817999857655	4.36000391033	-0.0891322857148	2.107694262	0.399352273359	-0.247609066234	-0.347713284588	0.546585210929	0.0637846677083	0.438249458912	0.0533632085754	0.0544135375072	-0.472461463667	0.389356740605	-0.0397448144258	0.0113694049533	0.317195853497	-0.0248855681071	0.344807896233	-13.8746506246	11.2399495799	12.4663154171
14	6.39486552513	1.49397461226	-5.70802129493	0.617220207076	-0.643146471209	6.87188453694	0.0188493442672	0.0911335727569	-0.510127562813	-1.2100540909	-0.2106112347	-0.671595450731	0.909374407072	0.968652939452	0.239930485651	0.671010369266	0.220805888955	0.0154762767175	0.444168629093	-0.0758102449628	0.454027283254	-4.15784000321	7.21442442922	1.6640412413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid -5 through 93)
2	X-RAY DIFFRACTION	2	(chain 'A' and resid 94 through 116)
3	X-RAY DIFFRACTION	3	(chain 'A' and resid 117 through 122)
4	X-RAY DIFFRACTION	4	(chain 'A' and resid 123 through 170)
5	X-RAY DIFFRACTION	5	(chain 'A' and resid 387 through 395)
6	X-RAY DIFFRACTION	6	(chain 'A' and resid 396 through 407)
7	X-RAY DIFFRACTION	7	(chain 'A' and resid 408 through 422)
8	X-RAY DIFFRACTION	8	(chain 'C' and resid 0 through 45)
9	X-RAY DIFFRACTION	9	(chain 'C' and resid 46 through 84)
10	X-RAY DIFFRACTION	10	(chain 'C' and resid 85 through 103)
11	X-RAY DIFFRACTION	11	(chain 'C' and resid 104 through 170)
12	X-RAY DIFFRACTION	12	(chain 'C' and resid 392 through 401)
13	X-RAY DIFFRACTION	13	(chain 'C' and resid 402 through 412)
14	X-RAY DIFFRACTION	14	(chain 'C' and resid 413 through 421)

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