PDB-8cuk: X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast

ID or keywords:

Entry

Database: PDB / ID: 8cuk

Title

X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast

Components

E3 ubiquitin-protein ligase PEP5

Keywords

TRANSPORT PROTEIN / membrane trafficking / HOPS complex / WD40 domain

Function / homology

Function and homology information

histone catabolic process / organelle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole fusion, non-autophagic / Golgi to endosome transport / endosome organization ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.22 Å

Authors

Port, S.A. / Baker, R.W. / Jeffrey, P.D. / Hughson, F.M.

Funding support

United States, 1items

Citation

Journal: to be published
Title: X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast
Authors: Port, S.A. / Baker, R.W. / Jeffrey, P.D. / Hughson, F.M.

History

Deposition	May 17, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cuk.cif.gz	494 KB	Display	PDBx/mmCIF format
PDB format	pdb8cuk.ent.gz	338.7 KB	Display	PDB format
PDBx/mmJSON format	8cuk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cuk_validation.pdf.gz	448 KB	Display	wwPDB validaton report
Full document	8cuk_full_validation.pdf.gz	454.8 KB	Display
Data in XML	8cuk_validation.xml.gz	38.5 KB	Display
Data in CIF	8cuk_validation.cif.gz	55.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/8cuk ftp://data.pdbj.org/pub/pdb/validation_reports/cu/8cuk	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	#88 - Apr 2007 Clathrin similarity (2) #163 - Jul 2013 HIV Capsid similarity (1) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: E3 ubiquitin-protein ligase PEP5

B: E3 ubiquitin-protein ligase PEP5

C: E3 ubiquitin-protein ligase PEP5

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

1

A: E3 ubiquitin-protein ligase PEP5

defined by author&software
Evidence: gel filtration
42.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: E3 ubiquitin-protein ligase PEP5

defined by author&software
Evidence: gel filtration
42.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: E3 ubiquitin-protein ligase PEP5

defined by author&software
Evidence: gel filtration
42.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.084, 113.159, 129.758
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	E3 ubiquitin-protein ligase PEP5 / Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin ...Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin transferase PEP5 / Vacuolar biogenesis protein END1 / Vacuolar morphogenesis protein 1 / Vacuolar protein sorting-associated protein 11 / Vacuolar protein-targeting protein 11 Mass: 42355.367 Da / Num. of mol.: 3 / Fragment: WD40 domain (1-350) of Yeast Vps11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c Gene: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13 Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) References: UniProt: P12868, RING-type E3 ubiquitin transferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

E3 ubiquitin-protein ligase PEP5 / Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin ...

Mass: 42355.367 Da / Num. of mol.: 3 / Fragment: WD40 domain (1-350) of Yeast Vps11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c
Gene: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13
Plasmid: pQLinkH / Production host:

Escherichia coli (E. coli)
References: UniProt: P12868, RING-type E3 ubiquitin transferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.68 Å³/Da / Density % sol: 54.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Tris pH 7.5, 11% PEG 6000, 3% glycerol, 0.5 mM TCEP. Cryoprotected with 30% glycerol supplementing the crystallization conditions.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.743 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.743 Å / Relative weight: 1

Reflection

Resolution: 2.22→50 Å / Num. obs: 62899 / % possible obs: 96.2 % / Redundancy: 6.9 % / R_merge(I) obs: 0.09 / Χ²: 0.927 / Net I/σ(I): 7.5 / Num. measured all: 432332

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.22-2.26	3.9	0.928	2741	0.623	1	85.5
2.26-2.3	5	0.839	2954	0.628	1	91.8
2.3-2.34	6	0.814	3046	0.648	1	93.9
2.34-2.39	6.7	0.761	3091	0.654	1	95.6
2.39-2.44	6.9	0.637	3049	0.686	1	95.1
2.44-2.5	7	0.548	3093	0.687	1	95.5
2.5-2.56	7	0.438	3094	0.723	1	95.6
2.56-2.63	7	0.369	3108	0.754	1	96
2.63-2.71	7.1	0.296	3123	0.786	1	96.3
2.71-2.8	7.1	0.26	3105	0.804	1	96.6
2.8-2.9	7.2	0.203	3170	0.853	1	96.9
2.9-3.01	7.3	0.163	3156	0.907	1	97.3
3.01-3.15	7.4	0.132	3169	0.951	1	97.2
3.15-3.32	7.5	0.096	3178	1.09	1	97.5
3.32-3.52	7.4	0.079	3232	1.174	1	98.3
3.52-3.8	7.4	0.067	3214	1.343	1	98.3
3.8-4.18	7.4	0.055	3253	1.365	1	98.7
4.18-4.78	7.3	0.041	3288	1.191	1	98.8
4.78-6.02	7.1	0.039	3332	1.035	1	99.3
6.02-50	7.2	0.032	3503	1.081	1	99.6

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
PHENIX	1.17-3644	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
SHELXCD		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.22→47.76 Å / SU ML: 0.2799 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.3609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2341	2985	4.87 %
R_work	0.1745	58314	-
obs	0.1773	61299	93.83 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.91 Å²

Refinement step

Cycle: LAST / Resolution: 2.22→47.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7853	0	0	392	8245

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	8052
X-RAY DIFFRACTION	f_angle_d	0.8926	10920
X-RAY DIFFRACTION	f_chiral_restr	0.0609	1286
X-RAY DIFFRACTION	f_plane_restr	0.0053	1402
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6358	2994

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 (%)
2.22-2.26	0.3251	106	0.2922	2168	X-RAY DIFFRACTION	74.44
2.26-2.3	0.3651	128	0.2749	2480	X-RAY DIFFRACTION	84.32
2.3-2.34	0.3233	121	0.2699	2583	X-RAY DIFFRACTION	88.25
2.34-2.38	0.3595	136	0.2474	2619	X-RAY DIFFRACTION	90.42
2.38-2.43	0.3566	138	0.2366	2677	X-RAY DIFFRACTION	91.34
2.43-2.48	0.3179	139	0.239	2695	X-RAY DIFFRACTION	91.42
2.48-2.54	0.3372	134	0.2213	2703	X-RAY DIFFRACTION	92.08
2.54-2.61	0.2529	147	0.2128	2718	X-RAY DIFFRACTION	93.47
2.61-2.68	0.2716	153	0.1927	2756	X-RAY DIFFRACTION	94.36
2.68-2.76	0.2797	145	0.1995	2782	X-RAY DIFFRACTION	94.94
2.76-2.84	0.3164	147	0.2065	2792	X-RAY DIFFRACTION	95.36
2.84-2.95	0.2513	157	0.1981	2819	X-RAY DIFFRACTION	95.94
2.95-3.06	0.2799	147	0.201	2833	X-RAY DIFFRACTION	96.01
3.06-3.2	0.2515	176	0.1936	2823	X-RAY DIFFRACTION	97.21
3.2-3.37	0.2556	138	0.1725	2901	X-RAY DIFFRACTION	97.65
3.37-3.58	0.1872	149	0.1642	2913	X-RAY DIFFRACTION	97.52
3.58-3.86	0.2018	158	0.159	2906	X-RAY DIFFRACTION	98.43
3.86-4.25	0.1891	128	0.1376	2971	X-RAY DIFFRACTION	98.47
4.25-4.86	0.1528	136	0.1158	2988	X-RAY DIFFRACTION	99.24
4.86-6.12	0.2132	149	0.1469	3019	X-RAY DIFFRACTION	99.22
6.12-47.76	0.1978	153	0.1673	3168	X-RAY DIFFRACTION	99.34

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	2.1829117422	-0.470605443074	0.994602387415	1.82966609205	1.19491918425	4.42065482653	-0.0599079474391	0.204861008357	0.441315548985	-0.105764830696	-0.0485224169243	-0.0774468633932	-0.291389449034	-0.0630825665362	0.0948566120207	0.235596442413	-0.031640686988	0.00775790562535	0.173479215932	0.021325506562	0.317908950398	1.91200914855	60.7468236741	30.1789658807
2	2.66867510583	-1.70175718694	1.29642508581	2.54502139079	-1.28919017795	3.17227259508	0.123838853737	0.444765074878	-0.153670497375	-0.296041983126	-0.16383596737	-0.0544106952254	0.283439488989	0.397228733105	0.0446493659995	0.237422085071	0.00988685081904	0.030063565572	0.27731398575	-0.0594252337072	0.32063840684	15.2541946582	43.611713603	32.8642221089
3	3.82967394831	-2.12361003511	0.770693930109	3.02537732209	-0.231868338415	2.6636417716	-0.178618605954	-0.311856725179	-0.16598627759	0.279868573997	0.0962259700165	0.18798081511	0.143470276025	-0.152644968543	0.0625677085026	0.275133408412	-0.0423100615779	0.0652356819299	0.273120507871	-0.0623777928415	0.23526216487	3.36083132263	54.7076380545	49.0904607271
4	1.99016847751	1.72047988757	-0.19071334381	7.8540199118	2.05727151419	0.90059341582	0.0973977720829	-0.354287824976	-0.0643851324861	0.55131591063	-0.0321422369696	-0.025993957154	0.192325033765	0.105890921927	-0.0831137742535	0.309752814301	0.0229181204963	-0.0542773187533	0.369755139158	0.0607643455002	0.229666556812	29.5493636213	19.8781881866	49.8090872945
5	4.41000190567	0.382241740171	-1.9727360566	5.79308693038	-0.131018258636	6.692425131	0.174244267968	-0.741653584719	0.66024112136	0.499646808116	-0.0748029194094	-0.328260610516	-0.413724228806	0.463850561485	-0.0290035805571	0.267852736157	-0.0202116904247	-0.0377116009793	0.379816038828	-0.114893237762	0.461546093408	40.6749006843	35.598624675	42.7939815867
6	4.79791559865	0.836874193133	-1.21884727737	4.40631731644	-0.268772344536	4.39185207566	-0.0799246454867	-0.0559618656556	0.12122646912	0.0376423923256	0.155544646679	-0.286772482172	-0.139882539427	0.294703261028	-0.0619677637143	0.175516814817	-0.00712583209343	-0.00255741034754	0.240786380938	0.0240557255995	0.297864762908	46.2593558184	25.9585290385	27.2505323898
7	7.7153530835	2.43946102845	-1.93828423449	3.446698254	-0.341987563725	3.28530474136	-0.344273213934	0.606933443347	-0.449566259354	-0.489719382938	0.303630012577	-0.130681038388	0.382625806927	-0.218004899644	0.0521608929025	0.368817891881	-0.0726410154077	0.00869915534386	0.242126363153	0.0249275679235	0.341145895825	34.0191040003	10.6899560106	26.304259833
8	4.6576113537	-0.870816402286	1.39606836769	6.55083962307	0.884489055241	6.35427200724	-0.182638275498	0.484630856423	-0.0130344743154	-0.0267433401499	-0.196008875194	-0.290304707118	0.4684491143	0.124276356997	0.303091626035	0.355746389409	-0.0579543573794	0.0232497441678	0.267650332133	0.0516345879923	0.425199766481	27.5615255851	5.61561927163	33.706744023
9	6.33537128177	2.10002743363	-1.61376360812	6.48511928561	2.0032414569	7.19384704025	0.0735526661295	-0.204069858521	0.127424708786	0.537069329903	-0.213704401208	-0.646962461115	0.287023569939	0.375381990364	0.175086663029	0.37077848577	-0.0359578277435	-0.075229747648	0.294450410355	0.0646410910702	0.366372379298	31.9553837628	12.5423511498	44.4195291929
10	1.56471264684	-0.378992748302	0.974024724962	3.47306298959	-2.89189242249	3.38763924237	0.136505471916	0.34639431718	-0.238631100569	-0.480438993	0.0907907056877	0.449821358298	0.316271770442	-0.184590946534	-0.204274586417	0.350991302716	0.00671470569474	-0.0611256550356	0.326893150066	-0.081475208271	0.256277203507	58.2651540645	27.5912037406	1.86317911791
11	1.84163476354	0.932767403684	0.392670970934	3.7251813155	0.300958411338	1.57746319981	-0.00208339241676	0.0531784325291	-0.120883223459	-0.00220673696872	-0.0214278068412	-0.193029788007	0.017854393305	0.164945364409	0.0213904160179	0.199928542778	0.0497373034061	-0.0162935006547	0.234600714789	-0.0058523235466	0.169343213621	73.0745905846	37.1533078475	18.1229472644
12	6.39759162975	2.15727298539	2.17769354772	4.72820824982	-0.876922277064	4.47049418341	-0.160047634246	0.250378819029	0.23526928413	-0.198032601821	0.0490333554633	0.0864800218163	-0.186680566101	0.0214183021343	0.0861041890683	0.321253815504	0.060012565237	-0.0546231200316	0.321875200147	0.026386361646	0.190213014628	60.798891138	45.0776359418	1.36118410347

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 93 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 94 through 234 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 235 through 350 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 6 through 69 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 70 through 130 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 131 through 234 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 235 through 297 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 298 through 320 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 321 through 350 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 6 through 69 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 70 through 248 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 249 through 350 )

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