PDB-9ex5: Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain...

ID or keywords:

Entry

Database: PDB / ID: 9ex5

Title

Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-5 peptide (LIDL)

Components

Clathrin heavy chain
Epsin-5

Keywords

ENDOCYTOSIS / Clathrin / Ent5 / Adaptor protein

Function / homology

Function and homology information

Lysosome Vesicle Biogenesis / VLDLR internalisation and degradation / Clathrin-mediated endocytosis / Recycling pathway of L1 / RHOV GTPase cycle / LDL clearance / RHOU GTPase cycle / clathrin vesicle coat / clathrin coat of trans-Golgi network vesicle / early endosome to Golgi transport ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae S288C (yeast)

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.011 Å

Authors

Defelipe, L.A. / Bento, I. / Garcia Alai, M.M.

Funding support

European Union, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast.
Authors: Defelipe, L.A. / Veith, K. / Burastero, O. / Kupriianova, T. / Bento, I. / Skruzny, M. / Kolbel, K. / Uetrecht, C. / Thuenauer, R. / Garcia-Alai, M.M.

History

Deposition	Apr 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ex5.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9ex5.ent.gz	725.7 KB	Display	PDB format
PDBx/mmJSON format	9ex5.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/ex/9ex5 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/9ex5	HTTPS FTP

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Related structure data

Related structure data	9exfC 9exgC 9extC 9eytC C: citing same article (ref.)
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 (12) #19 - Jul 2001 Actin similarity (1) #115 - Jul 2009 beta-Secretase similarity (1)

Deposited unit

A: Clathrin heavy chain

B: Clathrin heavy chain

C: Clathrin heavy chain

D: Epsin-5

E: Epsin-5

F: Epsin-5

G: Epsin-5

H: Epsin-5

I: Epsin-5

J: Epsin-5

L: Epsin-5

M: Epsin-5

132 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Clathrin heavy chain

E: Epsin-5

G: Epsin-5

M: Epsin-5

defined by author&software
Evidence: gel filtration
44.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Clathrin heavy chain

D: Epsin-5

F: Epsin-5

J: Epsin-5

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

3

C: Clathrin heavy chain

H: Epsin-5

I: Epsin-5

L: Epsin-5

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

Unit cell

Length a, b, c (Å)	76.995, 133.449, 285.527
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-572- HOH

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

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	GLY	GLY	5 - 365	9 - 369
2	1	1	PRO	PRO	GLY	GLY	5 - 365	9 - 369
3	2	2	LEU	LEU	ALA	ALA	4 - 366	8 - 370
4	2	2	LEU	LEU	ALA	ALA	4 - 366	8 - 370
5	3	3	PRO	PRO	GLY	GLY	5 - 365	9 - 369
6	3	3	PRO	PRO	GLY	GLY	5 - 365	9 - 369

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

#1: Protein	Clathrin heavy chain Mass: 40976.395 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CHC1, YGL206C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22137
#2: Protein/peptide	Epsin-5 Mass: 1028.112 Da / Num. of mol.: 9 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03769
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.77 Å³/Da / Density % sol: 55.67 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 10 %(w/v) PEG 1000 10 %(w/v) PEG 8000

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Data collection

Diffraction

Mean temperature: 196 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P14 (MX2) / Wavelength: 0.9763 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 19, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 2.01→142.76 Å / Num. obs: 93922 / % possible obs: 95.9 % / Redundancy: 12.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.049 / R_rim(I) all: 0.13 / Net I/σ(I): 15.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
11.01-142.76	11.3	0.03	681	1	0.012	0.032
2.01-2.05	3.5	0.692	1670	0.533	0.517	0.871

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.011→71.484 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.189 / WR_factor R_work: 0.161 / SU B: 9.797 / SU ML: 0.129 / Average fsc free: 0.9574 / Average fsc work: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2146	4607	4.909 %
R_work	0.1819	89243	-
all	0.184	-	-
obs	-	93850	95.872 %

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: 42.867 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.351 Å²	0 Å²	-0 Å²
2-	-	1.152 Å²	0 Å²
3-	-	-	-2.503 Å²

Refinement step

Cycle: LAST / Resolution: 2.011→71.484 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8901	0	0	604	9505

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	9058
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8787
X-RAY DIFFRACTION	r_angle_refined_deg	1.428	1.795	12320
X-RAY DIFFRACTION	r_angle_other_deg	0.458	1.741	20155
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.795	5	1133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.346	5	42
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.065	10	1523
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.745	10	405
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	1482
X-RAY DIFFRACTION	r_chiral_restr_other	0.001	0.2	3
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10581
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2053
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	1484
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	8192
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	4395
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4913
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	486
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.132	0.2	30
X-RAY DIFFRACTION	r_nbd_other	0.247	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.175	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	2.149	2.867	4568
X-RAY DIFFRACTION	r_mcbond_other	2.149	2.867	4568
X-RAY DIFFRACTION	r_mcangle_it	2.968	5.137	5689
X-RAY DIFFRACTION	r_mcangle_other	2.967	5.137	5690
X-RAY DIFFRACTION	r_scbond_it	3.429	3.282	4490
X-RAY DIFFRACTION	r_scbond_other	3.428	3.282	4491
X-RAY DIFFRACTION	r_scangle_it	5.237	5.864	6631
X-RAY DIFFRACTION	r_scangle_other	5.236	5.864	6632
X-RAY DIFFRACTION	r_lrange_it	6.548	37.071	36914
X-RAY DIFFRACTION	r_lrange_other	6.501	36.617	36526
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	11413
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.079	0.05	11468
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.067	0.05	11506

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	0.07488	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07488	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07948	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07948	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06694	0.05011
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06694	0.05011

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
2.011-2.063	0.321	160	0.314	3240	0.314	7201	0.896	0.906	47.2157	0.287
2.063-2.12	0.296	343	0.302	6434	0.301	6971	0.913	0.916	97.217	0.27
2.12-2.181	0.28	327	0.268	6425	0.268	6766	0.937	0.941	99.7931	0.239
2.181-2.248	0.281	302	0.243	6318	0.244	6623	0.938	0.956	99.9547	0.214
2.248-2.322	0.265	349	0.221	6053	0.223	6405	0.954	0.965	99.9532	0.192
2.322-2.403	0.266	296	0.221	5935	0.223	6233	0.954	0.967	99.9679	0.19
2.403-2.494	0.278	281	0.206	5676	0.209	5957	0.95	0.972	100	0.18
2.494-2.595	0.268	310	0.197	5431	0.201	5744	0.957	0.976	99.9478	0.168
2.595-2.711	0.234	270	0.185	5263	0.187	5535	0.972	0.98	99.9639	0.159
2.711-2.843	0.225	262	0.184	5094	0.186	5357	0.971	0.98	99.9813	0.158
2.843-2.996	0.238	230	0.185	4794	0.188	5024	0.971	0.979	100	0.16
2.996-3.178	0.231	276	0.175	4511	0.178	4791	0.968	0.982	99.9165	0.156
3.178-3.397	0.196	201	0.179	4294	0.18	4495	0.979	0.98	100	0.164
3.397-3.668	0.198	206	0.174	4011	0.176	4220	0.979	0.983	99.9289	0.163
3.668-4.017	0.196	202	0.158	3675	0.16	3878	0.978	0.986	99.9742	0.151
4.017-4.489	0.162	189	0.133	3334	0.135	3523	0.986	0.99	100	0.129
4.489-5.18	0.164	143	0.132	3002	0.134	3147	0.984	0.991	99.9364	0.132
5.18-6.336	0.243	121	0.182	2548	0.184	2669	0.972	0.985	100	0.175
6.336-8.926	0.137	80	0.16	2019	0.159	2101	0.989	0.986	99.9048	0.159
8.926-71.484	0.151	59	0.174	1186	0.173	1250	0.984	0.983	99.6	0.183

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	0.9076	-0.0444	-0.3216	0.9727	0.0079	2.7152	0.0173	-0.0049	-0.0137	-0.0257	-0.0097	0.0713	-0.0341	-0.1238	-0.0076	0.0036	-0.0077	-0.0072	0.058	0.02	0.0177	32.1725	-23.1099	-6.5061
2	0.954	-0.0621	0.0803	1.0137	0.2816	2.7266	-0.0168	-0.0043	-0.0598	0.0145	0.0171	0.04	0.1114	-0.0327	-0.0003	0.0517	-0.0288	-0.0165	0.0173	0.0121	0.0143	15.3552	6.1024	-41.157
3	1.034	0.0216	0.2037	0.8803	-0.273	2.8324	0.0088	-0.0276	0.0667	-0.0042	-0.01	0.0245	-0.0946	-0.0801	0.0012	0.064	0.0232	0.0226	0.0101	0.0056	0.0129	16.8482	-49.6757	54.0914
4	10.1712	-3.4135	-2.9496	5.1159	-0.206	4.0195	0.0532	-0.0702	0.3105	0.01	-0.0092	0.23	0.1949	-0.1776	-0.044	0.1707	-0.0043	-0.0282	0.12	-0.0137	0.1893	2.1283	9.0767	-65.5898
5	9.7117	-3.0067	12.4537	10.9106	-5.7098	16.5015	0.1439	-0.0755	-0.2162	-0.3202	0.0742	-0.1661	0.1544	0.0699	-0.2181	0.1416	-0.0445	0.0399	0.186	-0.0026	0.1721	48.222	-10.5858	-10.6329
6	6.0747	-0.5668	-3.6686	4.8761	-6.4206	11.7073	0.1539	-0.1499	0.2035	0.1156	-0.0776	-0.046	-0.2977	0.2583	-0.0763	0.1906	-0.0371	-0.0364	0.1905	-0.0337	0.2014	35.3463	14.4821	-37.4837
7	3.816	0.8713	-1.1873	10.488	3.1268	7.1263	0.0431	-0.0378	-0.0825	0.0358	0.0622	-0.2174	-0.0205	-0.1777	-0.1053	0.1025	0.0306	0.0304	0.1493	0.0231	0.2111	28.8474	-35.2093	19.0643
8	9.1724	2.6928	3.1117	6.4512	-0.5813	5.5869	0.0167	-0.0259	-0.165	-0.1359	0.0359	-0.0984	-0.089	0.0186	-0.0526	0.1322	0.0237	0.0062	0.1304	0.0391	0.2095	25.5709	-40.7419	28.459
9	14.7613	-2.5856	-10.7242	5.426	8.3329	16.1848	0.3293	-0.0612	-0.005	0.0987	-0.1123	-0.1845	0.0059	-0.0897	-0.217	0.1799	0.0063	-0.0206	0.1251	0.0476	0.1784	14.0691	-69.9205	58.2436
10	6.9994	2.832	0.7445	8.7509	-1.1504	0.39	-0.1138	0.0798	-0.1163	-0.0038	0.0191	-0.3559	0.0113	-0.0123	0.0947	0.1628	-0.0038	-0.0306	0.1278	-0.0107	0.157	21.892	-7.7076	-50.316
11	5.3141	-2.9224	-2.002	8.9688	0.3297	2.1339	-0.0853	-0.0123	-0.2762	-0.0829	0.0191	0.3004	-0.0294	-0.1445	0.0661	0.1368	0.0186	0.0161	0.1448	0.0224	0.1453	1.5277	-48.5228	44.8794
12	8.6973	0.9244	0.998	3.3373	0.0864	2.8277	0.0249	-0.0132	0.3124	0.0895	-0.1195	-0.0028	-0.1138	0.0217	0.0946	0.1297	0.0112	0.0107	0.1583	0.0296	0.1465	23.5294	-10.4252	2.734

Refinement TLS group

Selection: ALL

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