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

ID or keywords:

Entry

Database: PDB / ID: 9exg

Title

Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-2 peptide (LIDL)

Components

Clathrin heavy chain
Epsin-2

Keywords

ENDOCYTOSIS / Clathrin / Ent2 / 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 / Cargo recognition for clathrin-mediated endocytosis / RHOU GTPase cycle / actin cortical patch assembly / clathrin vesicle coat ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae S288C (yeast)

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.744 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 8, 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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PDBx/mmCIF format	9exg.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9exg.ent.gz	721.6 KB	Display	PDB format
PDBx/mmJSON format	9exg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9exg_validation.pdf.gz	502.8 KB	Display	wwPDB validaton report
Full document	9exg_full_validation.pdf.gz	509.4 KB	Display
Data in XML	9exg_validation.xml.gz	58.1 KB	Display
Data in CIF	9exg_validation.cif.gz	81.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/9exg ftp://data.pdbj.org/pub/pdb/validation_reports/ex/9exg	HTTPS FTP

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Related structure data

Related structure data	9ex5C 9exfC 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) #166 - Oct 2013 Proteasome similarity (2) #115 - Jul 2009 beta-Secretase similarity (1)

Deposited unit

A: Clathrin heavy chain

B: Clathrin heavy chain

C: Clathrin heavy chain

D: Epsin-2

E: Epsin-2

F: Epsin-2

G: Epsin-2

H: Epsin-2

I: Epsin-2

J: Epsin-2

L: Epsin-2

M: Epsin-2

hetero molecules

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

1

A: Clathrin heavy chain

D: Epsin-2

E: Epsin-2

F: Epsin-2

hetero molecules

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

2

B: Clathrin heavy chain

I: Epsin-2

J: Epsin-2

L: Epsin-2

hetero molecules

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

3

C: Clathrin heavy chain

G: Epsin-2

H: Epsin-2

M: Epsin-2

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

Unit cell

Length a, b, c (Å)	46.496, 94.289, 269.026
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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:

End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	-1 - 365	3 - 369
2	1	1	MET	MET	-1 - 365	3 - 369
3	2	2	ASP	ASP	3 - 361	7 - 365
4	2	2	ASP	ASP	3 - 361	7 - 365
5	3	3	ASP	ASP	3 - 361	7 - 365
6	3	3	ASP	ASP	3 - 361	7 - 365

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-2 Mass: 715.837 Da / Num. of mol.: 9 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05785
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 929 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.28 Å³/Da / Density % sol: 46.06 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium sulfate 0.1M Bis-Tris pH 5.5 25% (w/v) PEG3350

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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: Oct 30, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 1.74→67.347 Å / Num. obs: 121808 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.037 / R_rim(I) all: 0.097 / Net I/σ(I): 16.7

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
9.55-67.26	9.7	0.042	884	0.999	0.018	0.046
1.74-1.77	12.9	1.102	5957	0.788	0.457	1.194

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
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: 1.744→67.347 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.946 / WR_factor R_free: 0.216 / WR_factor R_work: 0.182 / SU B: 6.14 / SU ML: 0.1 / Average fsc free: 0.9608 / Average fsc work: 0.9709 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2261	6253	5.14 %
R_work	0.1913	115407	-
all	0.193	-	-
obs	-	121660	99.837 %

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: 32.856 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.231 Å²	0 Å²	-0 Å²
2-	-	-2.74 Å²	0 Å²
3-	-	-	-1.491 Å²

Refinement step

Cycle: LAST / Resolution: 1.744→67.347 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8921	0	23	929	9873

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	9108
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8798
X-RAY DIFFRACTION	r_angle_refined_deg	1.532	1.785	12385
X-RAY DIFFRACTION	r_angle_other_deg	0.5	1.737	20181
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.067	5	1148
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.565	5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.205	10	1524
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.921	10	397
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1497
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10656
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2058
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	1418
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	8349
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	4437
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4961
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	619
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.016	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.245	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.179	0.2	40
X-RAY DIFFRACTION	r_mcbond_it	0.585	0.322	4617
X-RAY DIFFRACTION	r_mcbond_other	0.585	0.322	4617
X-RAY DIFFRACTION	r_mcangle_it	0.945	0.571	5748
X-RAY DIFFRACTION	r_mcangle_other	0.945	0.571	5749
X-RAY DIFFRACTION	r_scbond_it	0.806	0.404	4491
X-RAY DIFFRACTION	r_scbond_other	0.799	0.401	4487
X-RAY DIFFRACTION	r_scangle_it	1.245	0.701	6632
X-RAY DIFFRACTION	r_scangle_other	1.243	0.696	6627
X-RAY DIFFRACTION	r_lrange_it	4.047	5.132	38557
X-RAY DIFFRACTION	r_lrange_other	3.98	3.969	37545
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.132	0.05	11002
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.128	0.05	10792
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.135	0.05	10731

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	0.13179	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13179	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12802	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.12802	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.13549	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.13549	0.05008

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
1.744-1.789	0.307	455	0.277	8452	0.279	8931	0.929	0.944	99.7313	0.268
1.789-1.838	0.289	444	0.255	8169	0.257	8623	0.946	0.954	99.884	0.241
1.838-1.891	0.262	420	0.242	8009	0.243	8433	0.954	0.96	99.9526	0.224
1.891-1.949	0.256	409	0.23	7826	0.231	8239	0.957	0.966	99.9515	0.21
1.949-2.013	0.243	411	0.21	7501	0.211	7933	0.965	0.972	99.7353	0.19
2.013-2.084	0.245	400	0.208	7264	0.21	7666	0.964	0.973	99.9739	0.186
2.084-2.163	0.239	406	0.202	7029	0.204	7439	0.962	0.975	99.9462	0.179
2.163-2.251	0.225	364	0.201	6809	0.202	7192	0.964	0.974	99.7358	0.177
2.251-2.351	0.253	361	0.199	6533	0.202	6896	0.961	0.976	99.971	0.175
2.351-2.465	0.245	322	0.202	6266	0.204	6596	0.965	0.976	99.8787	0.18
2.465-2.598	0.262	294	0.202	5998	0.205	6302	0.963	0.976	99.8413	0.181
2.598-2.756	0.254	320	0.204	5654	0.207	5976	0.958	0.975	99.9665	0.186
2.756-2.946	0.22	294	0.202	5304	0.203	5615	0.967	0.976	99.6972	0.187
2.946-3.181	0.23	263	0.184	4955	0.186	5224	0.967	0.979	99.8851	0.176
3.181-3.484	0.204	277	0.175	4567	0.176	4855	0.972	0.981	99.7734	0.173
3.484-3.894	0.189	229	0.162	4205	0.163	4441	0.978	0.984	99.8424	0.164
3.894-4.494	0.177	183	0.146	3688	0.148	3883	0.979	0.987	99.691	0.153
4.494-5.498	0.19	184	0.153	3161	0.155	3361	0.981	0.987	99.5239	0.165
5.498-7.749	0.246	135	0.196	2537	0.198	2678	0.973	0.977	99.776	0.206
7.749-67.347	0.228	82	0.217	1480	0.218	1573	0.969	0.973	99.3007	0.235

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	0.8012	-0.1208	-0.1382	1.1478	0.3388	1.1987	-0.0252	0.0101	-0.0196	-0.0002	0.0372	-0.0078	-0.009	0.0456	-0.012	0.0011	-0.0077	0.0041	0.2954	0.0109	0.2999	4.047	2.732	66.5482
2	0.4396	-0.0283	0.1209	0.4692	-0.0904	0.837	0.0507	0.0293	0.0511	-0.1076	-0.0245	-0.0055	0.0203	0.0242	-0.0262	0.3405	-0.0428	0.0365	0.3367	-0.0037	0.3093	0.3654	-12.5796	20.3442
3	0.5595	0.3718	-0.0562	3.047	-0.7678	0.752	0.0541	-0.039	-0.0393	0.3322	-0.0055	0.0331	-0.0643	0.0088	-0.0486	0.3429	0.0256	-0.0059	0.407	-0.0029	0.3082	-0.09	32.8043	19.8655
4	8.6182	0.2648	-1.1189	2.83	-0.5956	0.2615	-0.1406	0.0488	-0.0875	0.0312	0.1145	0.0833	0.0241	-0.056	0.0261	0.1953	-0.0288	-0.0188	0.4108	-0.0117	0.374	-15.9296	-4.2348	58.0329
5	3.1808	-2.7062	1.8892	4.0687	1.8541	7.9219	-0.0996	0.1216	0.3429	0.0475	0.0867	-0.3852	-0.205	0.3546	0.0129	0.2899	0.0108	0.0237	0.3508	0.0193	0.3319	3.767	17.6002	90.6532
6	6.2305	2.8351	-3.04	5.4126	-4.2711	3.5277	0.0006	-0.2267	-0.0672	0.1081	0.1244	0.2134	0.0086	-0.0238	-0.1251	0.3638	0.0068	0.0011	0.3768	0.0067	0.3833	4.8224	-9.7692	79.5625
7	7.5117	0.066	-1.7705	1.3294	0.6149	1.6198	-0.1356	-0.1018	0.1063	0.077	0.1015	-0.254	0.0902	0.3079	0.0341	0.3895	0.0315	-0.0035	0.4125	0.0044	0.4113	12.1795	28.8408	8.0906
8	8.982	3.0036	2.052	7.4867	-0.0147	3.573	0.0561	-0.0337	0.0858	-0.2107	-0.1364	0.3462	0.0395	-0.2866	0.0803	0.3777	-0.0048	0.0419	0.409	-0.0167	0.3303	3.299	56.3225	5.5659
9	5.7433	-2.2119	0.3552	5.8801	1.6526	7.7205	-0.0719	0.4431	0.0957	-0.1915	0.0016	-0.0876	-0.0285	0.4416	0.0703	0.4269	-0.03	0.005	0.46	0.001	0.3874	-4.6507	-11.4369	-7.6651
10	6.0633	0.0365	-2.8979	1.9563	-1.9642	4.0644	0.0326	0.1025	0.1606	0.0667	0.1025	0.1864	-0.1554	-0.1083	-0.1351	0.395	-0.0014	0.013	0.3681	-0.0045	0.378	-4.2771	3.4472	19.2301
11	6.7637	0.5558	1.7388	0.4299	0.6225	1.0606	0.0772	-0.14	-0.0438	-0.0306	-0.0704	0.0358	-0.0886	-0.0972	-0.0068	0.3936	-0.0068	0.0089	0.3904	0.0006	0.401	-15.6961	-17.6653	36.5738
12	0.662	1.7262	-0.3773	4.6609	0.2682	11.4518	0.0818	0.0173	0.032	0.1324	0.1974	0.0381	-0.375	0.3018	-0.2792	0.5849	-0.0054	-0.0856	0.6093	-0.0053	0.5384	10.8287	27.3225	36.8259

Refinement TLS group

Selection: ALL

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