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

ID or keywords:

Entry

Database: PDB / ID: 9exf

Title

Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to YAP1801 peptide (LIDM)

Components

Clathrin coat assembly protein AP180A
Clathrin heavy chain

Keywords

ENDOCYTOSIS / Clathrin / YAP1801 / 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 / 1-phosphatidylinositol binding / prospore membrane / 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: 1.95 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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Download

PDBx/mmCIF format	9exf.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9exf.ent.gz	969.5 KB	Display	PDB format
PDBx/mmJSON format	9exf.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/9exf ftp://data.pdbj.org/pub/pdb/validation_reports/ex/9exf	HTTPS FTP

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Related structure data

Related structure data	9ex5C 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: Clathrin heavy chain

E: Clathrin coat assembly protein AP180A

F: Clathrin coat assembly protein AP180A

G: Clathrin coat assembly protein AP180A

H: Clathrin coat assembly protein AP180A

J: Clathrin coat assembly protein AP180A

K: Clathrin coat assembly protein AP180A

O: Clathrin coat assembly protein AP180A

N: Clathrin coat assembly protein AP180A

M: Clathrin coat assembly protein AP180A

P: Clathrin coat assembly protein AP180A

hetero molecules

172 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Clathrin heavy chain

E: Clathrin coat assembly protein AP180A

G: Clathrin coat assembly protein AP180A

hetero molecules

defined by author
Evidence: gel filtration
42.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Clathrin heavy chain

F: Clathrin coat assembly protein AP180A

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

3

C: Clathrin heavy chain

J: Clathrin coat assembly protein AP180A

hetero molecules

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

4

D: Clathrin heavy chain

H: Clathrin coat assembly protein AP180A

K: Clathrin coat assembly protein AP180A

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

Unit cell

Length a, b, c (Å)	51.083, 89.739, 188.122
Angle α, β, γ (deg.)	90, 90.392, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	ASP	ASP	A	A	-1 - 368	3 - 372
2	1	1	MET	MET	ASP	ASP	B	B	-1 - 368	3 - 372
3	2	2	MET	MET	ALA	ALA	A	A	-1 - 366	3 - 370
4	2	2	MET	MET	ALA	ALA	C	C	-1 - 366	3 - 370
5	3	3	MET	MET	LEU	LEU	A	A	-1 - 369	3 - 373
6	3	3	MET	MET	LEU	LEU	D	D	-1 - 369	3 - 373
7	4	4	MET	MET	ALA	ALA	B	B	-1 - 366	3 - 370
8	4	4	MET	MET	ALA	ALA	C	C	-1 - 366	3 - 370
9	5	5	ALA	ALA	LEU	LEU	B	B	-2 - 369	2 - 373
10	5	5	ALA	ALA	LEU	LEU	D	D	-2 - 369	2 - 373
11	6	6	MET	MET	ASP	ASP	C	C	-1 - 367	3 - 371
12	6	6	MET	MET	ASP	ASP	D	D	-1 - 367	3 - 371

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
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Clathrin heavy chain Mass: 40976.395 Da / Num. of mol.: 4 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	Clathrin coat assembly protein AP180A Mass: 831.978 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38856
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.55 Å³/Da / Density % sol: 51.82 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M TRIS-HCl pH 8.5 0.28182M Lithium Sfate monohydrate 30% (w/v) PEG4000

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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: 0.9793 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 31, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.95→81 Å / Num. obs: 116855 / % possible obs: 95.3 % / Redundancy: 7.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.108 / Net I/σ(I): 11
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 7.1 % / R_merge(I) obs: 1.242 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5172 / CC_1/2: 0.499 / R_pim(I) all: 0.553 / Χ²: 0.99 / % possible all: 86.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.82)	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→65.013 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.951 / SU B: 8.196 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.212	5916	5.063 %
R_work	0.1814	110932	-
all	0.183	-	-
obs	-	116848	94.399 %

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: 37.123 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.427 Å²	-0 Å²	0.109 Å²
2-	-	-0.182 Å²	-0 Å²
3-	-	-	-0.246 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→65.013 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11928	0	7	614	12549

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	12171
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	11759
X-RAY DIFFRACTION	r_angle_refined_deg	1.517	1.788	16542
X-RAY DIFFRACTION	r_angle_other_deg	0.499	1.742	26948
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.691	5	1527
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.653	5	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.827	10	2060
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.437	10	552
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1977
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	14309
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2791
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	1891
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	10873
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	5885
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	6806
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	549
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.193	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.147	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	119
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.151	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	1.655	1.953	6141
X-RAY DIFFRACTION	r_mcbond_other	1.655	1.953	6141
X-RAY DIFFRACTION	r_mcangle_it	2.529	3.491	7654
X-RAY DIFFRACTION	r_mcangle_other	2.529	3.492	7655
X-RAY DIFFRACTION	r_scbond_it	2.592	2.28	6030
X-RAY DIFFRACTION	r_scbond_other	2.592	2.281	6031
X-RAY DIFFRACTION	r_scangle_it	4.061	4.044	8887
X-RAY DIFFRACTION	r_scangle_other	4.061	4.045	8888
X-RAY DIFFRACTION	r_lrange_it	5.944	24.583	50258
X-RAY DIFFRACTION	r_lrange_other	5.915	24.353	49810
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.095	0.05	11465
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.097	0.05	11454
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.086	0.05	11506
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.093	0.05	11510
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.09	0.05	11487
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.101	0.05	11345

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	0.09511	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09511	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09723	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09723	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08591	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.08591	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.09321	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.09321	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09046	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.09046	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.10122	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.10122	0.05009

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
1.95-2.001	0.299	396	0.27	7606	0.272	9050	0.94	0.952	88.4199	0.255
2.001-2.055	0.27	413	0.25	8107	0.251	8883	0.953	0.96	95.9135	0.231
2.055-2.115	0.259	356	0.23	7986	0.231	8651	0.957	0.966	96.4282	0.209
2.115-2.18	0.262	378	0.224	7639	0.226	8332	0.957	0.969	96.2194	0.202
2.18-2.251	0.247	385	0.214	7433	0.215	8176	0.963	0.972	95.6213	0.192
2.251-2.33	0.239	408	0.2	6945	0.202	7891	0.964	0.976	93.1821	0.176
2.33-2.418	0.219	391	0.194	6803	0.196	7588	0.972	0.978	94.8076	0.171
2.418-2.517	0.253	344	0.189	6771	0.192	7332	0.964	0.98	97.0404	0.167
2.517-2.628	0.247	348	0.195	6396	0.198	6987	0.968	0.978	96.5221	0.173
2.628-2.756	0.242	336	0.189	6165	0.192	6695	0.965	0.98	97.1023	0.169
2.756-2.905	0.234	312	0.193	5858	0.195	6427	0.968	0.978	96.0012	0.176
2.905-3.081	0.215	306	0.18	5371	0.182	6027	0.972	0.981	94.1928	0.166
3.081-3.293	0.216	288	0.192	5137	0.193	5705	0.972	0.979	95.092	0.18
3.293-3.556	0.212	237	0.186	4871	0.188	5322	0.972	0.982	95.979	0.179
3.556-3.895	0.2	255	0.167	4423	0.169	4900	0.977	0.986	95.4694	0.163
3.895-4.352	0.16	177	0.136	3965	0.137	4423	0.987	0.99	93.6469	0.133
4.352-5.022	0.141	181	0.123	3326	0.124	3917	0.989	0.992	89.5328	0.124
5.022-6.141	0.203	204	0.176	2733	0.178	3340	0.985	0.987	87.9341	0.176
6.141-8.647	0.183	123	0.171	2193	0.172	2607	0.985	0.987	88.8377	0.171
8.647-65.013	0.159	78	0.148	1204	0.148	1484	0.989	0.989	86.3881	0.157

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	0.889	0.4563	-0.1714	2.337	-0.4158	0.6978	-0.0049	0.0144	0.0263	-0.0035	0.041	-0.0447	-0.0055	-0.0016	-0.0361	0.0075	-0.0089	-0.0188	0.0454	-0.0127	0.0881	18.1806	-0.0735	75.7318
2	1.1271	-0.3117	0.1901	1.3616	-0.3849	1.7933	-0.0192	0.1796	0.0991	-0.1476	0.0257	-0.0517	-0.0412	0.0291	-0.0065	0.0411	-0.02	0.0167	0.0372	0.0224	0.1653	43.1852	35.1332	69.0063
3	1.0458	-0.3889	0.2239	1.3722	-0.4522	1.7757	-0.0247	0.0812	-0.0664	-0.0925	0.0261	0.0731	0.0053	-0.0913	-0.0014	0.1033	-0.0614	-0.0116	0.1019	0.0182	0.1162	53.3614	66.7661	44.0639
4	1.1381	0.4149	-0.5604	1.2488	-0.6992	1.9341	0.0321	0.0712	0.0607	0.0313	-0.0926	-0.0051	-0.1266	0.0189	0.0605	0.0642	0.0221	-0.0152	0.1286	0.0029	0.1337	78.2683	82.0588	11.6207
5	4.1672	-0.637	0.143	9.6724	0.3935	6.5665	0.0312	-0.1522	0.0401	0.0626	0.0015	0.0571	0.0531	0.0627	-0.0327	0.1202	-0.0197	0.0044	0.1724	0.0177	0.1929	39.9796	-6.4383	73.4419
6	6.5644	-3.4838	9.0641	5.9093	-6.4052	13.1518	0.0972	-0.0074	-0.0803	0.1407	-0.0622	-0.1712	0.1071	-0.0015	-0.035	0.2324	-0.0249	0.0289	0.2196	0.0014	0.2327	33.3403	49.1811	81.5924
7	8.5078	5.9008	0.6496	7.0044	-1.0586	9.2673	0.0485	0.5189	-0.2441	-0.3702	0.0851	0.3376	-0.1216	-0.2752	-0.1336	0.2392	-0.0181	0.0212	0.2249	-0.0122	0.255	-1.041	-21.1056	81.5013
8	1.8359	-2.2966	0.6082	3.7595	-1.5054	7.3522	0.0645	-0.0259	0.0279	-0.0894	0.011	0.0321	-0.0493	-0.0913	-0.0756	0.1793	-0.0125	0.014	0.2256	0.0165	0.2258	56.6987	81.5971	4.7891
9	2.7253	0.5324	-3.0132	5.807	3.3868	7.4185	0.0312	0.2881	0.3959	-0.0393	0.0886	-0.138	-0.1198	-0.06	-0.1197	0.2816	-0.0083	0.0042	0.2779	0.0246	0.3059	58.3287	40.8105	36.3915
10	8.3272	-5.4044	2.9721	3.5138	-1.8756	8.5998	0.1166	-0.1922	-0.1446	-0.1029	0.1535	0.0762	0.3825	0.0939	-0.2701	0.2831	-0.0453	0.0196	0.2745	0.0069	0.2651	97.1428	92.486	-5.1767
11	0.361	-0.3942	-1.5307	0.4354	1.6585	6.5435	0.03	-0.0434	-0.0136	-0.0441	0.0394	0.0558	-0.1827	0.1571	-0.0694	0.3264	-0.0086	-0.0309	0.3031	0.017	0.358	38.4793	36.4819	40.5495
12	8.7241	1.9011	1.7218	0.7631	-0.601	3.0888	0.449	-0.9925	0.3061	0.094	-0.1608	0.1983	0.0826	-0.2265	-0.2882	0.4262	0.0354	-0.0227	0.3942	0.0085	0.3221	78.5422	98.2589	16.2104
13	3.22	3.426	-1.0017	7.6392	2.6518	3.8914	-0.1146	0.0362	-0.4997	0.3793	-0.2855	-0.0792	0.2529	-0.1232	0.4001	0.5313	-0.0634	0.0389	0.5415	-0.019	0.4987	42.969	57.3294	54.0203
14	1.7062	3.5053	-1.4752	8.708	-2.2288	1.7074	0.0332	0.0381	0.073	-0.0773	0.1153	0.0537	-0.0935	-0.0205	-0.1485	0.2921	0.0134	0.0102	0.2886	0.0019	0.2863	53.3845	47.0036	62.2754

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	-1 - 401
2	X-RAY DIFFRACTION	2	ALL	Bp	-2 - 369
3	X-RAY DIFFRACTION	3	ALL	Cp	-1 - 367
4	X-RAY DIFFRACTION	4	ALL	Dp	-2 - 369
5	X-RAY DIFFRACTION	5	ALL	Ep	1 - 7
6	X-RAY DIFFRACTION	6	ALL	Fp	2 - 7
7	X-RAY DIFFRACTION	7	ALL	Gp	1 - 7
8	X-RAY DIFFRACTION	8	ALL	Hp	1 - 7
9	X-RAY DIFFRACTION	9	ALL	Jp	3 - 6
10	X-RAY DIFFRACTION	10	ALL	Kp	3 - 6
11	X-RAY DIFFRACTION	11	ALL	Op	2 - 6
12	X-RAY DIFFRACTION	12	ALL	Np	4 - 7
13	X-RAY DIFFRACTION	13	ALL	Mp	2 - 7
14	X-RAY DIFFRACTION	14	ALL	Pp	2 - 7

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