PDB-9hdb: Sla1 SH3_3 domain (residues 355-414)

ID or keywords:

Entry

Database: PDB / ID: 9hdb

Title

Sla1 SH3_3 domain (residues 355-414)

Components

Actin cytoskeleton-regulatory complex protein SLA1

Keywords

ENDOCYTOSIS / SH3 domain / Membrane trafficking / protein-protein interaction

Function / homology

Function and homology information

actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.491 Å

Authors

Draper-Barr, G. / Defelipe, L.A. / Ruiz-Carillo, D. / Garcia-Alai, M.M.

Funding support

Germany, 1items

Citation

Journal: Structure / Year: 2025
Title: Sla2 is a core interaction hub for clathrin light chain and the Pan1/End3/Sla1 complex.
Authors: George Draper-Barr / Lucas A Defelipe / David Ruiz-Carrillo / Emil Gustavsson / Meytal Landau / Maria García-Alai /

Abstract: The interaction network of Sla2, a vital endocytic mid-coat adaptor protein, undergoes constant rearrangement. Sla2 serves as a scaffold linking the membrane to the actin cytoskeleton, with its role ...

History

Deposition	Nov 12, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 21, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9hdb.cif.gz	136 KB	Display	PDBx/mmCIF format
PDB format	pdb9hdb.ent.gz	87.5 KB	Display	PDB format
PDBx/mmJSON format	9hdb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hd/9hdb ftp://data.pdbj.org/pub/pdb/validation_reports/hd/9hdb	HTTPS FTP

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Related structure data

Related structure data	52061C 9hddC 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 (1)

Deposited unit

B: Actin cytoskeleton-regulatory complex protein SLA1

A: Actin cytoskeleton-regulatory complex protein SLA1

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

1

B: Actin cytoskeleton-regulatory complex protein SLA1

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

2

A: Actin cytoskeleton-regulatory complex protein SLA1

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

Unit cell

Length a, b, c (Å)	38.533, 50.423, 51.967
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	B
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 6 - 63 / Label seq-ID: 6 - 63

Dom-ID	Auth asym-ID	Label asym-ID
1	B	A
2	A	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Actin cytoskeleton-regulatory complex protein SLA1 Mass: 7262.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residues 355-414 of Sla1. Purified from an N-terminal GST fusion construct leaving the GAMA sequence prior to the domain of interest after TEV cleavage. Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SLA1, YBL007C, YBL0321 / Plasmid: pETM30 Details (production host): 6xHis-GST-'TEV cleavage site'-POI Production host: Escherichia coli (E. coli) / References: UniProt: P32790
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.74 Å³/Da / Density % sol: 29.22 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5 20% PEG 10000 1mM peptide (PVSTPARTPARTPTP) dissolved in 0.03M HEPES pH 8, 0.15M NaCl, 0.5mM TCEP

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.9762 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2024

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 1.49→51.97 Å / Num. obs: 17131 / % possible obs: 100 % / Redundancy: 10 % / CC_1/2: 0.998 / R_merge(I) obs: 0.078 / R_pim(I) all: 0.037 / R_rim(I) all: 0.087 / Χ²: 0.98 / Net I/σ(I): 15.6

Reflection shell

Χ²: 0.98 / Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
8.16-51.97	7.2	0.071	24.2	139	0.989	0.036	0.08	99.7
1.49-1.52	9.3	0.422	4.8	820	0.943	0.211	0.473	99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
Aimless		data scaling
autoPROC		data reduction
PHENIX		model building
Coot		model building
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.491→36.214 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.961 / SU B: 2.543 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1895	848	4.964 %	RANDOM
R_work	0.143	16235	-	-
all	0.145	-	-	-
obs	-	17083	99.947 %	-

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: 18.897 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.915 Å²	0 Å²	0 Å²
2-	-	0.226 Å²	-0 Å²
3-	-	-	0.689 Å²

Refinement step

Cycle: LAST / Resolution: 1.491→36.214 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	982	0	0	111	1093

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	1007
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	967
X-RAY DIFFRACTION	r_angle_refined_deg	1.965	1.809	1354
X-RAY DIFFRACTION	r_angle_other_deg	0.664	1.809	2244
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.153	5	123
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.048	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.145	10	195
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.885	10	44
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	143
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1169
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	215
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	125
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	854
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	470
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	561
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	62
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.157	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.155	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.19	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	4.4	1.092	495
X-RAY DIFFRACTION	r_mcbond_other	4.375	1.091	495
X-RAY DIFFRACTION	r_mcangle_it	5.992	1.963	617
X-RAY DIFFRACTION	r_mcangle_other	5.995	1.964	618
X-RAY DIFFRACTION	r_scbond_it	6.214	1.322	512
X-RAY DIFFRACTION	r_scbond_other	6.208	1.321	513
X-RAY DIFFRACTION	r_scangle_it	8.545	2.334	737
X-RAY DIFFRACTION	r_scangle_other	8.54	2.332	738
X-RAY DIFFRACTION	r_lrange_it	11.566	16.541	4028
X-RAY DIFFRACTION	r_lrange_other	11.097	15.69	3956
X-RAY DIFFRACTION	r_rigid_bond_restr	5.644	3	1974
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.147	0.05	1719

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.1468	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.1468	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
1.491-1.529	0.211	52	0.129	1180	0.132	1233	0.979	0.99	99.9189	0.119
1.529-1.571	0.235	83	0.106	1116	0.114	1199	0.965	0.992	100	0.099
1.571-1.617	0.168	61	0.097	1128	0.101	1189	0.983	0.994	100	0.089
1.617-1.666	0.179	67	0.106	1056	0.11	1125	0.977	0.993	99.8222	0.098
1.666-1.721	0.216	48	0.116	1072	0.12	1120	0.972	0.992	100	0.107
1.721-1.781	0.2	50	0.118	1016	0.122	1067	0.978	0.991	99.9063	0.111
1.781-1.848	0.212	36	0.119	1010	0.122	1047	0.969	0.991	99.9045	0.115
1.848-1.923	0.163	37	0.125	972	0.126	1009	0.982	0.99	100	0.122
1.923-2.009	0.203	42	0.12	922	0.124	964	0.974	0.991	100	0.121
2.009-2.106	0.177	63	0.121	856	0.125	921	0.983	0.991	99.7828	0.126
2.106-2.22	0.195	53	0.124	822	0.128	875	0.982	0.991	100	0.129
2.22-2.354	0.233	34	0.135	808	0.139	842	0.975	0.989	100	0.143
2.354-2.516	0.188	42	0.142	742	0.145	784	0.98	0.987	100	0.152
2.516-2.716	0.216	34	0.148	706	0.151	740	0.972	0.986	100	0.161
2.716-2.974	0.177	45	0.146	640	0.148	685	0.982	0.987	100	0.166
2.974-3.322	0.145	31	0.143	598	0.143	630	0.988	0.986	99.8413	0.164
3.322-3.83	0.195	22	0.151	535	0.153	558	0.982	0.986	99.8208	0.179
3.83-4.678	0.144	21	0.128	457	0.129	478	0.989	0.99	100	0.167
4.678-6.561	0.198	21	0.199	367	0.199	388	0.973	0.977	100	0.241
6.561-36.214	0.37	6	0.32	232	0.321	238	0.959	0.938	100	0.415

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	1.9328	0.3527	0.0737	2.6627	0.0752	2.3278	0.0181	-0.0679	0.0255	0.0303	0.0016	-0.0761	0.0537	0.0542	-0.0197	0.0084	0.0012	0.0013	0.0188	-0.0056	0.0049	-9.7501	-5.2405	-9.1819
2	3.3624	0.2839	-0.3691	2.6116	0.5613	3.3646	0.0186	-0.0117	0.1837	0.0057	-0.029	0.0646	-0.1388	-0.0731	0.0104	0.0064	0.0019	0.0001	0.0045	-0.0012	0.0111	8.8075	-6.9381	-16.864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Bp	1 - 64
2	X-RAY DIFFRACTION	2	ALL	Ap	6 - 64

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