PDB-8r02: Crystal structure of the retromer complex VPS29/VPS35 with the li...

ID or keywords:

Entry

Database: PDB / ID: 8r02

Title

Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a

Components

Vacuolar protein sorting-associated protein 29
Vacuolar protein sorting-associated protein 35

Keywords

PROTEIN TRANSPORT / Complex / transport / recycling / ligand

Function / homology

Function and homology information

neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / WNT ligand biogenesis and trafficking ...neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / positive regulation of locomotion involved in locomotory behavior / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / vesicle-mediated transport in synapse / positive regulation of dopamine biosynthetic process / mitochondrial fragmentation involved in apoptotic process / positive regulation of dopamine receptor signaling pathway / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / retromer complex / voluntary musculoskeletal movement / dopaminergic synapse / regulation of protein metabolic process / transcytosis / regulation of synapse maturation / endocytic recycling / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / positive regulation of protein localization to cell periphery / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / regulation of presynapse assembly / regulation of macroautophagy / D1 dopamine receptor binding / intracellular protein transport / modulation of chemical synaptic transmission / protein destabilization / regulation of protein stability / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / early endosome / lysosome / neuron projection / postsynaptic density / endosome / endosome membrane / lysosomal membrane / negative regulation of gene expression / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / metal ion binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Milani, M. / Fagnani, E.

Funding support

Italy, 1items

Citation

Journal: Comput Struct Biotechnol J / Year: 2024
Title: Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface.
Authors: Fagnani, E. / Boni, F. / Seneci, P. / Gornati, D. / Muzio, L. / Mastrangelo, E. / Milani, M.

History

Deposition	Oct 30, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r02.cif.gz	515.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8r02.ent.gz	330.9 KB	Display	PDB format
PDBx/mmJSON format	8r02.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/r0/8r02 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/8r02	HTTPS FTP

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Related structure data

Related structure data	8r0jC 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	#225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: Vacuolar protein sorting-associated protein 29

B: Vacuolar protein sorting-associated protein 29

C: Vacuolar protein sorting-associated protein 35

D: Vacuolar protein sorting-associated protein 35

hetero molecules

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

1

A: Vacuolar protein sorting-associated protein 29

C: Vacuolar protein sorting-associated protein 35

defined by author&software
Evidence: gel filtration
56.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Vacuolar protein sorting-associated protein 29

D: Vacuolar protein sorting-associated protein 35

hetero molecules

defined by author&software
Evidence: gel filtration
56.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.500, 140.830, 141.340
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	1 - 182
2	1	1	A	1 - 182
3	2	2	A	489 - 778
4	2	2	A	489 - 778

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein	Vacuolar protein sorting-associated protein 29 Mass: 20930.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ0
#2: Protein	Vacuolar protein sorting-associated protein 35 Mass: 35243.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QK1
#3: Chemical	ChemComp-XFZ / Bis-1,3-phenyl guanylhydrazon / 2-[(E)-[3-[(E)-[bis(azanyl)methylidenehydrazinylidene]methyl]phenyl]methylideneamino]guanidine Mass: 246.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₈ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91788 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91788 Å / Relative weight: 1
Reflection	Resolution: 2.5→19.919 Å / Num. obs: 40494 / % possible obs: 99.7 % / Redundancy: 13.6 % / CC_1/2: 0.999 / Net I/σ(I): 16.1
Reflection shell	Resolution: 2.5→2.55 Å / Num. unique obs: 2913 / CC_1/2: 0.597

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→19.919 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.938 / WR_factor R_free: 0.256 / WR_factor R_work: 0.196 / SU B: 33.081 / SU ML: 0.323 / Average fsc free: 0.9279 / Average fsc work: 0.9448 / Cross valid method: FREE R-VALUE / ESU R: 0.537 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2639	2021	4.998 %
R_work	0.2017	38415	-
all	0.205	-	-
obs	-	40436	99.729 %

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: 115.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.565 Å²	0 Å²	0 Å²
2-	-	-3.074 Å²	0 Å²
3-	-	-	-2.491 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.919 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7729	0	18	64	7811

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	7914
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7567
X-RAY DIFFRACTION	r_angle_refined_deg	1.444	1.839	10691
X-RAY DIFFRACTION	r_angle_other_deg	0.804	1.771	17431
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.848	5	960
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.753	5	39
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.184	10	1425
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.914	10	386
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1183
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9209
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1821
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	1694
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	6677
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	3822
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4156
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	137
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.025	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.177	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.336	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.103	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	6.839	9.556	3846
X-RAY DIFFRACTION	r_mcbond_other	6.839	9.556	3846
X-RAY DIFFRACTION	r_mcangle_it	9.957	17.173	4801
X-RAY DIFFRACTION	r_mcangle_other	9.956	17.173	4802
X-RAY DIFFRACTION	r_scbond_it	7.041	10.263	4068
X-RAY DIFFRACTION	r_scbond_other	7.041	10.262	4069
X-RAY DIFFRACTION	r_scangle_it	10.748	18.606	5889
X-RAY DIFFRACTION	r_scangle_other	10.747	18.605	5890
X-RAY DIFFRACTION	r_lrange_it	13.71	90.16	8692
X-RAY DIFFRACTION	r_lrange_other	13.71	90.167	8691
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.097	0.05	5636
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.113	0.05	9324

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	0.09709	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09709	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11308	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11308	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
2.5-2.564	0.397	143	0.417	2716	0.416	2861	0.859	0.849	99.9301	0.403
2.564-2.633	0.355	142	0.398	2699	0.395	2841	0.866	0.85	100	0.377
2.633-2.708	0.351	137	0.36	2615	0.36	2752	0.902	0.898	100	0.338
2.708-2.79	0.365	133	0.311	2546	0.314	2680	0.901	0.928	99.9627	0.282
2.79-2.879	0.37	132	0.284	2513	0.288	2645	0.904	0.94	100	0.248
2.879-2.978	0.343	125	0.27	2374	0.273	2500	0.917	0.951	99.96	0.235
2.978-3.088	0.32	122	0.232	2315	0.236	2437	0.93	0.964	100	0.201
3.088-3.211	0.285	119	0.238	2261	0.241	2380	0.945	0.961	100	0.208
3.211-3.349	0.292	113	0.226	2139	0.229	2252	0.94	0.968	100	0.2
3.349-3.508	0.297	109	0.215	2066	0.219	2175	0.944	0.972	100	0.194
3.508-3.691	0.263	103	0.213	1978	0.215	2082	0.962	0.972	99.952	0.195
3.691-3.907	0.284	100	0.199	1911	0.204	2011	0.951	0.975	100	0.189
3.907-4.165	0.257	92	0.178	1749	0.182	1841	0.958	0.981	100	0.171
4.165-4.483	0.208	87	0.15	1664	0.153	1751	0.969	0.986	100	0.149
4.483-4.886	0.225	82	0.157	1541	0.16	1623	0.968	0.984	100	0.165
4.886-5.422	0.237	75	0.172	1416	0.175	1491	0.963	0.982	100	0.181
5.422-6.185	0.291	66	0.206	1264	0.21	1330	0.953	0.976	100	0.216
6.185-7.399	0.26	59	0.207	1106	0.21	1165	0.957	0.973	100	0.226
7.399-9.808	0.198	48	0.145	905	0.148	953	0.98	0.988	100	0.187
9.808-19.919	0.226	34	0.175	637	0.177	671	0.956	0.98	100	0.223

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	0.2254	0.1076	-0.014	2.1213	-0.0371	0.6608	-0.0259	0.1223	-0.0785	0.4719	0.0285	0.2129	-0.1403	-0.1173	-0.0025	0.2034	0.0468	0.1087	0.1518	0.005	0.0965	-11.4609	1.587	1.0646
2	0.1214	0.1176	0.1835	3.5154	1.1082	0.6646	-0.021	0.0136	0.0791	1.0937	0.1065	-0.434	0.333	-0.0787	-0.0855	0.4101	0.0463	-0.2041	0.1607	0.0082	0.1621	-12.55	-44.3099	-16.2045
3	0.0804	0.0878	-0.2141	0.9548	-0.7051	0.9759	0.0646	0.045	-0.0031	-0.0658	-0.2004	-0.1717	-0.2328	0.0808	0.1358	0.1879	0.0242	-0.0169	0.1276	0.0762	0.0821	3.0702	8.4066	-12.6731
4	0.0667	0.2228	0.2306	3.198	1.0292	0.8809	-0.0235	-0.003	0.0399	-0.1886	-0.0652	0.2	0.0041	0.0278	0.0887	0.0736	0.0447	-0.0259	0.0668	-0.0453	0.1111	-23.3645	-45.8542	-34.3822

Refinement TLS group

Selection: ALL

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