PDB-8blu: The PDZ domains of human SDCBP

ID or keywords:

Entry

Database: PDB / ID: 8blu

Title

The PDZ domains of human SDCBP

Components

Syntenin-1

Keywords

SIGNALING PROTEIN / Apo / cytosolic

Function / homology

Function and homology information

interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Bradshaw, W.J. / Katis, V.L. / Daniel-Mozo, M. / Bountra, C. / von Delft, F. / Brennan, P.E.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The PDZ domains of human SDCBP
Authors: Bradshaw, W.J. / Katis, V.L. / Daniel-Mozo, M. / Bountra, C. / von Delft, F. / Brennan, P.E.

History

Deposition	Nov 10, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 30, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8blu.cif.gz	193.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8blu.ent.gz	147.7 KB	Display	PDB format
PDBx/mmJSON format	8blu.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/bl/8blu ftp://data.pdbj.org/pub/pdb/validation_reports/bl/8blu	HTTPS FTP

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Related structure data

Related structure data	1n99S S: Starting model for refinement
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	#245 - May 2020 Spliceosomes similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #56 - Aug 2004 Caspases similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Syntenin-1

B: Syntenin-1

C: Syntenin-1

D: Syntenin-1

hetero molecules

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

1

A: Syntenin-1

hetero molecules

defined by author
Evidence: gel filtration
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Syntenin-1

hetero molecules

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

3

C: Syntenin-1

hetero molecules

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

4

D: Syntenin-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	79.603, 49.588, 118.194
Angle α, β, γ (deg.)	90.000, 93.928, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	106 - 297	3 - 194
2	1	1	GLU	GLU	106 - 297	3 - 194
3	2	2	VAL	VAL	106 - 298	3 - 195
4	2	2	VAL	VAL	106 - 298	3 - 195
5	3	3	VAL	VAL	106 - 298	3 - 195
6	3	3	VAL	VAL	106 - 298	3 - 195
7	4	4	GLU	GLU	106 - 297	3 - 194
8	4	4	GLU	GLU	106 - 297	3 - 194
9	5	5	GLU	GLU	106 - 297	3 - 194
10	5	5	GLU	GLU	106 - 297	3 - 194
11	6	6	VAL	VAL	106 - 298	3 - 195
12	6	6	VAL	VAL	106 - 298	3 - 195

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

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Syntenin-1 / Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain- ...Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain-interacting protein 18 / TACIP18 / Scaffold protein Pbp1 / Syndecan-binding protein 1 Mass: 21430.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O00560

#1: Protein

Syntenin-1 / Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain- ...

Mass: 21430.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Plasmid: pNIC28-Bsa4 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: O00560

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Non-polymers , 8 types, 796 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-DGL / D-GLUTAMIC ACID Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#6: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#7: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#8: Chemical	ChemComp-ALA / ALANINE Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.71 Å³/Da / Density % sol: 54.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 50 mM imidazole, 50 mM MES, 100 mM Morpheus amino acid mix, 8.3% PEG 8000, 16.6% Ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 12, 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: 1.5→68.07 Å / Num. obs: 147705 / % possible obs: 100 % / Redundancy: 26 % / CC_1/2: 1 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.024 / R_rim(I) all: 0.088 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 18.9 % / R_merge(I) obs: 5.446 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7241 / CC_1/2: 0.416 / R_pim(I) all: 1.84 / R_rim(I) all: 5.754 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1N99

1n99

Resolution: 1.5→63.955 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.961 / WR_factor R_free: 0.207 / WR_factor R_work: 0.169 / SU B: 2.082 / SU ML: 0.07 / Average fsc free: 0.9454 / Average fsc work: 0.9554 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2229	2055	1.392 %
R_work	0.183	145584	-
all	0.184	-	-
obs	-	147639	99.966 %

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: 31.328 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.933 Å²	-0 Å²	0.63 Å²
2-	-	1.169 Å²	0 Å²
3-	-	-	0.671 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→63.955 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5950	0	121	774	6845

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	6448
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	6233
X-RAY DIFFRACTION	r_angle_refined_deg	1.727	1.641	8716
X-RAY DIFFRACTION	r_angle_other_deg	0.581	1.57	14610
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.112	5	859
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.349	5	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.695	10	1252
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.409	10	268
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1026
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7237
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1163
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	1183
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	5724
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	3097
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	3594
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	575
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.195	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	135
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	36
X-RAY DIFFRACTION	r_mcbond_it	3.252	3.229	3219
X-RAY DIFFRACTION	r_mcbond_other	3.251	3.23	3219
X-RAY DIFFRACTION	r_mcangle_it	4.369	4.827	4026
X-RAY DIFFRACTION	r_mcangle_other	4.372	4.828	4027
X-RAY DIFFRACTION	r_scbond_it	4.661	3.642	3229
X-RAY DIFFRACTION	r_scbond_other	4.658	3.642	3227
X-RAY DIFFRACTION	r_scangle_it	6.538	5.287	4647
X-RAY DIFFRACTION	r_scangle_other	6.537	5.287	4648
X-RAY DIFFRACTION	r_lrange_it	8.127	48.148	7313
X-RAY DIFFRACTION	r_lrange_other	8.048	44.187	7124
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.108	0.05	5760
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.127	0.05	5754
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.128	0.05	5734
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.108	0.05	5999
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.11	0.05	5955
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.1	0.05	6063

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	0.10772	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10772	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12666	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.12666	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.12777	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.12777	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.10788	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.10788	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.11049	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.11049	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09972	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09972	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
1.5-1.539	0.385	177	0.411	10667	0.41	10844	0.876	0.867	100	0.398
1.539-1.581	0.391	179	0.356	10359	0.357	10538	0.905	0.896	100	0.345
1.581-1.627	0.343	144	0.313	10164	0.313	10315	0.902	0.915	99.9321	0.296
1.627-1.677	0.323	150	0.283	9806	0.284	9964	0.905	0.934	99.9197	0.262
1.677-1.732	0.311	128	0.258	9596	0.258	9729	0.945	0.951	99.9486	0.232
1.732-1.793	0.258	157	0.235	9235	0.236	9401	0.958	0.963	99.9043	0.21
1.793-1.86	0.256	118	0.219	8914	0.219	9040	0.956	0.97	99.9115	0.192
1.86-1.936	0.224	104	0.196	8613	0.196	8720	0.973	0.976	99.9656	0.17
1.936-2.022	0.205	117	0.19	8239	0.191	8356	0.974	0.977	100	0.169
2.022-2.121	0.225	115	0.18	7895	0.181	8014	0.971	0.98	99.9501	0.161
2.121-2.235	0.229	93	0.171	7566	0.171	7662	0.968	0.982	99.9608	0.155
2.235-2.371	0.218	106	0.168	7122	0.169	7228	0.973	0.983	100	0.154
2.371-2.534	0.214	86	0.162	6701	0.162	6787	0.971	0.984	100	0.15
2.534-2.737	0.162	88	0.157	6244	0.158	6332	0.981	0.985	100	0.15
2.737-2.998	0.158	77	0.164	5749	0.164	5826	0.983	0.984	100	0.158
2.998-3.35	0.228	74	0.173	5256	0.173	5330	0.968	0.983	100	0.17
3.35-3.867	0.206	43	0.169	4641	0.169	4684	0.977	0.985	100	0.17
3.867-4.732	0.192	43	0.144	3948	0.145	3991	0.979	0.988	100	0.15
4.732-6.673	0.252	41	0.172	3088	0.173	3129	0.98	0.986	100	0.179
6.673-63.955	0.195	15	0.18	1781	0.18	1796	0.986	0.976	100	0.185

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