PDB-5k70: Sidekick-2 immunoglobulin domains 1-4 H18R/N22S mutant

ID or keywords:

Entry

Database: PDB / ID: 5k70

Title

Sidekick-2 immunoglobulin domains 1-4 H18R/N22S mutant

Components

Protein sidekick-2

Keywords

CELL ADHESION / immunoglobulin

Function / homology

Function and homology information

SDK interactions / camera-type eye photoreceptor cell differentiation / retina layer formation / homophilic cell adhesion via plasma membrane adhesion molecules / synapse assembly / synapse / plasma membrane
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Goodman, K.M. / Mannepalli, S. / Honig, B. / Shapiro, L.

Citation

Journal: Elife / Year: 2016
Title: Molecular basis of sidekick-mediated cell-cell adhesion and specificity.
Authors: Goodman, K.M. / Yamagata, M. / Jin, X. / Mannepalli, S. / Katsamba, P.S. / Ahlsen, G. / Sergeeva, A.P. / Honig, B. / Sanes, J.R. / Shapiro, L.

History

Deposition	May 25, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2016	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Apr 3, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5k70.cif.gz	583.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5k70.ent.gz	485.2 KB	Display	PDB format
PDBx/mmJSON format	5k70.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5k70_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5k70_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5k70_validation.xml.gz	52.4 KB	Display
Data in CIF	5k70_validation.cif.gz	71.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k7/5k70 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k70	HTTPS FTP

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Related structure data

Related structure data	5k6uC 5k6vC 5k6wC 5k6xC 5k6yC 5k6zC C: citing same article (ref.)
Similar structure data	5xx0-1 5xwx-2 5xx0-2 5k6u-d 5k6y-2 5k6y-3 2om5-d 4iqa-d 5xpw-1 5e4i-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#185 - May 2015 Titin similarity (3) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (3) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Protein sidekick-2

B: Protein sidekick-2

C: Protein sidekick-2

D: Protein sidekick-2

hetero molecules

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

1

A: Protein sidekick-2

hetero molecules

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

2

B: Protein sidekick-2

hetero molecules

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

3

C: Protein sidekick-2

hetero molecules

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

4

D: Protein sidekick-2

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.890, 113.430, 185.906
Angle α, β, γ (deg.)	90.00, 103.69, 90.00
Int Tables number	5
Space group name H-M	I121

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Protein sidekick-2 Mass: 42381.191 Da / Num. of mol.: 4 / Mutation: H18R/N22S mutant Source method: isolated from a genetically manipulated source Details: N-terminal residues GPAGA are expression construct-derived and would be cleaved in the native protein Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sdk2, Kiaa1514 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6V4S5

#1: Protein

Protein sidekick-2

Mass: 42381.191 Da / Num. of mol.: 4 / Mutation: H18R/N22S mutant
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GPAGA are expression construct-derived and would be cleaved in the native protein
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Sdk2, Kiaa1514 / Cell line (production host): HEK293 / Production host:

Homo sapiens (human) / References: UniProt: Q6V4S5

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Sugars , 3 types, 7 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-6DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 76 molecules

#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.35 Å³/Da / Density % sol: 63.29 %
Crystal grow	Temperature: 295 K / Method: batch mode Details: 13.5% PEG3350 (w/v), 0.1M ammonium sulfate, 0.2M sodium dihydrogen phosphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.7→65 Å / Num. obs: 61442 / % possible obs: 100 % / Redundancy: 3.6 % / R_merge(I) obs: 0.101 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.546 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Sdk1

Resolution: 2.7→39.516 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.76

	R_factor	Num. reflection	% reflection
R_free	0.2434	3112	5.06 %
R_work	0.206	-	-
obs	0.2079	61442	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.7→39.516 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11311	0	222	62	11595

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11806
X-RAY DIFFRACTION	f_angle_d	1.064	16146
X-RAY DIFFRACTION	f_dihedral_angle_d	13.255	4263
X-RAY DIFFRACTION	f_chiral_restr	0.04	1886
X-RAY DIFFRACTION	f_plane_restr	0.004	2086

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7-2.7422	0.3712	144	0.3182	2615	X-RAY DIFFRACTION	100
2.7422-2.7871	0.3784	150	0.3095	2622	X-RAY DIFFRACTION	100
2.7871-2.8352	0.368	154	0.2918	2649	X-RAY DIFFRACTION	100
2.8352-2.8867	0.3233	143	0.2829	2616	X-RAY DIFFRACTION	100
2.8867-2.9422	0.3101	119	0.2803	2675	X-RAY DIFFRACTION	100
2.9422-3.0023	0.31	153	0.2646	2635	X-RAY DIFFRACTION	100
3.0023-3.0675	0.286	117	0.2478	2653	X-RAY DIFFRACTION	100
3.0675-3.1388	0.2775	154	0.2461	2633	X-RAY DIFFRACTION	100
3.1388-3.2173	0.2622	146	0.24	2625	X-RAY DIFFRACTION	100
3.2173-3.3042	0.2801	143	0.2345	2655	X-RAY DIFFRACTION	100
3.3042-3.4014	0.244	125	0.2332	2638	X-RAY DIFFRACTION	100
3.4014-3.5111	0.303	150	0.2238	2657	X-RAY DIFFRACTION	100
3.5111-3.6366	0.2544	127	0.2107	2641	X-RAY DIFFRACTION	100
3.6366-3.782	0.2503	145	0.2065	2674	X-RAY DIFFRACTION	100
3.782-3.954	0.2683	156	0.1889	2624	X-RAY DIFFRACTION	100
3.954-4.1623	0.2061	152	0.1779	2639	X-RAY DIFFRACTION	100
4.1623-4.4227	0.1764	142	0.1604	2648	X-RAY DIFFRACTION	100
4.4227-4.7637	0.1644	123	0.1466	2680	X-RAY DIFFRACTION	100
4.7637-5.2421	0.199	152	0.1596	2654	X-RAY DIFFRACTION	100
5.2421-5.9984	0.206	151	0.17	2662	X-RAY DIFFRACTION	100
5.9984-7.5487	0.2381	136	0.1982	2693	X-RAY DIFFRACTION	100
7.5487-39.52	0.1905	130	0.1878	2742	X-RAY DIFFRACTION	100

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	6.4511	0.1046	1.0731	0.7254	0.2466	1.796	0.0546	-0.2923	0.0127	0.0269	0.0124	0.0268	-0.021	0.0169	-0.0446	0.2722	0.0321	0.0384	0.3292	0.0036	0.2032	-15.0158	-37.4761	-5.6012
2	4.6236	-1.8563	1.999	4.8155	-1.057	3.9139	0.2427	0.0089	-0.7405	-0.0443	-0.0428	-0.0838	0.6491	0.2464	-0.1503	0.4133	0.0075	-0.02	0.3028	-0.0213	0.3063	-32.3609	-49.1508	-35.4935
3	1.5068	0.1894	-0.877	1.3624	-0.4198	3.6725	-0.1997	-0.4611	0.0259	0.1559	0.334	0.2617	-0.3066	-1.2	-0.1277	0.6572	-0.0013	-0.0385	0.9913	-0.0075	0.3211	-83.0119	-48.9784	-75.0881
4	2.4618	-0.6169	1.2921	5.1516	-0.7787	2.6439	-0.1849	0.1176	0.2816	0.0191	-0.0044	-0.0134	-0.3938	-0.0464	0.2641	0.3722	-0.0938	-0.0491	0.3588	-0.0512	0.2878	-53.8861	-37.6695	-56.99
5	3.5675	-0.7325	0.9652	1.2668	-0.3344	3.1427	-0.0503	-0.2374	-0.1967	0.01	0.0888	0.0864	-0.095	-0.1684	-0.0375	0.2764	0.0097	0.0126	0.2662	0.0053	0.266	-55.2639	-27.3511	-14.1339
6	4.9236	-0.4249	1.4967	2.5791	-0.659	1.6038	0.2319	0.5125	-0.9932	0.061	0.029	0.1328	0.4931	0.2405	-0.1799	0.4563	0.1174	-0.019	0.4193	-0.0916	0.4531	3.6701	-66.5838	-20.4198
7	4.3983	-1.3419	0.5666	2.3794	0.6592	3.4379	-0.0176	-0.3966	-0.4004	0.5881	0.0754	0.3423	0.0508	-0.7809	-0.076	0.716	-0.1495	0.0873	0.6155	-0.0241	0.322	-74.4566	-61.178	-35.1749
8	0.801	0.0505	0.1488	0.1062	-0.0198	0.3919	-0.8323	-0.1798	1.2018	-1.2668	-0.2125	0.3439	-2.8476	-0.1394	0.2384	2.6672	-0.0115	-0.4926	0.1862	0.3888	0.5382	-68.3555	-19.224	-92.5044
9	4.9247	-1.1117	-0.8806	1.6572	0.5772	1.6819	-0.014	0.4313	0.2351	-0.2117	0.0259	-0.1177	-0.3148	-0.0014	-0.0115	0.3567	0.0075	-0.0339	0.2296	0.0176	0.214	-45.3288	-19.2046	-33.0835
10	1.1514	-1.2121	0.3819	2.476	0.2969	1.7894	0.2401	0.7595	0.3608	-0.2799	-0.2826	-0.5011	-0.0113	0.2819	0.0503	0.335	0.0754	0.0707	0.6409	0.0196	0.3342	10.9018	-45.2973	-23.5611
11	3.9459	0.6626	-0.0351	4.0928	-0.6231	3.4771	-0.0029	-0.2499	-0.6362	0.2692	0.1382	-0.3586	0.3964	0.1893	-0.1206	0.5115	-0.0808	-0.0593	0.3196	-0.0086	0.4146	-55.2452	-68.3578	-45.6569
12	0.9006	0.521	-0.7371	0.8647	-0.9285	2.1035	-0.3407	0.8414	0.0031	-1.1772	-0.0604	-0.2955	-0.597	0.4324	0.4599	1.2447	-0.1875	0.0419	0.8035	0.0728	0.4211	-64.861	-40.0236	-100.0439
13	4.3152	-0.5394	1.2477	2.8155	-0.0528	1.2633	-0.3353	0.6693	1.7442	-0.0485	-0.205	-0.6733	-0.4944	0.6516	0.4074	0.4394	-0.0997	-0.0747	0.4481	0.1414	0.7067	-2.7844	-22.9715	-16.7537
14	3.8296	-0.5379	1.7477	0.8825	0.0762	2.9387	-0.1925	0.7276	0.4551	-0.2163	-0.0462	-0.1707	0.1211	0.3441	0.2252	0.3399	-0.0984	0.0364	0.5826	0.0895	0.2932	-25.9936	-30.8561	-46.9276
15	1.15	-0.3285	0.8915	0.7725	-0.3403	2.5138	0.0681	0.3658	-0.1596	-1.3071	0.1752	-0.1508	0.4576	0.2244	-0.2324	1.0674	-0.2165	0.0165	0.5081	-0.0421	0.3895	-70.9539	-62.5048	-88.1285
16	1.9367	0.1071	1.6157	1.739	0.0921	3.4692	0.1436	0.7384	-0.2845	-0.3939	0.2143	-0.4845	0.7189	1.1047	-0.3834	0.5024	-0.0169	0.0491	0.744	-0.2544	0.4443	-41.8966	-54.8238	-64.1727

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and ((resseq 1:90))
2	X-RAY DIFFRACTION	2	chain 'B' and ((resseq 1:90))
3	X-RAY DIFFRACTION	3	chain 'C' and ((resseq 1:90))
4	X-RAY DIFFRACTION	4	chain 'D' and ((resseq 1:90))
5	X-RAY DIFFRACTION	5	chain 'A' and ((resseq 91:184))
6	X-RAY DIFFRACTION	6	chain 'B' and ((resseq 91:184))
7	X-RAY DIFFRACTION	7	chain 'C' and ((resseq 91:184))
8	X-RAY DIFFRACTION	8	chain 'D' and ((resseq 91:183))
9	X-RAY DIFFRACTION	9	chain 'A' and ((resseq 192:285))
10	X-RAY DIFFRACTION	10	chain 'B' and ((resseq 192:285))
11	X-RAY DIFFRACTION	11	chain 'C' and ((resseq 192:285))
12	X-RAY DIFFRACTION	12	chain 'D' and ((resseq 193:285))
13	X-RAY DIFFRACTION	13	chain 'A' and ((resseq 286:379))
14	X-RAY DIFFRACTION	14	chain 'B' and ((resseq 286:379))
15	X-RAY DIFFRACTION	15	chain 'C' and ((resseq 286:379))
16	X-RAY DIFFRACTION	16	chain 'D' and ((resseq 286:378))

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Protein , 1 types, 4 molecules ABCD

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Sugars , 3 types, 7 molecules

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Non-polymers , 2 types, 76 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

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Protein , 1 types, 4 molecules ABCD

-
Sugars , 3 types, 7 molecules

-
Non-polymers , 2 types, 76 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi