PDB-6pll: Crystal structure of the ZIG-8 IG1 homodimer

ID or keywords:

Entry

Database: PDB / ID: 6pll

Title

Crystal structure of the ZIG-8 IG1 homodimer

Components

Zwei Ig domain protein zig-8

Keywords

CELL ADHESION /

Cell Surface Receptor /

Immunoglobulin Superfamily /

Nervous System /

Homodimer

Function / homology

Function and homology information

neuron projection membrane / synapse organization / extracellular region
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.693 Å

Authors

Cheng, S. / Ozkan, E.

Funding support

United States, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Family of neural wiring receptors in bilaterians defined by phylogenetic, biochemical, and structural evidence.
Authors: Cheng, S. / Park, Y. / Kurleto, J.D. / Jeon, M. / Zinn, K. / Thornton, J.W. / Ozkan, E.

History

Deposition	Jul 1, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6pll.cif.gz	157.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6pll.ent.gz	124.6 KB	Display	PDB format
PDBx/mmJSON format	6pll.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/pl/6pll ftp://data.pdbj.org/pub/pdb/validation_reports/pl/6pll	HTTPS FTP

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Related structure data

Related structure data	6on6C 6on9SC 6onbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3haw-2 3i2l-2 1cuo-d 4koc-d 3hgb-d 2hx7-2 2hx7-1 4hi4-5 3rur-4 3k2p-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (2) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (2) #63 - Mar 2005 T-Cell Receptor similarity (2) #132 - Dec 2010 Adenovirus similarity (2) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (2)

Deposited unit

A: Zwei Ig domain protein zig-8

B: Zwei Ig domain protein zig-8

C: Zwei Ig domain protein zig-8

hetero molecules

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

1

C: Zwei Ig domain protein zig-8

hetero molecules

defined by author
Evidence: gel filtration, Very weak dimer, approx KD of 5 millimolar
14.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Zwei Ig domain protein zig-8

B: Zwei Ig domain protein zig-8

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.560, 73.560, 270.631
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein

Zwei Ig domain protein zig-8 / 2 Ig domain protein zig-8

Mass: 14297.955 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Caenorhabditis elegans (invertebrata) / Gene: zig-8, Y39E4B.8 / Cell line (production host): High Five cells / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: G5ED00

#2: Chemical

ChemComp-SO4 / SULFATE ION /

Sulfate

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

#3: 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 /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O

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: 2.46 Å³/Da / Density % sol: 50.08 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium dihydrogen phosphate, 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 120 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791928 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 13, 2019
Radiation	Monochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791928 Å / Relative weight: 1
Reflection	Resolution: 2.69→50 Å / Num. obs: 12889 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 21.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.225 / R_rim(I) all: 0.23 / Net I/σ(I): 15.33
Reflection shell	Resolution: 2.69→2.86 Å / Redundancy: 17.7 % / R_merge(I) obs: 2.597 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 1967 / CC_1/2: 0.529 / R_rim(I) all: 2.673 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.16_3549: ???)	refinement
XDS	20190315	data reduction
XDS	20190315	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6ON9

6on9

Resolution: 2.693→46.381 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.63

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2695	662	5.17 %	Random selection
R_work	0.2368	-	-	-
obs	0.2385	12800	99.65 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.693→46.381 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2742	0	24	13	2779

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2821
X-RAY DIFFRACTION	f_angle_d	0.753	3852
X-RAY DIFFRACTION	f_dihedral_angle_d	11.994	1726
X-RAY DIFFRACTION	f_chiral_restr	0.052	438
X-RAY DIFFRACTION	f_plane_restr	0.005	504

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 (%)
2.6935-2.9014	0.4227	126	0.3577	2314	X-RAY DIFFRACTION	99
2.9014-3.1933	0.3292	130	0.309	2374	X-RAY DIFFRACTION	100
3.1933-3.6552	0.3175	130	0.2709	2384	X-RAY DIFFRACTION	100
3.6552-4.6046	0.261	135	0.2061	2444	X-RAY DIFFRACTION	100
4.6046-46.3875	0.2159	141	0.2075	2622	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	4.1931	0.3789	3.8545	0.5172	-0.8434	6.6273	-0.5565	-0.6175	3.0277	-0.824	-0.1099	-0.6439	-1.6727	-0.9304	0.3704	0.4683	0.0123	-0.0185	0.4204	0.0572	1.0937	1.0373	43.0037	15.1242
2	5.6134	0.0237	-1.2694	2.0588	-0.753	2.6009	0.059	-0.4559	-0.3463	-0.0067	-0.2724	-0.0345	0.5791	-0.5735	0.0009	0.4385	-0.1691	-0.0336	0.5856	-0.0485	0.3291	0.7276	29.0177	11.5931
3	9.6005	-2.1964	-0.594	2.9831	0.4683	8.6398	-0.0873	0.3916	-0.4927	0.7347	0.1241	-0.7537	1.3285	0.6916	-0.2524	0.733	0.0157	-0.0835	0.512	-0.0601	0.5669	7.6943	21.2753	19.3026
4	3.0699	-0.365	-1.3159	1.3172	-1.1379	6.1442	-0.0373	-0.1647	-0.4011	0.1244	-0.1281	0.2015	0.6599	-0.5385	0.1755	0.4893	-0.1511	-0.071	0.4208	-0.0137	0.4775	-2.4614	25.9982	19.6197
5	4.5812	2.0703	4.652	2.5328	2.8654	5.0741	-0.6393	-0.4891	2.3669	0.7349	-0.5122	0.4064	-2.975	0.0331	0.9046	0.9468	0.1577	-0.0108	0.6092	-0.0994	0.8693	10.518	41.5194	43.0763
6	4.7622	-3.5812	5.1199	3.3281	-3.4154	5.6379	-0.4131	-1.2843	-0.0705	0.3406	0.6701	0.7869	-1.0429	-1.2363	-0.0476	0.5607	0.1922	0.0171	1.2952	0.0971	0.7698	-1.7536	32.7159	45.8184
7	6.6443	-1.285	1.7	5.6968	0.132	8.8642	-0.1878	-0.7032	-0.2921	0.4196	0.1078	-0.0027	1.099	-0.5375	-0.1154	0.5603	0.2142	-0.0197	0.6579	0.1461	0.4039	14.0454	24.7635	46.8148
8	8.7404	0.5537	-1.3289	4.2029	-1.0076	7.5658	-0.248	-0.1063	-0.0621	-0.5197	0.2844	0.0561	1.2869	-0.9436	0.0779	0.5192	0.0641	-0.0442	0.4838	0.0001	0.3208	6.1616	22.191	33.8733
9	3.2773	0.9901	-3.0772	6.7329	1.1003	3.367	-0.9151	0.4253	-0.7049	0.7828	0.4509	0.853	1.1875	-1.1367	0.5255	0.9681	-0.1536	-0.0163	0.6326	0.2164	0.7173	5.8623	18.1054	42.6665
10	7.559	-3.6889	-0.1624	3.5626	-2.4855	7.3779	0.0295	0.3833	-0.3223	-2.4972	0.5139	-1.3085	1.8982	2.2465	-0.457	0.8956	0.2771	0.0393	0.9902	0.0828	0.6895	21.5175	25.5746	39.7703
11	4.8035	5.0256	-4.3608	2.1762	-0.9746	6.4803	1.3519	1.162	-0.4332	0.6978	-0.3273	-0.4016	0.1108	-1.2702	-0.5267	0.4107	-0.0159	-0.0353	0.5445	0.0684	0.4286	4.9089	29.486	37.7729
12	6.3536	3.2293	3.8637	5.1086	-1.3079	5.4115	0.8433	-0.3047	1.772	1.5421	-0.0791	0.9651	-0.8376	-0.5753	-0.4688	0.7624	-0.0827	0.2568	0.795	-0.0092	0.6095	-7.8202	28.8407	35.7726
13	3.1751	-1.3339	1.4572	4.4552	-0.8938	4.8477	0.1721	-0.0462	0.8873	-0.0165	-0.1845	-0.409	0.148	0.7603	0.4936	0.5436	0.3144	-0.022	0.7434	0.0481	0.4412	13.9391	31.4746	44.371
14	2.3852	1.7006	-1.6326	5.3179	-5.4997	5.6841	-0.2604	-0.3234	0.2864	0.9403	1.1044	0.2765	-1.3433	-1.6592	-0.9533	0.6585	0.062	0.1268	0.7944	0.0437	0.6833	-13.7614	37.9969	26.7084
15	6.1083	-2.6643	1.8779	2.3806	0.6277	8.4077	-0.3321	1.3889	1.1783	0.2197	-0.8216	-1.9207	-0.7084	-0.1574	0.6406	0.7346	-0.1207	-0.0983	1.1535	-0.0033	0.6679	-21.873	28.2597	23.3153
16	1.9681	-1.5613	0.754	4.7222	0.8932	5.026	0.8563	0.4434	0.0959	-0.2321	-0.7377	1.3146	-0.1422	-1.9051	0.1961	0.6124	0.1522	-0.0061	1.4835	0.2609	0.835	-29.1921	34.9228	31.0191
17	6.8441	0.5245	2.0282	5.9681	0.4054	3.8956	0.1625	0.6825	-0.8332	0.2453	-0.0072	0.9765	-0.4729	-1.8284	-0.3757	0.6196	0.0418	0.0611	1.2613	0.0679	0.7083	-30.7814	34.1973	39.5591
18	6.3597	-0.5358	-2.2067	5.7028	0.5	6.5279	-0.067	-0.0051	0.0478	0.2261	-0.1435	-0.1332	-0.0386	-1.5686	0.2842	0.5231	0.1775	0.0707	1.0358	0.1648	0.5381	-25.5782	36.5898	32.8779

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 71 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 137 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 20 through 32 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 33 through 43 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 44 through 58 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 59 through 90 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 91 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 113 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 114 through 120 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 121 through 126 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 127 through 137 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 23 through 32 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 33 through 43 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 44 through 71 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 72 through 99 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 100 through 137 )

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