PDB-5gmi: Crystal Structure of GRASP55 GRASP domain in complex with JAM-C C...

ID or keywords:

Entry

Database: PDB / ID: 5gmi

Title

Crystal Structure of GRASP55 GRASP domain in complex with JAM-C C-terminus

Components

Golgi reassembly-stacking protein 2
Junctional adhesion molecule C

Keywords

STRUCTURAL PROTEIN/PEPTIDE / beta strand sandswish / classic PDZ peptide binding groove / conserved carboxylate-binding loop /

STRUCTURAL PROTEIN-PEPTIDE COMPLEX

Function / homology

Function and homology information

regulation of actin cytoskeleton organization by cell-cell adhesion / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of membrane permeability /

regulation of neutrophil chemotaxis / hematopoietic stem cell migration to bone marrow / positive regulation of cellular extravasation / granulocyte migration / establishment of protein localization to plasma membrane /

organelle assembly / organelle organization ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.71 Å

Authors

Shi, N. / Shi, X. / Morelli, X. / Betzi, S. / Huang, X.

Citation

Journal: PLoS Genet. / Year: 2017
Title: Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis
Authors: Cartier-Michaud, A. / Bailly, A.L. / Betzi, S. / Shi, X. / Lissitzky, J.C. / Zarubica, A. / Serge, A. / Roche, P. / Lugari, A. / Hamon, V. / Bardin, F. / Derviaux, C. / Lembo, F. / Audebert, ...

History

Deposition	Jul 14, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 24, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 5, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5gmi.cif.gz	197 KB	Display	PDBx/mmCIF format
PDB format	pdb5gmi.ent.gz	158.4 KB	Display	PDB format
PDBx/mmJSON format	5gmi.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/gm/5gmi ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gmi	HTTPS FTP

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Related structure data

Related structure data	5gmjC 3rleS 5gml C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5gml-1 5gmj-1 3lvk-1 6b4f-d 1muh-d 5lvc-d 5316 5l7o-d 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	#99 - Mar 2008 Cadherin similarity (1) #21 - Sep 2001 Antibodies similarity (1) #182 - Feb 2015 Insulin receptor similarity (1)

Deposited unit

A: Golgi reassembly-stacking protein 2

B: Golgi reassembly-stacking protein 2

C: Junctional adhesion molecule C

D: Junctional adhesion molecule C

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

1

A: Golgi reassembly-stacking protein 2

B: Golgi reassembly-stacking protein 2

C: Junctional adhesion molecule C

D: Junctional adhesion molecule C

A: Golgi reassembly-stacking protein 2

B: Golgi reassembly-stacking protein 2

C: Junctional adhesion molecule C

D: Junctional adhesion molecule C

defined by author&software
113 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.492, 132.492, 220.706
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A
2	1	1	CHAIN B
1	1	2	CHAIN C
2	1	2	CHAIN D

NCS ensembles :

ID
1
2

#1: Protein	Golgi reassembly-stacking protein 2 / GRS2 / Golgi reassembly-stacking protein of 55 kDa / GRASP55 Mass: 25945.014 Da / Num. of mol.: 2 / Fragment: GRASP DOMAIN, UNP RESIDUES 2-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gorasp2,GOLPH6 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99JX3
#2: Protein/peptide	Junctional adhesion molecule C / JAM-C / JAM-2 / Junctional adhesion molecule 3 / JAM-3 Mass: 2289.504 Da / Num. of mol.: 2 / Fragment: PEPTIDE OF JAMC C TERMIANL / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9D8B7
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 89 / 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: 4.29 Å³/Da / Density % sol: 74.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: SODIUM FORMATE, SODIUM ACETATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.71→71.42 Å / Num. obs: 27006 / % possible obs: 99.9 % / Redundancy: 6.1 % / R_merge(I) obs: 0.1366 / Net I/σ(I): 7.1
Reflection shell	Resolution: 2.711→2.81 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.6674 / Mean I/σ(I) obs: 2.38 / % possible all: 100

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Processing

Software

Name	Version	Classification
xia2		data scaling
PHASER		phasing
PHENIX	1.9_1692	refinement
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RLE

3rle

Resolution: 2.71→71.42 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.58

	R_factor	Num. reflection	% reflection
R_free	0.291	1890	7.46 %
R_work	0.256	-	-
obs	0.259	25347	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 72.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.71→71.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3504	0	0	89	3593

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3606
X-RAY DIFFRACTION	f_angle_d	1.066	4893
X-RAY DIFFRACTION	f_dihedral_angle_d	12.704	1316
X-RAY DIFFRACTION	f_chiral_restr	0.045	537
X-RAY DIFFRACTION	f_plane_restr	0.004	641

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	1941	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1941	X-RAY DIFFRACTION	POSITIONAL
2	1	C	30	X-RAY DIFFRACTION	POSITIONAL
2	2	D	30	X-RAY DIFFRACTION	POSITIONAL

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 (%)
2.7109-2.7452	0.373	143	0.3569	1749	X-RAY DIFFRACTION	100
2.7452-2.7814	0.3467	139	0.3215	1762	X-RAY DIFFRACTION	100
2.7814-2.8195	0.3788	142	0.3224	1752	X-RAY DIFFRACTION	100
2.8195-2.8598	0.3037	139	0.3044	1725	X-RAY DIFFRACTION	100
2.8598-2.9024	0.3478	140	0.2963	1762	X-RAY DIFFRACTION	100
2.9024-2.9478	0.3543	135	0.3017	1722	X-RAY DIFFRACTION	100
2.9478-2.9961	0.3075	141	0.3015	1742	X-RAY DIFFRACTION	100
2.9961-3.0478	0.3479	139	0.3107	1720	X-RAY DIFFRACTION	100
3.0478-3.1032	0.3445	142	0.2897	1748	X-RAY DIFFRACTION	100
3.1032-3.1629	0.3169	139	0.2719	1763	X-RAY DIFFRACTION	100
3.1629-3.2275	0.3367	144	0.2506	1732	X-RAY DIFFRACTION	100
3.2275-3.2976	0.2343	140	0.2565	1754	X-RAY DIFFRACTION	100
3.2976-3.3743	0.2628	140	0.2489	1732	X-RAY DIFFRACTION	100
3.3743-3.4587	0.261	136	0.2416	1715	X-RAY DIFFRACTION	100
3.4587-3.5522	0.2656	141	0.2362	1744	X-RAY DIFFRACTION	100
3.5522-3.6568	0.2677	136	0.2513	1758	X-RAY DIFFRACTION	100
3.6568-3.7748	0.3275	138	0.2538	1743	X-RAY DIFFRACTION	100
3.7748-3.9097	0.2429	138	0.2386	1752	X-RAY DIFFRACTION	100
3.9097-4.0662	0.2205	141	0.2411	1723	X-RAY DIFFRACTION	100
4.0662-4.2513	0.2894	145	0.2348	1749	X-RAY DIFFRACTION	100
4.2513-4.4754	0.2626	141	0.2203	1718	X-RAY DIFFRACTION	100
4.4754-4.7557	0.304	141	0.2169	1743	X-RAY DIFFRACTION	100
4.7557-5.1228	0.3179	143	0.2341	1744	X-RAY DIFFRACTION	99
5.1228-5.6381	0.2947	130	0.2593	1732	X-RAY DIFFRACTION	99
5.6381-6.4535	0.3068	140	0.2815	1723	X-RAY DIFFRACTION	99
6.4535-8.1289	0.286	137	0.2697	1680	X-RAY DIFFRACTION	96
8.1289-71.4442	0.2897	150	0.2553	1727	X-RAY DIFFRACTION	99

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	2.4441	0.4431	0.3903	1.0789	1.1717	1.4846	-0.0618	0.8882	1.6365	-0.1599	0.0549	0.9214	-0.3511	-0.0796	-0.2159	0.4619	-0.0534	-0.0863	0.4716	0.2409	0.7974	53.737	12.4083	13.5962
2	9.4749	-6.5836	8.1058	4.5772	-5.479	7.7627	-1.0352	0.4519	0.2298	1.1548	1.6582	0.9611	-1.1941	-0.8207	-0.5019	0.7753	-0.1006	0.0338	0.728	0.3702	0.7216	70.6411	26.2138	-2.5955
3	6.1719	3.0887	-3.4802	5.7429	-3.8316	4.2811	0.1231	0.2155	0.0884	0.0134	0.151	0.1021	-0.0778	-0.2162	-0.3219	0.5428	-0.1797	-0.1265	0.3659	0.0637	0.3632	82.0401	26.7616	0.8705
4	2.1602	3.3946	-0.8747	6.9581	-0.4308	2.7303	-0.033	-0.177	-0.6577	-0.5523	0.1187	0.1208	0.2776	-0.6293	0.0147	0.5805	-0.2648	-0.0472	0.602	0.1628	0.5208	84.523	20.645	-0.6813
5	6.6468	-2.1719	-0.713	7.1547	0.6673	4.8169	-0.4952	0.1247	0.0939	-0.3979	0.3391	-0.7504	-0.002	0.0474	0.3149	0.6288	-0.2562	0.1078	0.4218	0.006	0.4979	77.0316	0.4641	7.4575
6	2.2128	0.1639	-1.5082	1.3354	-0.442	5.4888	-0.4821	-0.1929	0.1438	-2.8975	1.1857	-0.1405	1.4347	-1.5531	-0.6229	1.7732	-0.2098	-0.016	0.9826	-0.0718	0.7815	74.1401	1.5864	-7.8618
7	3.6756	0.0431	0.4726	6.4187	-1.3414	1.7373	-0.4023	0.3862	-0.0198	-0.6414	0.4053	-0.6268	-0.032	0.1196	0.0053	0.6374	-0.2718	0.0695	0.5377	0.0149	0.3725	75.8667	5.0814	7.1624
8	6.9404	0.2974	-2.214	5.2963	-2.4568	2.2524	0.6028	0.3895	-0.4639	1.0174	-0.2896	-1.4311	0.1201	0.3917	-0.1663	0.5173	-0.0337	-0.1161	0.2038	0.0237	0.4672	77.9806	-12.5437	20.0745
9	2.6412	1.8065	0.0031	1.9919	2.0909	5.1113	0.1565	-0.2703	-0.8521	0.1006	0.1383	-0.1405	0.4754	0.4043	-0.1987	0.4734	0.0284	-0.1622	0.4574	0.1055	0.4891	89.246	13.1937	29.9216
10	6.6864	1.8892	2.7214	5.8049	1.691	4.9011	0.1476	-0.375	-0.4278	0.1573	0.1169	0.1722	0.0568	-0.1083	-0.24	0.3223	0.0588	-0.084	0.374	0.0336	0.3246	93.3694	15.6286	34.3525
11	7.9547	0.325	0.8013	2.9979	-0.2079	1.8687	0.129	-0.9033	0.207	0.5693	-0.1991	-0.0923	-0.0288	-0.159	0.1165	0.5487	-0.1142	-0.0486	0.3332	-0.0245	0.3456	69.1252	9.8475	29.7639
12	9.7514	-4.1503	3.1902	4.9935	1.9537	4.4302	0.4991	-0.4945	0.139	-0.4272	-0.2255	-0.2366	1.9801	-0.5846	-0.38	0.8598	-0.0463	-0.0733	0.5468	-0.0548	0.6143	84.371	19.5887	38.8176
13	8.2863	5.8965	5.5982	4.484	5.0532	7.8051	-0.3315	-0.2956	-2.2026	-0.5297	-1.304	2.5719	1.904	-2.0935	1.6826	1.7752	-0.6643	0.1708	1.2905	-0.4147	2.3251	85.3952	17.2809	-5.7434

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID -14 THROUGH 5 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 6 THROUGH 19 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 20 THROUGH 85 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 86 THROUGH 109 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 110 THROUGH 139 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 140 THROUGH 161 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 162 THROUGH 208 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID -14 THROUGH 5 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 6 THROUGH 37 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 38 THROUGH 109 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 110 THROUGH 208 )
12	X-RAY DIFFRACTION	12	CHAIN 'D' AND (RESID 306 THROUGH 310 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 306 THROUGH 310 )

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