PDB-4rey: Crystal Structure of the GRASP65-GM130 C-terminal peptide complex

ID or keywords:

Entry

Database: PDB / ID: 4rey

Title

Crystal Structure of the GRASP65-GM130 C-terminal peptide complex

Components

Golgi reassembly-stacking protein 1
Golgin subfamily A member 2

Keywords

MEMBRANE PROTEIN / PDZ fold six-stranded anti parallel-barrel capped by two-helices /

protein interaction

Function / homology

Function and homology information

meiotic spindle assembly / Golgi cis cisterna / positive regulation of protein glycosylation / Golgi disassembly / establishment of protein localization to plasma membrane /

asymmetric cell division / negative regulation of dendrite morphogenesis / Golgi ribbon formation /

microtubule nucleation / importin-alpha family protein binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Shi, N. / Hu, F. / Li, B.

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Interaction between the Golgi Reassembly-stacking Protein GRASP65 and the Golgi Matrix Protein GM130.
Authors: Hu, F. / Shi, X. / Li, B. / Huang, X. / Morelli, X. / Shi, N.

History

Deposition	Sep 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 18, 2015	Group: Database references
Revision 1.2	Nov 23, 2016	Group: Structure summary
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4rey.cif.gz	147.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4rey.ent.gz	119.1 KB	Display	PDB format
PDBx/mmJSON format	4rey.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/re/4rey ftp://data.pdbj.org/pub/pdb/validation_reports/re/4rey	HTTPS FTP

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Related structure data

Related structure data	4kfvS S: Starting model for refinement
Similar structure data	2eyi-d 3kbb-d 4wyu-2 5b21-d 4ygr-d 3vqm-2 2vga-d 2xmi-d 2v25-1 6tct-1 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	#79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #53 - May 2004 Serpins similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #14 - Feb 2001 Insulin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

PDB pages

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NCBI

Related items in Molecule of the Month

#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#53 - May 2004
Serpins
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#94 - Oct 2007
Superoxide Dismutase
similarity (1)
#14 - Feb 2001
Insulin
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)

Deposited unit

A: Golgi reassembly-stacking protein 1

B: Golgin subfamily A member 2

hetero molecules

26.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	129.725, 129.725, 37.104
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Golgi reassembly-stacking protein 1 / Golgi peripheral membrane protein p65 / Golgi phosphoprotein 5 / GOLPH5 / Golgi reassembly-stacking ...Golgi peripheral membrane protein p65 / Golgi phosphoprotein 5 / GOLPH5 / Golgi reassembly-stacking protein of 65 kDa / GRASP65 Mass: 23266.180 Da / Num. of mol.: 1 / Fragment: GRASP domain of GRAS65, UNP residues 1-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOLPH5, GORASP1, GRASP65 / Plasmid: RSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BQQ3
#2: Protein/peptide	Golgin subfamily A member 2 / 130 kDa cis-Golgi matrix protein / GM130 / GM130 autoantigen / Golgin-95 Mass: 3060.392 Da / Num. of mol.: 1 / Fragment: GM130 C-TERMINAL DOMAIN, UNP residues 980-1002 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GM130, GOLGA2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08379
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.09 Å³/Da / Density % sol: 60.21 %
Crystal grow	Temperature: 291 K / pH: 8.5 Details: 30% PEG 4000, 0.1M Tris, 0.2M Lithium sulfate, , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2013
Radiation	Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.96→64.84 Å / Num. obs: 25936 / % possible obs: 99.56 % / Observed criterion σ(I): 1 / Redundancy: 13.1 % / B_iso Wilson estimate: 32 Å² / R_merge(I) obs: 0.1033 / Net I/σ(I): 13.78
Reflection shell	Resolution: 1.96→2.03 Å / Redundancy: 13.4 % / R_merge(I) obs: 0.4814 / Mean I/σ(I) obs: 4.39 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
xia2		data reduction
xia2		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KFV

4kfv

Resolution: 1.96→64.86 Å / SU ML: 0.17 / Phase error: 18.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.19	1997	7.7 %
R_work	0.152	-	-
obs	0.155	25936	99.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 47 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→64.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1698	0	5	201	1904

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	1811
X-RAY DIFFRACTION	f_angle_d	1.774	2466
X-RAY DIFFRACTION	f_dihedral_angle_d	15.755	683
X-RAY DIFFRACTION	f_chiral_restr	0.082	262
X-RAY DIFFRACTION	f_plane_restr	0.01	329

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 (%)
1.9601-1.9849	0.2792	136	0.2421	1704	X-RAY DIFFRACTION	100
1.9849-2.011	0.199	146	0.185	1681	X-RAY DIFFRACTION	100
2.011-2.0386	0.2433	150	0.1887	1721	X-RAY DIFFRACTION	100
2.0386-2.0677	0.2083	138	0.1677	1745	X-RAY DIFFRACTION	100
2.0677-2.0985	0.2263	148	0.1703	1685	X-RAY DIFFRACTION	100
2.0985-2.1313	0.2271	138	0.1748	1715	X-RAY DIFFRACTION	100
2.1313-2.1663	0.2035	137	0.1842	1752	X-RAY DIFFRACTION	100
2.1663-2.2036	0.28	141	0.201	1670	X-RAY DIFFRACTION	100
2.2036-2.2437	0.2577	146	0.2202	1707	X-RAY DIFFRACTION	100
2.2437-2.2869	0.3057	144	0.2176	1711	X-RAY DIFFRACTION	100
2.2869-2.3335	0.2246	148	0.2043	1678	X-RAY DIFFRACTION	98
2.3335-2.3843	0.2138	139	0.1676	1687	X-RAY DIFFRACTION	100
2.3843-2.4398	0.1776	142	0.1535	1722	X-RAY DIFFRACTION	100
2.4398-2.5008	0.2002	144	0.1598	1732	X-RAY DIFFRACTION	100
2.5008-2.5684	0.1622	142	0.1455	1663	X-RAY DIFFRACTION	100
2.5684-2.644	0.1803	142	0.1402	1775	X-RAY DIFFRACTION	100
2.644-2.7293	0.1654	137	0.1386	1665	X-RAY DIFFRACTION	100
2.7293-2.8269	0.1885	145	0.1469	1724	X-RAY DIFFRACTION	100
2.8269-2.94	0.1667	144	0.1511	1699	X-RAY DIFFRACTION	100
2.94-3.0738	0.2084	152	0.1666	1722	X-RAY DIFFRACTION	100
3.0738-3.2359	0.2001	140	0.15	1695	X-RAY DIFFRACTION	100
3.2359-3.4386	0.1852	146	0.1504	1719	X-RAY DIFFRACTION	100
3.4386-3.7041	0.1616	135	0.1432	1713	X-RAY DIFFRACTION	100
3.7041-4.0768	0.1821	131	0.1331	1732	X-RAY DIFFRACTION	100
4.0768-4.6666	0.1801	145	0.1152	1714	X-RAY DIFFRACTION	100
4.6666-5.8788	0.132	144	0.1255	1695	X-RAY DIFFRACTION	100
5.8788-64.898	0.2156	131	0.1584	1509	X-RAY DIFFRACTION	88

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	7.2916	-4.0437	-0.0609	8.671	3.0566	2.9871	-0.2279	-0.4088	-0.5808	0.4197	0.1903	0.3109	0.28	0.0564	-0.0215	0.4067	0.1322	0.0425	0.247	0.0388	0.425	-110.3896	80.2572	1.0563
2	3.6173	-3.9744	-2.1938	5.2187	2.5278	8.1873	0.0009	-0.0389	0.8742	-0.1169	-0.1956	-0.9444	-0.6225	0.3534	0.0855	0.5493	0.0909	0.0113	0.2759	0.054	0.5776	-110.7501	94.3401	-1.6469
3	7.4374	-3.113	-1.2332	4.4597	1.488	6.5248	0.1177	0.4296	-0.7359	-0.0957	-0.29	0.9539	-0.0752	-0.2877	0.2326	0.4226	0.1007	0.0472	0.2035	-0.0062	0.5194	-116.9736	82.3484	-3.8948
4	2.8337	-5.1109	2.7457	9.9406	-3.7547	8.2084	-0.6689	-1.0521	-0.091	1.6406	0.3148	0.2052	0.1279	-0.5297	0.3204	0.8528	0.2208	0.1043	0.6532	0.0167	0.4761	-115.7679	86.9546	12.5927
5	5.824	-3.2455	-0.1927	7.0013	2.3671	1.157	0.4968	0.5014	1.1348	-1.0517	-0.0432	-1.2114	-0.991	0.0199	-0.4766	0.5807	0.1193	0.1168	0.3685	0.0899	0.568	-101.2733	81.6172	-6.2819
6	2.3653	-1.8734	2.6551	6.1615	-6.8411	7.869	0.252	0.3374	-0.0125	0.0258	-0.253	-0.0603	0.1597	0.5156	-0.0645	0.1644	0.0896	0.0518	0.3197	-0.0381	0.1808	-93.1053	60.431	-4.645
7	4.8866	-0.4721	0.8616	5.0421	0.5111	4.6927	-0.0028	-0.1255	0.6683	-0.2511	0.0717	-0.6609	-0.3324	0.4068	-0.0424	0.1515	0.0624	0.0511	0.2794	-0.0528	0.2978	-92.8125	66.6787	-0.6371
8	4.3249	0.4386	3.3297	4.1823	0.177	5.6429	-0.2178	-0.1786	0.3779	0.0931	0.1596	-0.6742	-0.3399	0.5853	0.058	0.1938	0.0439	0.006	0.3335	-0.0851	0.3615	-89.5563	67.2885	2.4113
9	6.0934	-0.0652	2.8141	2.8013	-0.986	4.5181	-0.0639	-0.2705	-0.0971	0.0578	0.1433	-0.1038	-0.0849	-0.0062	-0.0578	0.1958	0.0381	0.0331	0.2811	-0.061	0.2097	-92.6727	60.3575	2.8155
10	6.782	-1.2306	2.4544	5.5568	-1.9555	5.2542	0.0109	0.336	0.4929	-0.2186	-0.0193	0.1294	-0.1902	0.0236	0.0183	0.2358	0.0573	0.0475	0.2689	-0.0112	0.2006	-97.8098	64.3216	-10.2419
11	9.6234	1.0785	-4.8082	8.4949	-1.6019	2.6332	0.317	-0.9116	0.7409	1.1772	-0.0315	-0.7727	-1.0165	0.2709	-0.1145	0.6019	0.0297	0.0089	0.4395	-0.0536	0.5835	-95.5428	77.5652	2.3458
12	5.4695	1.5213	0.6242	1.0818	2.452	7.9742	-0.5202	-1.0269	4.2433	2.6203	-0.7414	-1.8272	-3.8557	0.6292	1.2528	1.3138	-0.3117	-0.1651	0.9803	-0.3742	2.0127	-89.3392	89.6228	1.3637
13	2.6794	1.0948	-3.0852	6.7651	-2.0223	3.6806	1.1063	-1.4091	2.0092	0.7602	0.2399	-1.7318	-1.9867	0.6795	-0.8548	0.7495	0.0698	-0.0865	0.6498	-0.2438	0.8424	-100.0934	87.0574	6.5189

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 97 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 122 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 123 through 148 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 149 through 167 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 168 through 189 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 190 through 205 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 969 through 978 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 979 through 983 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 984 through 990 )

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