PDB-2fu3: Crystal structure of gephyrin E-domain

ID or keywords:

Entry

Database: PDB / ID: 2fu3

Title

Crystal structure of gephyrin E-domain

Components

gephyrin

Keywords

BIOSYNTHETIC PROTEIN/STRUCTURAL PROTEIN / Glycine receptor / gephyrin / neuroreceptor anchoring / BIOSYNTHETIC PROTEIN-STRUCTURAL PROTEIN COMPLEX

Function / homology

Function and homology information

Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / and MAD / Resolution: 2.7 Å

Authors

Kim, E.Y. / Schindelin, H.

Citation

Journal: Embo J. / Year: 2006
Title: Deciphering the structural framework of glycine receptor anchoring by gephyrin.
Authors: Kim, E.Y. / Schrader, N. / Smolinsky, B. / Bedet, C. / Vannier, C. / Schwarz, G. / Schindelin, H.

History

Deposition	Jan 25, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2fu3.cif.gz	165.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2fu3_validation.pdf.gz	436.4 KB	Display	wwPDB validaton report
Full document	2fu3_full_validation.pdf.gz	463 KB	Display
Data in XML	2fu3_validation.xml.gz	31.8 KB	Display
Data in CIF	2fu3_validation.cif.gz	43.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fu/2fu3 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fu3	HTTPS FTP

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Related structure data

Related structure data	2ftsC C: citing same article (ref.)
Similar structure data	5eru-1 5g2s-1 6fgc-1 6fgd-1 6gb9-1 1fc5-d 5ers-1 6etf-1 4tk1-d 6etd-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

Deposited unit

A: gephyrin

B: gephyrin

91.3 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)	108.820, 156.195, 51.362
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	gephyrin Mass: 45652.395 Da / Num. of mol.: 2 / Fragment: E-domain, Residues 318-736 (NP 074056) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rattus norvegicus (Norway rat) / Plasmid: pTWIN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03555
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

gephyrin

Mass: 45652.395 Da / Num. of mol.: 2 / Fragment: E-domain, Residues 318-736 (NP 074056)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Rattus norvegicus (Norway rat) / Plasmid: pTWIN1 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03555

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.39 Å³/Da / Density % sol: 48.51 %
Crystal grow	Temperature: 311 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl (pH 7.5-8.5), 0.1M Na Acetate, and 25-30% PEG 4000, vapor diffusion, hanging drop, temperature 311K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X26C / Wavelength: 1.1 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2004

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

D res high: 3.5 Å / D res low: 50 Å / % possible obs: 100

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs
1	8.9	123833	0.163	3.35	21485
2	7.5	81870	0.169	3.79	21781

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	Chi squared
9.48	50	1087	99.5	1	0.07	10.847
7.53	9.48	1058	100	1	0.082	3.578
6.58	7.53	1086	100	1	0.131	3.862
5.98	6.58	1080	100	1	0.148	3.047
5.55	5.98	1070	99.9	1	0.169	3.257
5.23	5.55	1065	100	1	0.157	2.98
4.97	5.23	1074	100	1	0.149	3.102
4.75	4.97	1084	100	1	0.156	3.186
4.57	4.75	1075	100	1	0.143	3.523
4.41	4.57	1077	100	1	0.153	3.02
4.27	4.41	1050	100	1	0.168	3.094
4.15	4.27	1088	99.9	1	0.187	2.948
4.04	4.15	1059	100	1	0.211	2.932
3.94	4.04	1064	100	1	0.235	2.703
3.85	3.94	1106	100	1	0.265	2.812
3.77	3.85	1071	100	1	0.289	2.756
3.69	3.77	1065	100	1	0.333	2.454
3.63	3.69	1053	100	1	0.362	2.574
3.56	3.63	1094	100	1	0.37	2.491
3.5	3.56	1079	99.9	1	0.426	2.407
9.48	50	1099	99.8	2	0.06	19.3
7.53	9.48	1087	100	2	0.065	3.891
6.58	7.53	1087	100	2	0.126	3.112
5.98	6.58	1100	100	2	0.146	3.372
5.55	5.98	1084	100	2	0.158	3.136
5.23	5.55	1074	100	2	0.145	2.586
4.97	5.23	1111	100	2	0.14	2.773
4.75	4.97	1074	100	2	0.136	2.682
4.57	4.75	1096	100	2	0.14	3.441
4.41	4.57	1098	100	2	0.154	2.771
4.27	4.41	1061	99.9	2	0.168	2.709
4.15	4.27	1122	100	2	0.198	3.049
4.04	4.15	1053	100	2	0.22	2.813
3.94	4.04	1094	99.9	2	0.266	2.64
3.85	3.94	1113	99.9	2	0.28	2.71
3.77	3.85	1060	100	2	0.323	2.556
3.69	3.77	1055	100	2	0.416	3.581
3.63	3.69	1140	100	2	0.399	2.446
3.56	3.63	1082	100	2	0.51	3.658
3.5	3.56	1091	100	2	0.507	2.602

Reflection

Resolution: 2.7→50 Å / Num. obs: 35018 / % possible obs: 99.8 % / R_merge(I) obs: 0.095 / Χ²: 1.553 / Net I/σ(I): 16.4

Reflection shell

Resolution (Å)	% possible obs (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID
2.7-2.75	99.9	0.572	1173	1.507	1
2.75-2.8	99.9	0.482	1220	1.505	1
2.8-2.85	99.9	0.386	1235	1.462	1
2.85-2.91	99.9	0.332	1166	1.545	1
2.91-2.97	99.8	0.287	1231	1.565	1
2.97-3.04	100	0.258	1223	1.816	1
3.04-3.12	100	0.214	1210	1.527	1
3.12-3.2	99.9	0.178	1231	1.559	1
3.2-3.3	100	0.144	1199	1.52	1
3.3-3.4	100	0.13	1248	1.624	1
3.4-3.52	100	0.122	1209	1.708	1
3.52-3.66	99.9	0.107	1252	1.754	1
3.66-3.83	99.9	0.099	1206	1.59	1
3.83-4.03	99.9	0.095	1238	1.702	1
4.03-4.29	99.9	0.089	1253	1.622	1
4.29-4.62	99.9	0.084	1235	1.564	1
4.62-5.08	99.9	0.08	1249	1.485	1
5.08-5.81	100	0.08	1270	1.489	1
5.81-7.32	99.8	0.076	1287	1.454	1
7.32-50	98	0.058	1350	1.03	1

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Phasing

Phasing MR

R_factor: 0.419 / Cor.coef. F_o:F_c: 0.665

	Highest resolution	Lowest resolution
Rotation	3 Å	39.92 Å
Translation	3 Å	39.92 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	1.701	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure: and MAD / Resolution: 2.7→20 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.9 / SU B: 30.333 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.273	1259	5.1 %	RANDOM
R_work	0.202	-	-	-
all	0.205	-	-	-
obs	-	24732	99.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 63.896 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.44 Å²	0 Å²	0 Å²
2-	-	2.7 Å²	0 Å²
3-	-	-	-4.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6191	0	0	66	6257

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	6385
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6021
X-RAY DIFFRACTION	r_angle_refined_deg	1.541	1.983	8695
X-RAY DIFFRACTION	r_angle_other_deg	0.831	3	13999
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.217	5	836
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.832	24.378	249
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.218	15	1051
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.119	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1019
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7129
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1153
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1410
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	6593
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	3112
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.2	4184
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	183
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.019	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.159	0.2	29
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.252	0.2	73
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.12	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.493	1.5	4314
X-RAY DIFFRACTION	r_mcbond_other	0.089	1.5	1690
X-RAY DIFFRACTION	r_mcangle_it	0.838	2	6754
X-RAY DIFFRACTION	r_scbond_it	1.28	3	2327
X-RAY DIFFRACTION	r_scangle_it	2.081	4.5	1941

LS refinement shell

Resolution: 2.7→2.769 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	83	-
R_work	0.283	1646	-
obs	-	1729	99.88 %

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	5.3939	4.3348	0.0324	7.2674	0.0447	2.8113	0.2092	-0.052	0.0796	0.8094	-0.2311	0.2488	-0.3146	0.12	0.0219	-0.1984	-0.0097	-0.0314	-0.2618	0.0806	-0.3859	43.6427	22.456	29.673
2	5.5956	2.4189	0.2809	13.8561	-1.2546	15.3887	-0.2483	0.5209	0.7988	-1.6726	0.5392	0.1788	-0.1819	-0.3856	-0.2909	0.4507	-0.3205	-0.3251	0.3031	0.3111	0.8476	61.4622	65.3676	18.493
3	9.4216	9.5264	-0.4298	17.5371	-7.8533	8.9109	0.2685	1.065	1.3427	0.4131	-0.2734	2.8312	0.0658	0.2402	0.005	0.1455	-0.1382	-0.0466	0.0711	0.1221	0.3631	54.1817	51.3145	30.9948
4	2.3323	2.581	0.4143	6.6849	1.0705	3.7813	0.1091	-0.1203	-0.2462	0.2811	-0.2283	-0.2748	-0.0858	0.3194	0.1192	-0.4444	0.0167	-0.0565	-0.3078	0.1029	-0.2707	48.2455	17.4761	22.8735
5	3.1341	2.1786	-0.1046	1.5144	-0.066	6.4787	-0.2563	0.0936	-0.7424	-0.5043	0.0912	-0.3866	0.7012	-0.0762	0.1651	-0.2119	0.0217	0.0196	-0.3674	-0.0296	-0.0401	42.144	1.8897	12.7474
6	1.2356	-0.3133	-2.8048	11.2731	-2.6502	7.3765	-0.1105	0.2257	-0.9481	-0.1574	-0.1014	0.8821	1.3136	-0.8442	0.2119	-0.0511	-0.043	-0.03	-0.2126	0.0616	0.2217	38.532	-6.0108	24.0591
7	3.5389	1.8254	-0.2157	4.3083	-0.4295	4.6908	0.0212	0.0691	-0.3546	0.3137	-0.0192	0.3124	0.3519	-0.2594	-0.002	-0.3197	-0.0144	0.019	-0.3197	0.0596	-0.1681	34.0365	5.6905	25.9212
8	5.6837	-1.4946	1.2412	5.1574	-2.7751	2.6658	0.0084	-0.0424	-0.6424	-0.4271	-0.0508	0.3804	0.1196	-0.5078	0.0424	-0.3743	-0.0109	0.0377	-0.2054	-0.0087	-0.0748	22.5306	18.6654	12.7163
9	13.4899	-5.9009	1.7895	39.5069	6.2187	9.0226	-0.0488	1.3585	-0.9339	-2.5081	0.412	0.1593	0.6584	0.1441	-0.3632	-0.1411	0.0308	0.051	0.0972	0.083	-0.184	25.0682	21.4218	4.5951
10	6.8541	-0.1365	-0.8548	5.261	0.0418	6.2435	0.222	0.1927	-0.3496	-0.2384	-0.0775	0.5031	0.0504	-0.4417	-0.1445	-0.336	0.0295	-0.0281	-0.2184	0.0669	-0.0918	21.7714	18.7359	11.3588
11	4.1419	-2.0906	-1.2916	20.8952	1.9247	3.6299	-0.432	0.1107	0.6449	-0.5555	0.574	0.0926	-0.6316	-0.0493	-0.1421	-0.2753	-0.0542	-0.0613	-0.1577	0.0723	-0.2538	48.6288	40.2397	-2.2083
12	3.5538	4.9308	0.9608	7.8357	-0.6963	4.401	-0.4591	0.3897	-0.5116	-0.7348	0.4711	-0.5683	0.936	-0.2866	-0.012	-0.0649	-0.1198	0.2239	-0.2542	-0.0983	-0.1169	40.9111	5.566	-0.6792
13	6.0109	0.4517	0.7657	21.9647	-6.7811	4.4893	0.5255	-0.6865	-0.5211	-0.4186	0.7613	2.5175	0.5367	-1.0753	-1.2867	0.5724	-0.5586	-0.1643	0.6576	0.2192	0.3297	18.4484	-17.6761	7.0878
14	2.4925	2.3259	0.7452	3.9593	0.6515	3.0635	-0.1745	0.0642	-0.1421	-0.0996	0.0444	-0.2207	0.1705	0.1861	0.1301	-0.4139	0.0316	0.0573	-0.3315	0.0415	-0.2178	49.9292	21.8972	8.1652
15	7.0476	4.6919	-0.5383	6.6932	-1.0598	5.6468	0.0641	-0.1886	0.6868	0.2014	-0.215	-0.32	-0.8596	0.8484	0.1509	-0.2768	-0.1139	-0.0116	-0.127	0.0599	-0.0471	63.2432	37.4774	7.4968
16	2.8733	0.8913	0.2952	5.2439	-0.0264	3.1924	-0.1492	0.1108	0.4059	0.0892	-0.0081	-0.1522	-0.4015	0.2624	0.1573	-0.3381	-0.0724	-0.0219	-0.2905	0.0524	-0.2277	53.6119	39.401	2.7703
17	7.5238	-0.4401	-3.3268	5.1691	-0.8447	4.3173	0.4723	-0.3896	0.8315	0.4803	-0.1381	0.0866	-0.9434	0.0222	-0.3342	-0.1599	0.0215	0.0462	-0.2742	0.0269	-0.0525	35.488	41.1466	14.6042
18	24.6334	1.6142	-0.5054	9.91	-0.3188	11.9343	0.7315	-2.1922	0.5504	2.1219	-0.2929	-0.5101	-0.8917	0.8234	-0.4386	0.1207	0.0161	0.0592	-0.0219	-0.0152	-0.1221	33.9913	38.3334	24.1851
19	3.0721	0.0946	0.1963	8.6796	-6.1189	9.7621	0.0452	-0.5827	1.2152	0.9179	0.4277	0.2038	-1.4056	-0.3363	-0.4728	0.0134	0.0567	0.1527	-0.106	-0.0468	0.1765	35.6888	44.8552	17.1803
20	18.0405	-5.1647	-5.7256	9.0071	-1.3232	9.6164	0.3933	-0.5722	0.7314	0.7325	0.331	0.2899	-0.3412	0.0299	-0.7243	-0.2389	0.0203	-0.0002	-0.2568	-0.0339	-0.1918	32.8418	38.1854	16.1539

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	318 - 373	1 - 56
2	2	A	A	374 - 453	57 - 136
3	3	A	A	454 - 466	137 - 149
4	4	A	A	467 - 517	150 - 200
5	5	A	A	518 - 549	201 - 232
6	6	A	A	550 - 587	233 - 270
7	7	A	A	588 - 652	271 - 335
8	8	A	A	653 - 680	336 - 363
9	9	A	A	681 - 700	364 - 383
10	10	A	A	701 - 736	384 - 419
11	11	B	B	318 - 343	1 - 26
12	12	B	B	344 - 371	27 - 54
13	13	B	B	372 - 458	55 - 141
14	14	B	B	459 - 534	142 - 217
15	15	B	B	535 - 583	218 - 266
16	16	B	B	584 - 650	267 - 333
17	17	B	B	651 - 680	334 - 363
18	18	B	B	681 - 700	364 - 383
19	19	B	B	701 - 721	384 - 404
20	20	B	B	722 - 736	405 - 419

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