PDB-4fvj: SPFH domain of the mouse stomatin (Crystal form 2)

ID or keywords:

Entry

Database: PDB / ID: 4fvj

Title

SPFH domain of the mouse stomatin (Crystal form 2)

Components

Stomatin

Keywords

MEMBRANE PROTEIN / mixed alpha-beta fold / membrane scaffold

Function / homology

Function and homology information

positive regulation of viral process / RHOH GTPase cycle / RHOQ GTPase cycle / RHOC GTPase cycle / RHOB GTPase cycle / RHOA GTPase cycle / positive regulation by host of viral genome replication / Stimuli-sensing channels / regulation of monoatomic ion transmembrane transport / RNA polymerase binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.69 Å

Authors

Brand, J. / Schwefel, D. / Daumke, O.

Citation

Journal: Embo J. / Year: 2012
Title: A stomatin dimer modulates the activity of acid-sensing ion channels.
Authors: Brand, J. / Smith, E.S. / Schwefel, D. / Lapatsina, L. / Poole, K. / Omerbasic, D. / Kozlenkov, A. / Behlke, J. / Lewin, G.R. / Daumke, O.

History

Deposition	Jun 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2012	Group: Database references
Revision 1.2	Sep 13, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fvj.cif.gz	355.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4fvj.ent.gz	294.3 KB	Display	PDB format
PDBx/mmJSON format	4fvj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fvj_validation.pdf.gz	486.5 KB	Display	wwPDB validaton report
Full document	4fvj_full_validation.pdf.gz	502.4 KB	Display
Data in XML	4fvj_validation.xml.gz	31.9 KB	Display
Data in CIF	4fvj_validation.cif.gz	44 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fv/4fvj ftp://data.pdbj.org/pub/pdb/validation_reports/fv/4fvj	HTTPS FTP

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Related structure data

Related structure data	4fvfSC 4fvgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2lfr-d 5b5k-d 6n0a-2 6m98-d 1ud0-1 6h0r-d 1qd0-2 3n1b-3 1d4r-1 6n0a-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) 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

4fvfSC

4fvgC

S: Starting model for refinement

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	#80 - Aug 2006 AAA+ Proteases similarity (2) #114 - Jun 2009 Vaults similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #88 - Apr 2007 Clathrin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#80 - Aug 2006
AAA+ Proteases
similarity (2)
#114 - Jun 2009
Vaults
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#176 - Aug 2014
Dynein
similarity (1)
#177 - Sep 2014
Apoptosomes
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)

Deposited unit

A: Stomatin

B: Stomatin

C: Stomatin

D: Stomatin

E: Stomatin

F: Stomatin

G: Stomatin

H: Stomatin

116 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Stomatin

E: Stomatin

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

2

B: Stomatin

F: Stomatin

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

3

C: Stomatin

H: Stomatin

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

4

D: Stomatin

G: Stomatin

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

Unit cell

Length a, b, c (Å)	178.530, 91.380, 86.138
Angle α, β, γ (deg.)	90.00, 111.88, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Stomatin / Protein 7.2b / Erythrocyte band 7 integral membrane protein Mass: 14504.312 Da / Num. of mol.: 8 / Mutation: C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epb7.2, Epb72, Stom, Stomatin / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 phage resistant Rosetta / References: UniProt: P54116
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Stomatin / Protein 7.2b / Erythrocyte band 7 integral membrane protein

Mass: 14504.312 Da / Num. of mol.: 8 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Epb7.2, Epb72, Stom, Stomatin / Plasmid: pGEX6P1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21DE3 phage resistant Rosetta / References: UniProt: P54116

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.81 Å³/Da / Density % sol: 56.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 7% ethanol, 5% glycerol, 0.8 M sodium acetate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 8, 2009 / Details: double mirror
Radiation	Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2.67→82.76 Å / Num. all: 35622 / Num. obs: 32523 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / R_sym value: 0.108 / Net I/σ(I): 6.8
Reflection shell	Resolution: 2.69→2.74 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1751 / R_sym value: 0.328 / % possible all: 76.2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.5.0110	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4FVF

4fvf

Resolution: 2.69→82.76 Å / Cor.coef. F_o:F_c: 0.9 / Cor.coef. F_o:F_c free: 0.86 / SU B: 30.653 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.932 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29009	1608	4.9 %	RANDOM
R_work	0.2456	-	-	-
all	0.24783	33912	-	-
obs	0.24783	30899	91.1 %	-

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: 54.57 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.85 Å²	0 Å²	0.76 Å²
2-	-	-2.85 Å²	0 Å²
3-	-	-	2.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.69→82.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7028	0	0	19	7047

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	6831
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.92	1.963	9295
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.89	5	900
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.773	25.451	288
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.92	15	1163
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.054	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	1154
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.021	5046
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.335	1.5	4468
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.598	2	7235
X-RAY DIFFRACTION	r_scbond_it	0.239	3	2363
X-RAY DIFFRACTION	r_scangle_it	0.442	4.5	2060
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.694→2.764 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.341	91	-
R_work	0.297	1846	-
obs	-	-	73.79 %

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	3.4009	-2.124	1.4575	2.0469	-0.5334	0.8238	0.2632	0.2224	-0.1527	-0.2733	-0.2125	0.119	0.0626	0.0743	-0.0507	0.1239	0.0231	-0.0057	0.2081	0.0106	0.0361	43.7179	-4.4431	26.0418
2	3.7257	-1.1466	1.6206	1.5355	-0.2326	1.2584	0.0378	0.0296	0.0939	-0.17	-0.0563	0.014	0.0729	0.0819	0.0185	0.1333	0.0132	-0.0382	0.1884	0.0474	0.0334	42.0952	1.1677	27.4933
3	0.4721	1.7353	0.3051	8.099	0.3352	0.6872	-0.0207	0.0177	-0.0167	-0.0074	0.0504	-0.1083	0.0311	-0.1577	-0.0298	0.1085	-0.0342	0.01	0.2827	-0.0143	0.0757	73.1876	-13.4185	12.4492
4	0.613	0.9164	0.7075	4.5406	1.1531	0.9102	-0.0569	-0.0145	0.0931	-0.0884	0.0153	0.1572	-0.0283	-0.0827	0.0416	0.0957	-0.0008	-0.0102	0.2606	0.0056	0.0663	69.9991	-8.868	10.2348
5	8.75	-2.6093	-1.0799	1.9762	1.5839	1.5245	-0.1243	0.2221	-0.2001	-0.054	-0.0271	0.1183	-0.1441	-0.0481	0.1513	0.1252	0.0148	-0.0371	0.2166	0.0103	0.0643	97.9166	0.0496	28.4566
6	4.3151	-1.1833	1.7727	1.2899	-0.1683	1.4729	-0.217	-0.2042	0.321	0.0424	0.0649	-0.013	-0.2187	0.0123	0.1522	0.0983	0.0221	-0.0515	0.1872	-0.0452	0.0769	96.5287	4.855	32.0048
7	0.3428	0.395	0.5018	5.6803	-0.4807	0.9632	0.0019	0.0118	0.0573	-0.1423	-0.0076	0.2993	0.0309	0.0126	0.0057	0.1016	0.0146	0.0075	0.1836	-0.0116	0.0859	101.1495	-6.575	12.1886
8	0.8229	0.9223	-0.2898	3.711	-1.9575	1.7526	0.0162	-0.0074	-0.0048	-0.141	-0.0543	-0.0906	0.0834	0.1175	0.0381	0.0979	0.0267	0.021	0.1886	-0.0099	0.0681	105.3731	-11.3325	10.2763
9	7.6604	-3.5735	0.2223	2.3628	-0.1044	0.3292	0.0637	-0.1035	0.0858	-0.0419	-0.0541	-0.0578	-0.0189	0.0208	-0.0096	0.0828	-0.0268	0.0273	0.2857	0.0056	0.0287	75.6097	-22.2578	27.0705
10	2.4304	-0.727	-0.4913	0.2395	0.052	1.4684	0.0239	0.0253	-0.1563	-0.0006	-0.0524	0.0695	-0.0053	0.1165	0.0285	0.0835	0.0084	0.0282	0.2623	-0.0039	0.0605	77.1457	-28.0037	29.2344
11	0.1377	-0.2608	-0.2103	9.6008	-1.1824	0.6291	-0.0511	-0.0569	0.0126	-0.0061	0.142	0.1456	0.0152	0.1438	-0.0909	0.1338	-0.0562	-0.0956	0.1915	0.0147	0.1461	70.5255	-49.6915	10.8801
12	0.8299	1.3629	-0.8641	6.0031	-0.4898	1.1583	-0.0826	-0.0427	-0.1315	-0.3046	-0.0018	-0.2319	0.0088	0.1189	0.0844	0.0506	-0.0404	-0.0159	0.1477	0.0042	0.1531	74.2228	-54.7435	10.0707
13	0.1908	0.8587	-0.1591	10.4629	0.2877	0.3011	-0.023	0.03	-0.0294	-0.0597	-0.1076	0.2261	-0.0131	-0.0484	0.1306	0.1262	0.0042	-0.1264	0.133	0.017	0.1875	103.3211	28.6927	12.3742
14	2.0999	1.9687	0.7098	7.8784	2.2856	0.6794	0.0107	0.1014	-0.0679	-0.2076	-0.1783	0.6986	-0.07	-0.0464	0.1676	0.108	0.0421	-0.1155	0.1145	-0.0134	0.2142	98.724	34.0505	11.7412
15	10.9963	-5.5942	-4.3883	5.5212	2.3184	1.7712	0.1179	-1.0931	0.886	0.324	0.2178	-0.9715	-0.0545	0.3654	-0.3357	0.1366	-0.0053	-0.1467	0.3987	-0.0198	0.2662	131.1567	-17.199	23.9629
16	5.9659	-0.9449	-0.74	0.9975	-0.0874	0.174	-0.2015	-0.1031	-0.2353	0.1408	0.1206	-0.1896	-0.0067	-0.0912	0.0808	0.0744	0.0472	-0.0158	0.2091	-0.0255	0.1215	131.2434	-22.8965	24.6305

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	89 - 127
2	X-RAY DIFFRACTION	2	A	128 - 201
3	X-RAY DIFFRACTION	3	B	90 - 127
4	X-RAY DIFFRACTION	4	B	128 - 203
5	X-RAY DIFFRACTION	5	C	90 - 127
6	X-RAY DIFFRACTION	6	C	128 - 201
7	X-RAY DIFFRACTION	7	D	89 - 127
8	X-RAY DIFFRACTION	8	D	128 - 200
9	X-RAY DIFFRACTION	9	E	90 - 127
10	X-RAY DIFFRACTION	10	E	128 - 202
11	X-RAY DIFFRACTION	11	F	89 - 127
12	X-RAY DIFFRACTION	12	F	128 - 201
13	X-RAY DIFFRACTION	13	G	89 - 127
14	X-RAY DIFFRACTION	14	G	128 - 201
15	X-RAY DIFFRACTION	15	H	90 - 127
16	X-RAY DIFFRACTION	16	H	128 - 203

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