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- PDB-4fvg: SPFH domain of mouse stomatin (Crystal form 3) -

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Basic information

Entry
Database: PDB / ID: 4fvg
TitleSPFH domain of mouse stomatin (Crystal form 3)
ComponentsStomatin
KeywordsMEMBRANE PROTEIN / mixed alpha-beta fold / membrane scaffold
Function / homology
Function and homology information


positive regulation of viral process / RHOH GTPase cycle / RHOQ GTPase cycle / RHOB GTPase cycle / RHOC 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 ...positive regulation of viral process / RHOH GTPase cycle / RHOQ GTPase cycle / RHOB GTPase cycle / RHOC 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 / ion channel inhibitor activity / positive regulation of protein targeting to membrane / Neutrophil degranulation / melanosome / cytoskeleton / membrane raft / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Band 7 domain / Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily / Tetrahydropterin Synthase; Chain A ...Band 7 domain / Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrand, J. / Schwefel, D. / Daumke, O.
CitationJournal: 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
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300AUTHORS STATE THE BIOLOGICAL ASSEMBLY IS AN OLIGOMER

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6453
Polymers14,4201
Non-polymers2252
Water1,72996
1
A: Stomatin
hetero molecules

A: Stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2906
Polymers28,8402
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.489, 84.489, 68.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

DetailsA continuous tube like oligomer is created by crystallographic symmetry.

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Components

#1: Protein Stomatin / Protein 7.2b / Erythrocyte band 7 integral membrane protein


Mass: 14420.151 Da / Num. of mol.: 1 / Mutation: C87S, L91A, I92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epb7.2, Epb72, Stom / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 phage resistant Rosetta / References: UniProt: P54116
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% ethanol, 0.02 cadmium sulfate, 0.1 HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 15, 2009 / Details: mirrors
RadiationMonochromator: Si111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→73.17 Å / Num. all: 16540 / Num. obs: 16492 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 37.736 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.25
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.97 / Num. unique all: 2576 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0110refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FVF

4fvf


Resolution: 1.8→73.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.013 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24512 704 5 %RANDOM
Rwork0.19356 ---
all0.19592 13291 --
obs0.19592 13259 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.724 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→73.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 2 96 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9521211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95124.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37715155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.344157
X-RAY DIFFRACTIONr_chiral_restr0.150.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021662
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3191.5568
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9672930
X-RAY DIFFRACTIONr_scbond_it3.123317
X-RAY DIFFRACTIONr_scangle_it4.7274.5281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 52 -
Rwork0.239 942 -
obs--98.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
118.7587-0.9348-5.816727.248-1.809117.58290.4215-1.4310.56820.9470.15070.9238-1.3186-0.3247-0.57210.56410.1557-0.05420.47380.16280.3276-29.1036-11.2819-7.4685
211.0726-5.25574.19679.2225-2.79579.22-0.16790.25950.8006-0.06340.0725-0.4301-0.54030.10440.09540.2267-0.0142-0.05670.11860.11030.1917-17.2363-16.4881-0.985
36.666-2.40812.51734.6064-1.74318.07560.1041-0.1244-0.01940.20220.06540.0582-0.4298-0.2467-0.16950.09280.0201-0.0480.19770.03770.1925-7.6656-27.02668.6505
411.14313.19724.34430.52651.56835.66210.17210.2279-0.53520.08460.012-0.14450.00770.3792-0.18410.19850.037-0.06220.2671-0.03210.2964-5.8489-31.06315.0815
510.5918-0.54251.22966.738-0.6638.32610.04420.41350.02-0.36710.05280.4319-0.4862-0.4866-0.0970.22270.0585-0.08930.22160.13990.175-25.008-18.4959-5.5917
66.6795-0.4328.57870.2925-4.340331.76720.1316-0.54811.00020.12360.0820.24490.2304-2.7639-0.21360.42580.16960.02890.82090.03370.687-35.5221-16.07144.7018
77.5202-0.8575-0.33853.2141.02045.781-0.0535-0.15280.53430.2660.12510.2928-1.0094-0.3372-0.07160.3120.0685-0.02050.12610.0670.1786-23.9626-18.14175.5315
89.1408-2.75760.238212.9006-1.30695.25210.0129-0.1796-0.15980.43740.0403-0.3302-0.01160.1147-0.05310.11820.0086-0.05380.14720.06080.1139-16.1131-29.07045.7689
91.6409-1.3605-3.77216.50013.67287.3847-0.26890.131-0.13030.13560.2175-0.32720.4788-0.06160.05140.26190.0316-0.13710.3908-0.10420.5032-8.7157-37.84671.5701
1014.3606-6.38674.63622.1729-2.236314.63530.96360.5423-0.7246-0.4113-0.18230.2474-0.24410.6897-0.78120.3314-0.00990.05750.3887-0.00350.5658-10.8123-34.232-6.2295
112.9527-0.9196-7.55468.50272.706818.5266-0.08970.2825-0.1115-0.6044-0.1325-0.07710.2492-0.40580.22220.18880.0292-0.07860.35170.00320.144-20.5141-31.1844-4.9841
1211.6238-2.8705-1.51276.46260.69724.95950.0523-0.01290.3268-0.01030.03010.7286-0.1354-0.5658-0.08240.10020.0169-0.03210.17330.06850.1794-29.4516-25.26781.4204
1325.855-4.43291.18351.0110.01355.91810.350.7896-0.0179-0.4742-0.08170.114-0.3342-0.0287-0.26820.4818-0.0309-0.14140.24670.14640.1648-22.1085-23.4178-7.6476
1416.1075-2.6557.28332.4783-2.715714.0166-0.17380.08170.82560.13310.064-0.2648-0.38260.53510.10980.1513-0.034-0.00540.23-0.03010.265-2.6977-25.52041.3133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 98
2X-RAY DIFFRACTION2A99 - 104
3X-RAY DIFFRACTION3A105 - 110
4X-RAY DIFFRACTION4A111 - 120
5X-RAY DIFFRACTION5A121 - 127
6X-RAY DIFFRACTION6A128 - 136
7X-RAY DIFFRACTION7A137 - 147
8X-RAY DIFFRACTION8A148 - 155
9X-RAY DIFFRACTION9A156 - 163
10X-RAY DIFFRACTION10A164 - 170
11X-RAY DIFFRACTION11A171 - 176
12X-RAY DIFFRACTION12A177 - 187
13X-RAY DIFFRACTION13A188 - 193
14X-RAY DIFFRACTION14A194 - 202

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