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- PDB-4fvf: SPFH domain of mouse stomatin (Crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 4fvf
TitleSPFH domain of mouse stomatin (Crystal form 1)
ComponentsStomatin
KeywordsMEMBRANE PROTEIN / mixed alpha-beta / scaffolding protein
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
ACETATE ION / : / Stomatin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 1.2Apr 25, 2018Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Sep 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stomatin
B: Stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,73816
Polymers28,2182
Non-polymers1,52014
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-74 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 55.500, 343.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 14108.921 Da / Num. of mol.: 2 / Mutation: C86S
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): BL21 DE3 Rosetta / References: UniProt: P54116
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 M sodium acetate, 0.05 M cadmium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2008 / Details: mirrors
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.46→57.26 Å / Num. all: 12433 / Num. obs: 12351 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 55.254 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.67
Reflection shellResolution: 2.46→2.61 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.851 / Mean I/σ(I) obs: 4.12 / Num. unique all: 1932 / Rsym value: 0.626 / % possible all: 0.958

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0086refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RPB

2rpb


Resolution: 2.46→57.26 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.083 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26849 597 4.8 %RANDOM
Rwork0.21745 ---
all0.21975 11820 --
obs0.21975 11753 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.46→57.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 17 77 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221830
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.9652491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1865232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60125.55681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53815333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8461512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211334
LS refinement shellResolution: 2.462→2.526 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 37 -
Rwork0.309 808 -
obs--92.35 %
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)
15.6711-0.12184.5561.8161-0.26975.6227-0.18290.2540.0424-0.0320.1179-0.1696-0.2523-0.05320.0650.06060.01460.04010.10520.01350.052717.53687.789318.5928
25.5094-0.7987-4.23361.67930.50074.9149-0.26030.1253-0.1541-0.02910.04620.25180.32990.0080.21410.06030.0121-0.00950.0964-0.00050.067948.9671-11.300416.6221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 202
2X-RAY DIFFRACTION2B89 - 205

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