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- PDB-5c1f: Structure of the Imp2 F-BAR domain -

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Basic information

Entry
Database: PDB / ID: 5c1f
TitleStructure of the Imp2 F-BAR domain
ComponentsSeptation protein imp2Septum
KeywordsCELL CYCLE / Imp2 F-BAR Membrane binding
Function / homology
Function and homology information


Clathrin-mediated endocytosis / : / mitotic actomyosin contractile ring maturation / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring assembly / cytoskeletal protein-membrane anchor activity / phosphatidylinositol-4-phosphate binding / cell division site ...Clathrin-mediated endocytosis / : / mitotic actomyosin contractile ring maturation / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring assembly / cytoskeletal protein-membrane anchor activity / phosphatidylinositol-4-phosphate binding / cell division site / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / cytoskeleton organization / phospholipid binding / cytoskeleton / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
FORMIC ACID / Septation protein imp2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3551 Å
AuthorsVander Kooi, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101035 United States
CitationJournal: Cell Rep / Year: 2016
Title: The Tubulation Activity of a Fission Yeast F-BAR Protein Is Dispensable for Its Function in Cytokinesis.
Authors: McDonald, N.A. / Takizawa, Y. / Feoktistova, A. / Xu, P. / Ohi, M.D. / Vander Kooi, C.W. / Gould, K.L.
History
DepositionJun 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septation protein imp2
B: Septation protein imp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9613
Polymers71,9152
Non-polymers461
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-90 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.337, 33.802, 120.765
Angle α, β, γ (deg.)90.00, 122.54, 90.00
Int Tables number5
Space group name H-MC121
DetailsAnalytical ultracentrifugation, homology

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Components

#1: Protein Septation protein imp2 / Septum


Mass: 35957.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: imp2, SPBC11C11.02 / Plasmid: pET28 / Production host: escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q10199
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 18% PEG 3350, 0.2 M AmFormate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM11
SYNCHROTRONAPS 22-ID20.9792
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJul 28, 2011
MARMOSAIC 300 mm CCD2CCDAug 17, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
ReflectionResolution: 2.35→20 Å / Num. obs: 26635 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3551→19.968 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1330 5 %
Rwork0.1904 --
obs0.1929 26626 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3551→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 3 154 5021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035030
X-RAY DIFFRACTIONf_angle_d0.5316767
X-RAY DIFFRACTIONf_dihedral_angle_d13.3251910
X-RAY DIFFRACTIONf_chiral_restr0.02715
X-RAY DIFFRACTIONf_plane_restr0.002881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3551-2.44920.25681200.22512424X-RAY DIFFRACTION85
2.4492-2.56050.29161420.23122786X-RAY DIFFRACTION98
2.5605-2.69520.27461480.22282781X-RAY DIFFRACTION100
2.6952-2.86360.28621330.22182872X-RAY DIFFRACTION100
2.8636-3.08390.26921630.22482858X-RAY DIFFRACTION100
3.0839-3.39290.25391540.20632834X-RAY DIFFRACTION100
3.3929-3.88070.24491460.18042846X-RAY DIFFRACTION100
3.8807-4.87750.19681480.1572924X-RAY DIFFRACTION100
4.8775-19.96890.20331760.15972971X-RAY DIFFRACTION100
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)
12.30070.71631.70910.54340.75332.38030.0211-0.1765-0.17170.0510.0264-0.06830.05980.2349-0.05170.25890.00990.03980.25970.0310.21656.63147.582422.8972
22.52530.02372.86571.21840.34016.659-0.02950.1407-0.11240.0775-0.01970.29560.430.098-0.0750.3319-0.0205-0.04240.44660.01970.326889.284214.292661.7235
32.15790.44971.35650.4456-0.49583.9313-0.22360.4129-0.03950.1823-0.2047-0.1266-0.58080.99370.03410.3498-0.0184-0.00350.43290.02430.326197.512217.784673.2149
42.18370.44451.73110.34990.54042.5395-0.2360.20110.0998-0.09070.03650.0765-0.20120.26210.11810.1922-0.00560.0430.14420.00340.220341.51649.8294.9098
50.7328-0.7119-0.43591.6718-1.00482.3506-0.02680.1602-0.28210.0209-0.2035-0.44530.5458-0.1287-0.32321.20290.01840.00791.3529-0.5181.0386-0.2921-22.0235-40.4451
62.36870.43621.97611.6151.35565.7206-0.45010.54250.0213-0.67570.33440.1119-0.6011-0.25440.04470.31390.0158-0.0060.5117-0.07030.47569.1471-1.1496-26.6539
72.1850.72641.46770.74540.97712.50070.1722-0.3653-0.17580.155-0.18420.13490.4656-0.37830.03810.2789-0.03270.07330.1670.02740.277629.18161.33749.4744
81.26391.79960.69692.00480.88360.69730.22410.1848-0.7414-0.13920.0918-0.72420.17650.0184-0.10610.6796-0.1569-0.10590.6885-0.23080.9429-7.0529-32.6901-35.1097
93.01291.6661.6992.0171.642.54310.050.06070.12970.0159-0.26720.48130.2236-0.64920.20810.3054-0.0760.01080.4003-0.11950.4952.0364-9.097-20.3554
102.5740.49812.25410.55270.37481.7725-0.2511-0.50750.32770.0945-0.06750.0587-0.2173-0.12750.13160.25490.02120.02190.4036-0.0570.221953.956120.256930.2243
111.2525-0.3881-1.18482.33390.13581.1340.2581-0.49550.17130.2970.6076-0.00540.3457-0.377-0.13111.14720.04710.01851.5021-0.17640.774589.144326.405673.0567
123.36491.10271.96862.50452.18794.5266-0.7059-0.71820.46930.48360.052-0.2068-0.36440.34260.07220.90330.0688-0.18610.7155-0.05960.495378.323731.322649.6721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:119)
2X-RAY DIFFRACTION2(chain A and resid 120:150)
3X-RAY DIFFRACTION3(chain A and resid 151:206)
4X-RAY DIFFRACTION4(chain A and resid 207:281)
5X-RAY DIFFRACTION5(chain A and resid 282:292)
6X-RAY DIFFRACTION6(chain A and resid 293:302)
7X-RAY DIFFRACTION7(chain B and resid 5:123)
8X-RAY DIFFRACTION8(chain B and resid 124:176)
9X-RAY DIFFRACTION9(chain B and resid 177:221)
10X-RAY DIFFRACTION10(chain B and resid 222:283)
11X-RAY DIFFRACTION11(chain B and resid 284:292)
12X-RAY DIFFRACTION12(chain B and resid 293:302)

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