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- PDB-6xj1: Crystal Structure of CDC15 F-BAR Domain from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 6xj1
TitleCrystal Structure of CDC15 F-BAR Domain from Schizosaccharomyces pombe
ComponentsCell division control protein 15
KeywordsCELL CYCLE / Cell division control protein 15 / cytoskeletal protein binding / cytoskeletal protein membrane adaptor / phospholipid binding
Function / homology
Function and homology information


medial membrane band / endoplasmic reticulum polarization => GO:0061163 / : / mitotic actomyosin contractile ring maturation / protein localization to mitotic actomyosin contractile ring / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / medial cortical node / mitotic actomyosin contractile ring, proximal layer / Clathrin-mediated endocytosis / mitotic actomyosin contractile ring assembly ...medial membrane band / endoplasmic reticulum polarization => GO:0061163 / : / mitotic actomyosin contractile ring maturation / protein localization to mitotic actomyosin contractile ring / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / medial cortical node / mitotic actomyosin contractile ring, proximal layer / Clathrin-mediated endocytosis / mitotic actomyosin contractile ring assembly / cytoskeletal protein-membrane anchor activity / mitotic actomyosin contractile ring / actin cortical patch / cell tip / clathrin-dependent endocytosis / mating projection tip / cell division site / cytoskeleton organization / phospholipid binding / cytoskeleton / plasma membrane / 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
Cell division control protein 15
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsChandra, M. / Jackson, L.P. / Snider, C.E. / Gould, K.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R35GM119525 United States
CitationJournal: Cell Rep / Year: 2020
Title: Opposite Surfaces of the Cdc15 F-BAR Domain Create a Membrane Platform That Coordinates Cytoskeletal and Signaling Components for Cytokinesis.
Authors: Snider, C.E. / Chandra, M. / McDonald, N.A. / Willet, A.H. / Collier, S.E. / Ohi, M.D. / Jackson, L.P. / Gould, K.L.
History
DepositionJun 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 15
B: Cell division control protein 15


Theoretical massNumber of molelcules
Total (without water)68,0742
Polymers68,0742
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-70 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.777, 75.171, 93.239
Angle α, β, γ (deg.)90.000, 95.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division control protein 15


Mass: 34037.227 Da / Num. of mol.: 2 / Mutation: E30K, E152K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: cdc15, SPAC20G8.05c / Production host: Escherichia coli (E. coli) / References: UniProt: Q09822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 100 mM HEPES (pH 7.0), 1.1 M Sodium Malonate Dibasic Monohydrate (pH 7.0) and 1% Jeffamine ED 2003 (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→37.59 Å / Num. obs: 59833 / % 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 / Num. unique obs: 688 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C1F

5c1f


Resolution: 3.52→37.59 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3096 483 5.37 %
Rwork0.2667 8516 -
obs0.2691 26635 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.26 Å2 / Biso mean: 48.5412 Å2 / Biso min: 0.64 Å2
Refinement stepCycle: final / Resolution: 3.52→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 0 55 4459
Biso mean---22.96 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.52-4.030.37381350.26162647278288
4.03-5.070.28721860.24362926311299
5.07-37.590.28421620.30042943310596

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