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- PDB-2efk: Crystal structure of the EFC domain of Cdc42-interacting protein 4 -

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Basic information

Entry
Database: PDB / ID: 2efk
TitleCrystal structure of the EFC domain of Cdc42-interacting protein 4
ComponentsCdc42-interacting protein 4
KeywordsENDOCYTOSIS/EXOCYTOSIS / EFC domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


cell communication / RHOQ GTPase cycle / phagocytic cup / cell projection / endocytosis / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / lysosome / cytoskeleton ...cell communication / RHOQ GTPase cycle / phagocytic cup / cell projection / endocytosis / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / lysosome / cytoskeleton / intracellular membrane-bounded organelle / lipid binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / HR1 rho-binding domain / REM-1 domain profile. / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / HR1 rho-binding domain / REM-1 domain profile. / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cdc42-interacting protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsShimada, A. / Niwa, H. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Curved EFC/F-BAR-Domain Dimers Are Joined End to End into a Filament for Membrane Invagination in Endocytosis
Authors: Shimada, A. / Niwa, H. / Tsujita, K. / Suetsugu, S. / Nitta, K. / Hanawa-Suetsugu, K. / Akasaka, R. / Nishino, Y. / Toyama, M. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Yamamoto, M. / Terada, ...Authors: Shimada, A. / Niwa, H. / Tsujita, K. / Suetsugu, S. / Nitta, K. / Hanawa-Suetsugu, K. / Akasaka, R. / Nishino, Y. / Toyama, M. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Yamamoto, M. / Terada, T. / Miyazawa, A. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Nagayama, K. / Takenawa, T. / Yokoyama, S.
History
DepositionFeb 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cdc42-interacting protein 4


Theoretical massNumber of molelcules
Total (without water)34,9701
Polymers34,9701
Non-polymers00
Water2,504139
1
A: Cdc42-interacting protein 4

A: Cdc42-interacting protein 4


Theoretical massNumber of molelcules
Total (without water)69,9402
Polymers69,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7920 Å2
ΔGint-54 kcal/mol
Surface area30470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.817, 70.410, 65.679
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z

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Components

#1: Protein Cdc42-interacting protein 4 / Thyroid receptor-interacting protein 10 / TRIP-10 / Protein Felic / Salt-tolerant protein / hSTP / CIP4


Mass: 34970.078 Da / Num. of mol.: 1 / Fragment: EFC DOMAIN, residues 10-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / References: UniProt: Q15642
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 8
Details: 20mM Tris-HCl, 150mM NaCl, 2mM DTT, pH 8.0, SMALL TUBES, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.9794, 0.9795, 1.0000
SYNCHROTRONSPring-8 BL26B121
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDAug 19, 2005
RIGAKU JUPITER 2102CCDSep 28, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI DOUBLE CRYSTALMADMx-ray1
2SI DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
311
ReflectionResolution: 2.3→50 Å / Num. all: 16924 / Num. obs: 16924 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1120 / % possible all: 61.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→45.29 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2725144.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1397 8.7 %RANDOM
Rwork0.228 ---
all0.233 16924 --
obs0.228 16014 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.185 Å2 / ksol: 0.329316 e/Å3
Displacement parametersBiso mean: 60.8 Å2
Baniso -1Baniso -2Baniso -3
1--17.51 Å20 Å223.63 Å2
2--0.85 Å20 Å2
3---16.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 0 139 2376
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.531.5
X-RAY DIFFRACTIONc_mcangle_it7.252
X-RAY DIFFRACTIONc_scbond_it8.472
X-RAY DIFFRACTIONc_scangle_it12.722.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 123 7 %
Rwork0.357 1634 -
obs--57.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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