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- PDB-4cc2: Complex of human Tuba C-terminal SH3 domain with human N-WASP pro... -

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Basic information

Entry
Database: PDB / ID: 4cc2
TitleComplex of human Tuba C-terminal SH3 domain with human N-WASP proline- rich peptide - P212121
Components
  • DYNAMIN-BINDING PROTEIN
  • NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
KeywordsSTRUCTURAL PROTEIN / SRC HOMOLOGY 3 / SH3 DOMAIN / PROLINE-RICH PEPTIDE / ACTIN CYTOSKELETON / CORTICAL TENSION
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / actin cap / vesicle organization / Golgi stack / vesicle budding from membrane ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / actin cap / vesicle organization / Golgi stack / vesicle budding from membrane / vesicle transport along actin filament / actin polymerization or depolymerization / protein-containing complex localization / dendritic spine morphogenesis / Nephrin family interactions / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / regulation of postsynapse organization / positive regulation of filopodium assembly / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / cilium assembly / RHO GTPases Activate WASPs and WAVEs / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / guanyl-nucleotide exchange factor activity / response to bacterium / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / endocytic vesicle membrane / regulation of protein localization / cell-cell junction / actin cytoskeleton / presynapse / lamellipodium / Clathrin-mediated endocytosis / actin binding / regulation of cell shape / cytoplasmic vesicle / microtubule binding / protein-containing complex assembly / cytoskeleton / intracellular signal transduction / cell division / synapse / glutamatergic synapse / endoplasmic reticulum membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / BAR domain / BAR domain profile. / BAR ...Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / BAR domain / BAR domain profile. / BAR / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / BAR domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / AH/BAR domain superfamily / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Actin nucleation-promoting factor WASL / Dynamin-binding protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPolle, L. / Rigano, L. / Julian, R. / Ireton, K. / Schubert, W.-D.
CitationJournal: Structure / Year: 2014
Title: Structural Details of Human Tuba Recruitment by Inlc of Listeria Monocytogenes Elucidate Bacterial Cell-Cell Spreading.
Authors: Polle, L. / Rigano, L.A. / Julian, R. / Ireton, K. / Schubert, W.
History
DepositionOct 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DYNAMIN-BINDING PROTEIN
B: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
C: DYNAMIN-BINDING PROTEIN
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,23216
Polymers17,5804
Non-polymers65212
Water2,612145
1
A: DYNAMIN-BINDING PROTEIN
B: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1377
Polymers8,7902
Non-polymers3475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-24.2 kcal/mol
Surface area4740 Å2
MethodPISA
2
C: DYNAMIN-BINDING PROTEIN
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0959
Polymers8,7902
Non-polymers3057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-59.6 kcal/mol
Surface area4490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.750, 70.310, 38.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DYNAMIN-BINDING PROTEIN / SCAFFOLD PROTEIN TUBA


Mass: 7712.617 Da / Num. of mol.: 2
Fragment: C-TERMINAL SH3 DOMAIN OF HUMAN TUBA, RESIDUES 1513-1577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: Q6XZF7
#2: Protein/peptide NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN / N-WASP / N-WASP


Mass: 1077.188 Da / Num. of mol.: 2 / Fragment: N-WASP PROLINE-RICH PEPTIDE, RESIDUES 346-357 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O00401
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES, GP, DERIVE FROM FUSION PROTEIN CLEAVAGE SITE

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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: 1.81 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growpH: 5.5 / Details: 3 M NACL, 0.1 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 18318 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.5
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.7 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUU

1zuu


Resolution: 1.55→40.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.624 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21802 921 5 %RANDOM
Rwork0.17003 ---
obs0.17232 17487 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---18.89 Å20 Å2
3---19.47 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 32 145 1340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021304
X-RAY DIFFRACTIONr_bond_other_d0.0080.021266
X-RAY DIFFRACTIONr_angle_refined_deg2.3611.9731765
X-RAY DIFFRACTIONr_angle_other_deg1.60732943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20125.57461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.025154
X-RAY DIFFRACTIONr_chiral_restr0.1550.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211432
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02292
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.547→1.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 68 -
Rwork0.233 1294 -
obs--94.26 %
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)
13.25270.4183-0.14933.6915-0.25431.26270.00790.03160.0198-0.0652-0.0377-0.1668-0.01810.00190.02970.1123-0.00560.00680.2034-0.00120.0085-1.282-0.252-19.243
21.8319-0.04170.23773.52410.80311.5912-0.01780.05950.1059-0.2331-0.0026-0.0687-0.10110.04590.02040.125-0.0070.00660.20940.00640.01-9.12816.943-8.758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1514 - 1577
2X-RAY DIFFRACTION1B2 - 13
3X-RAY DIFFRACTION2C1514 - 1575
4X-RAY DIFFRACTION2D3 - 13

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