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- PDB-4cc7: Crystal structure of the sixth or C-terminal SH3 domain of human ... -

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Basic information

Entry
Database: PDB / ID: 4cc7
TitleCrystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41
Components
  • DYNAMIN-BINDING PROTEIN
  • NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
KeywordsSTRUCTURAL PROTEIN / SRC HOMOLOGY 3 / PROLINE-RICH PEPTIDE / ACTIN CYTOSKELETON / CORTICAL TENSION / CELL-CELL CONTACTS
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / vesicle transport along actin filament / GTPase regulator activity / actin cap / NOSTRIN mediated eNOS trafficking / vesicle organization / vesicle budding from membrane ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / vesicle transport along actin filament / GTPase regulator activity / actin cap / NOSTRIN mediated eNOS trafficking / vesicle organization / vesicle budding from membrane / dendritic spine morphogenesis / actin polymerization or depolymerization / protein-containing complex localization / Golgi stack / Nephrin family interactions / DCC mediated attractive signaling / regulation of postsynapse organization / regulation of small GTPase mediated signal transduction / 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 / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / FCGR3A-mediated phagocytosis / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / cell-cell junction / endocytic vesicle membrane / regulation of cell shape / presynapse / lamellipodium / actin cytoskeleton / regulation of protein localization / Clathrin-mediated endocytosis / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / cytoskeleton / intracellular signal transduction / nuclear body / cell division / synapse / endoplasmic reticulum membrane / nucleolus / glutamatergic synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / 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 / 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 / BAR domain / BAR domain profile. / BAR / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. / BAR domain / WH2 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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: 1.97 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 18, 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 / 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_database_status.status_code_sf / _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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_asym_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.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_conn.ptnr2_label_seq_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: DYNAMIN-BINDING PROTEIN
B: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
C: DYNAMIN-BINDING PROTEIN
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
E: DYNAMIN-BINDING PROTEIN
F: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
G: DYNAMIN-BINDING PROTEIN
H: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
I: DYNAMIN-BINDING PROTEIN
J: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
K: DYNAMIN-BINDING PROTEIN
L: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
M: DYNAMIN-BINDING PROTEIN
N: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,54837
Polymers61,52914
Non-polymers1,02023
Water3,981221
1
A: DYNAMIN-BINDING PROTEIN
B: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9535
Polymers8,7902
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21.2 kcal/mol
Surface area4210 Å2
MethodPISA
2
C: DYNAMIN-BINDING PROTEIN
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9886
Polymers8,7902
Non-polymers1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-34.7 kcal/mol
Surface area4640 Å2
MethodPISA
3
E: DYNAMIN-BINDING PROTEIN
F: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8614
Polymers8,7902
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-23.5 kcal/mol
Surface area4580 Å2
MethodPISA
4
G: DYNAMIN-BINDING PROTEIN
H: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8614
Polymers8,7902
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-21.7 kcal/mol
Surface area4430 Å2
MethodPISA
5
I: DYNAMIN-BINDING PROTEIN
J: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8253
Polymers8,7902
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-13.1 kcal/mol
Surface area4480 Å2
MethodPISA
6
K: DYNAMIN-BINDING PROTEIN
L: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0137
Polymers8,7902
Non-polymers2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-38.3 kcal/mol
Surface area4190 Å2
MethodPISA
7
M: DYNAMIN-BINDING PROTEIN
N: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0488
Polymers8,7902
Non-polymers2586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-46.9 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.570, 88.570, 69.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein / Protein/peptide , 2 types, 14 molecules ACEGIKMBDFHJLN

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


Mass: 7712.617 Da / Num. of mol.: 7 / Fragment: C-TERMINAL SH3 DOMAIN OF 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.: 7 / Fragment: PROLINE-RICH REGION, RESIDUES 346-357 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O00401

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Non-polymers , 4 types, 244 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE TWO N-TERMINAL RESIDUES GP ARE REMNANTS OF THE 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: 2.17 Å3/Da / Density % sol: 43.37 % / 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: 1.97→50 Å / Num. obs: 38387 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.7
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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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: 1.97→46.59 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.047 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21459 1920 5 %RANDOM
Rwork0.1761 ---
obs0.17798 36465 99.8 %-
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: 42.248 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 43 221 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024295
X-RAY DIFFRACTIONr_bond_other_d0.0130.024197
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9615834
X-RAY DIFFRACTIONr_angle_other_deg2.18239719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7845505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37224.815189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95915747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8451516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214728
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02968
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: 1.966→2.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 140 -
Rwork0.236 2645 -
obs--97.96 %
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)
17.5466-2.862-1.27676.21210.61926.28910.21710.8321-0.0736-0.603-0.3507-0.1931-0.1569-0.23910.13360.28820.0380.02690.3005-0.01930.091340.671-70.017-23.054
25.62940.55270.52554.13950.58332.0594-0.029-0.1299-0.42610.06750.03320.19060.0687-0.0847-0.00420.1905-0.0006-0.00240.23960.01310.082222.566-62.19-12.536
34.15860.20880.25363.6051-0.86215.2622-0.1187-0.27070.20520.10750.14550.2277-0.2502-0.3221-0.02680.19790.0133-0.01290.2611-0.00380.15725.863-51.46-21.761
47.35040.74640.61654.56680.58013.7869-0.20260.2283-0.0154-0.18110.05760.1346-0.0475-0.11980.1450.2293-0.0119-0.02190.2890.02510.1477-9.58-60.735-34.523
55.9132.4598-1.60214.2393-2.47696.6809-0.0925-0.0382-0.14990.0567-0.148-0.17820.21810.01220.24040.2876-0.01160.04140.2941-0.01620.2252-24.854-74.184-26.584
62.74330.31140.66925.7389-0.30964.65840.0586-0.13910.09870.23620.02140.1013-0.3266-0.0166-0.080.23050.02170.01440.260800.012534.966-42.683-1.518
73.6989-0.97290.32624.55330.81194.6820.031-0.1627-0.04020.09790.1042-0.18760.17260.1053-0.13510.2678-0.03640.01050.2554-0.00380.09638.28-84.421-10.495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1514 - 1577
2X-RAY DIFFRACTION1B2 - 13
3X-RAY DIFFRACTION2C1514 - 1577
4X-RAY DIFFRACTION2D2 - 13
5X-RAY DIFFRACTION3E1514 - 1577
6X-RAY DIFFRACTION3F2 - 13
7X-RAY DIFFRACTION4G1514 - 1577
8X-RAY DIFFRACTION4H2 - 13
9X-RAY DIFFRACTION5I1514 - 1577
10X-RAY DIFFRACTION5J2 - 13
11X-RAY DIFFRACTION6K1514 - 1577
12X-RAY DIFFRACTION6L2 - 13
13X-RAY DIFFRACTION7M1514 - 1577
14X-RAY DIFFRACTION7N2 - 13

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